1
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Jogdeo CM, Siddhanta K, Das A, Ding L, Panja S, Kumari N, Oupický D. Beyond Lipids: Exploring Advances in Polymeric Gene Delivery in the Lipid Nanoparticles Era. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404608. [PMID: 38842816 PMCID: PMC11384239 DOI: 10.1002/adma.202404608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/23/2024] [Indexed: 06/07/2024]
Abstract
The recent success of gene therapy during the COVID-19 pandemic has underscored the importance of effective and safe delivery systems. Complementing lipid-based delivery systems, polymers present a promising alternative for gene delivery. Significant advances have been made in the recent past, with multiple clinical trials progressing beyond phase I and several companies actively working on polymeric delivery systems which provides assurance that polymeric carriers can soon achieve clinical translation. The massive advantage of structural tunability and vast chemical space of polymers is being actively leveraged to mitigate shortcomings of traditional polycationic polymers and improve the translatability of delivery systems. Tailored polymeric approaches for diverse nucleic acids and for specific subcellular targets are now being designed to improve therapeutic efficacy. This review describes the recent advances in polymer design for improved gene delivery by polyplexes and covalent polymer-nucleic acid conjugates. The review also offers a brief note on novel computational techniques for improved polymer design. The review concludes with an overview of the current state of polymeric gene therapies in the clinic as well as future directions on their translation to the clinic.
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Affiliation(s)
- Chinmay M Jogdeo
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kasturi Siddhanta
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ashish Das
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ling Ding
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sudipta Panja
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Neha Kumari
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Oupický
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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2
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Gras M, Adler P, Smietana M. A Catalytic Approach for the Synthesis of Peptide-Oligonucleotides Conjugates in Aqueous Solution or On-Column. Chemistry 2024; 30:e202401069. [PMID: 38709711 DOI: 10.1002/chem.202401069] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene-targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post-synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA-Encoded Libraries.
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Affiliation(s)
- Marion Gras
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Pauline Adler
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Michael Smietana
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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3
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Bonde S, Osmani RAM, Trivedi R, Patravale V, Angolkar M, Prasad AG, Ravikumar AA. Harnessing DNA origami's therapeutic potential for revolutionizing cardiovascular disease treatment: A comprehensive review. Int J Biol Macromol 2024; 270:132246. [PMID: 38735608 DOI: 10.1016/j.ijbiomac.2024.132246] [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: 12/05/2023] [Revised: 03/25/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
DNA origami is a cutting-edge nanotechnology approach that creates precise and detailed 2D and 3D nanostructures. The crucial feature of DNA origami is how it is created, which enables precise control over its size and shape. Biocompatibility, targetability, programmability, and stability are further advantages that make it a potentially beneficial technique for a variety of applications. The preclinical studies of sophisticated programmable nanomedicines and nanodevices that can precisely respond to particular disease-associated triggers and microenvironments have been made possible by recent developments in DNA origami. These stimuli, which are endogenous to the targeted disorders, include protein upregulation, pH, redox status, and small chemicals. Oncology has traditionally been the focus of the majority of past and current research on this subject. Therefore, in this comprehensive review, we delve into the intricate world of DNA origami, exploring its defining features and capabilities. This review covers the fundamental characteristics of DNA origami, targeting DNA origami to cells, cellular uptake, and subcellular localization. Throughout the review, we emphasised on elucidating the imperative for such a therapeutic platform, especially in addressing the complexities of cardiovascular disease (CVD). Moreover, we explore the vast potential inherent in DNA origami technology, envisioning its promising role in the realm of CVD treatment and beyond.
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Affiliation(s)
- Smita Bonde
- Department of Pharmaceutics, SSR College of Pharmacy, Silvassa 396230, UT of Dadra and Nagar Haveli, India.
| | - Riyaz Ali M Osmani
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Rashmi Trivedi
- Department of Pharmaceutics, Smt. Kishoritai Bhoyar College of Pharmacy, Kamptee, Nagpur 441002, Maharashtra, India.
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga (E), Mumbai 400019, Maharashtra, India.
| | - Mohit Angolkar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Aprameya Ganesh Prasad
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Akhila Akkihebbal Ravikumar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
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4
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Shioi R, Xiao L, Kool ET. Aqueous Activation of RNA 2'-OH for Conjugation with Amines and Thiols. Bioconjug Chem 2024; 35:43-50. [PMID: 38150592 DOI: 10.1021/acs.bioconjchem.3c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Strategies for covalent modification of RNA are important for enabling biological studies of the biopolymer and for enhancing properties of therapeutic RNAs. While a number of electrophiles have been observed to react with RNA, few methods exist for reaction with nucleophiles. Here, we describe new reagents that enable efficient conjugation of amines and other nucleophiles to unmodified RNA postsynthetically via transient activation of 2'-OH groups. Reaction of single-stranded RNA in aqueous solution with phenolic imidazolecarbamates at room temperature results in stoichiometric and superstoichiometric yields of imidazolecarbonyl group adducts, and control experiments with DNA confirm the site of reaction in RNA as 2'-OH. Subsequent incubation of imidazolecarbonyl-activated RNAs with primary or selected secondary amines results in rapid, high-yield conversion to carbamate conjugates. The activation and subsequent nucleophile reaction can be carried out either stepwise or in a one-pot reaction. Thiols and phenol species react to yield (thio)carbonate adducts, and amino acid sidechains also react, suggesting possible future utility for protein conjugates and analysis of protein-RNA interactions. The activation method is found to be selective to unpaired regions of RNA, and can be directed to a specific location in a strand by use of a loop-inducing helper DNA. The results establish novel and efficient reagents and methods for modifying RNA postsynthetically with nucleophiles.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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5
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Hales LT, Thompson PE. Solid-Phase Synthesis of PROTACs and SNIPERs on Backbone Amide Linked (BAL) Resin. Chemistry 2023; 29:e202301975. [PMID: 37526498 DOI: 10.1002/chem.202301975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/02/2023]
Abstract
Developing straightforward but flexible approaches to PROTAC synthesis that can incorporate the structural elements of emerging designs can improve the quality and efficiency of PROTAC development. Solid-phase approaches could offer many advantages over conventional PROTAC synthesis if diverse chemistries and topographies can be incorporated. We have exploited the backbone-amide-linked (BAL) resin to employ an array of solid-phase organic reactions, providing access to VHL- and IAP-targeting degraders using the BRD4-targeting JQ1 conjugates as examples.
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Affiliation(s)
- Liam Thomas Hales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, Parkville, VIC, Australia
| | - Philip Evan Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, Parkville, VIC, Australia
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6
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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7
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Convenient Solid-Phase Attachment of Small-Molecule Ligands to Oligonucleotides via a Biodegradable Acid-Labile P-N-Bond. Molecules 2023; 28:molecules28041904. [PMID: 36838892 PMCID: PMC9961013 DOI: 10.3390/molecules28041904] [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: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
One of the key problems in the design of therapeutic and diagnostic oligonucleotides is the attachment of small-molecule ligands for targeted deliveries in such a manner that provides the controlled release of the oligonucleotide at a certain moment. Here, we propose a novel, convenient approach for attaching ligands to the 5'-end of the oligonucleotide via biodegradable, acid-labile phosphoramide linkage. The method includes the activation of the 5'-terminal phosphate of the fully protected, support-bound oligonucleotide, followed by interaction with a ligand bearing the primary amino group. This technique is simple to perform, allows for forcing the reaction to completion by adding excess soluble reactant, eliminates the problem of the limited solubility of reagents, and affords the possibility of using different solvents, including water/organic media. We demonstrated the advantages of this approach by synthesizing and characterizing a wide variety of oligonucleotide 5'-conjugates with different ligands, such as cholesterol, aliphatic oleylamine, and p-anisic acid. The developed method suits different types of oligonucleotides (deoxyribo-, 2'-O-methylribo-, ribo-, and others).
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8
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Matsumoto M, Sutrisno L, Ariga K. Covalent nanoarchitectonics: Polymer synthesis with designer structures and sequences. JOURNAL OF POLYMER SCIENCE 2023. [DOI: 10.1002/pol.20220755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Michio Matsumoto
- International Center for Materials Nanoarchitectonics (WPI‐MANA) National Institute for Materials Science (NIMS) Ibaraki Japan
| | - Linawati Sutrisno
- International Center for Materials Nanoarchitectonics (WPI‐MANA) National Institute for Materials Science (NIMS) Ibaraki Japan
| | - Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (WPI‐MANA) National Institute for Materials Science (NIMS) Ibaraki Japan
- Graduate School of Frontier Sciences The University of Tokyo Chiba Japan
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9
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Fàbrega C, Aviñó A, Navarro N, Jorge AF, Grijalvo S, Eritja R. Lipid and Peptide-Oligonucleotide Conjugates for Therapeutic Purposes: From Simple Hybrids to Complex Multifunctional Assemblies. Pharmaceutics 2023; 15:320. [PMID: 36839642 PMCID: PMC9959333 DOI: 10.3390/pharmaceutics15020320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Antisense and small interfering RNA (siRNA) oligonucleotides have been recognized as powerful therapeutic compounds for targeting mRNAs and inducing their degradation. However, a major obstacle is that unmodified oligonucleotides are not readily taken up into tissues and are susceptible to degradation by nucleases. For these reasons, the design and preparation of modified DNA/RNA derivatives with better stability and an ability to be produced at large scale with enhanced uptake properties is of vital importance to improve current limitations. In the present study, we review the conjugation of oligonucleotides with lipids and peptides in order to produce oligonucleotide conjugates for therapeutics aiming to develop novel compounds with favorable pharmacokinetics.
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Affiliation(s)
- Carme Fàbrega
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Anna Aviñó
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Natalia Navarro
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Andreia F. Jorge
- Department of Chemistry, Coimbra Chemistry Centre (CQC), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Santiago Grijalvo
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Colloidal and Interfacial Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
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10
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Marchesi E, Bovolenta M, Preti L, Capobianco ML, Mamchaoui K, Bertoldo M, Perrone D. Synthesis and Exon-Skipping Properties of a 3'-Ursodeoxycholic Acid-Conjugated Oligonucleotide Targeting DMD Pre-mRNA: Pre-Synthetic versus Post-Synthetic Approach. Molecules 2021; 26:7662. [PMID: 34946743 PMCID: PMC8707236 DOI: 10.3390/molecules26247662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Steric blocking antisense oligonucleotides (ASO) are promising tools for splice modulation such as exon-skipping, although their therapeutic effect may be compromised by insufficient delivery. To address this issue, we investigated the synthesis of a 20-mer 2'-OMe PS oligonucleotide conjugated at 3'-end with ursodeoxycholic acid (UDCA) involved in the targeting of human DMD exon 51, by exploiting both a pre-synthetic and a solution phase approach. The two approaches have been compared. Both strategies successfully provided the desired ASO 51 3'-UDC in good yield and purity. It should be pointed out that the pre-synthetic approach insured better yields and proved to be more cost-effective. The exon skipping efficiency of the conjugated oligonucleotide was evaluated in myogenic cell lines and compared to that of unconjugated one: a better performance was determined for ASO 51 3'-UDC with an average 9.5-fold increase with respect to ASO 51.
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Affiliation(s)
- Elena Marchesi
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Matteo Bovolenta
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Lorenzo Preti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (L.P.); (M.B.)
| | - Massimo L. Capobianco
- Institute of Organic Synthesis and Photoreactivity, Italian National Research Council, 40129 Bologna, Italy;
| | - Kamel Mamchaoui
- Centre de Recherche en Myologie, Institut de Myologie, Sorbonne Université, Inserm, F-75013 Paris, France;
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (L.P.); (M.B.)
- Institute of Organic Synthesis and Photoreactivity, Italian National Research Council, 40129 Bologna, Italy;
| | - Daniela Perrone
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy;
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11
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Wang J, Shang J, Xiang Y, Tong A. Post-Synthetic Modification of Oligonucleotides Through Oxidative Amination of 4-Thio-2'-Deoxyuridine. Curr Protoc 2021; 1:e274. [PMID: 34644451 DOI: 10.1002/cpz1.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target recognition molecules for biosensing and gene regulation. Herein, we describe a general method for post-synthetic modification of ONs based on the oxidative amination of 4-thio-2'-deoxyuridine (4SdU) with sodium periodate and several amines. Alkyne-/azide-, biotin-, and fluorophore-modified ONs were prepared by modifying 4SdU-containing ONs with the corresponding amines and characterized for their bioorthogonal reactivity, streptavidin-binding affinity, and fluorescence properties, respectively. We synthesized three fluorophore-modified ONs with and without the aromatic fluorophores conjugated to modified nucleobases and investigated their emission properties. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Post-synthetic modification of ONs Supporting Protocol: Preparation of dansyl ethylenediamine Basic Protocol 2: Quantification of ON reaction yields Basic Protocol 3: Characterization of modified ONs.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
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12
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Meschaninova MI, Entelis NS, Chernolovskaya EL, Venyaminova AG. A Versatile Solid-Phase Approach to the Synthesis of Oligonucleotide Conjugates with Biodegradable Hydrazone Linker. Molecules 2021; 26:molecules26082119. [PMID: 33917095 PMCID: PMC8067880 DOI: 10.3390/molecules26082119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 12/02/2022] Open
Abstract
One of the ways to efficiently deliver various drugs, including therapeutic nucleic acids, into the cells is conjugating them with different transport ligands via labile or stable bonds. A convenient solid-phase approach for the synthesis of 5′-conjugates of oligonucleotides with biodegradable pH-sensitive hydrazone covalent bonds is proposed in this article. The approach relies on introducing a hydrazide of the ligand under aqueous/organic media to a fully protected support-bound oligonucleotide containing aldehyde function at the 5′-end. We demonstrated the proof-of-principle of this approach by synthesizing 5′-lipophilic (e.g., cholesterol and α-tocopherol) conjugates of modified siRNA and non-coding RNAs imported into mitochondria (antireplicative RNAs and guide RNAs for Mito-CRISPR/system). The developed method has the potential to be extended for the synthesis of pH-sensitive conjugates of oligonucleotides of different types (ribo-, deoxyribo-, 2′-O-methylribo-, and others) with ligands of different nature.
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
- Correspondence: ; Tel.: +7-383-363-5129
| | - Nina S. Entelis
- UMR Genetique Moleculaire, Genomique, Microbiologie (GMGM), Strasbourg University—CNRS, 67084 Strasbourg, France;
| | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.L.C.); (A.G.V.)
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13
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Wang J, Shang J, Xiang Y, Tong A. General Method for Post-Synthetic Modification of Oligonucleotides Based on Oxidative Amination of 4-Thio-2'-deoxyuridine. Bioconjug Chem 2021; 32:721-728. [PMID: 33730486 DOI: 10.1021/acs.bioconjchem.1c00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target binding molecules for biosensing and regulators for gene expression. Numerous efforts have been focused on developing facile methods for preparing these useful ONs carrying diverse modifications. Herein, we present a general method for postsynthetic modification of ONs via oxidative amination of 4-thio-2'-deoxyuridine (4SdU). 4SdU-containing ON can be derived by both alkyl and aromatic amines. Using this approach, ONs are successfully attached with alkyne/azide, biotin and dansylamide moieties, and these as-prepared ONs possess the expected biorthogonal reactivity, streptavidin affinity and fluorescent property, respectively. Furthermore, we also directly install fluorophores to the ON nucleobase based on oxidative amination of 4SdU, and these fluorophores exhibit distinct luminescence behaviors before and after conjugation. We believe our method will be a versatile strategy for constructing various functionalized ONs used in a wide range of nucleic acid applications.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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14
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Martín-Nieves V, Fàbrega C, Guasch M, Fernández S, Sanghvi YS, Ferrero M, Eritja R. Oligonucleotides Containing 1-Aminomethyl or 1-Mercaptomethyl-2-deoxy-d-ribofuranoses: Synthesis, Purification, Characterization, and Conjugation with Fluorophores and Lipids. Bioconjug Chem 2021; 32:350-366. [PMID: 33543930 PMCID: PMC9122261 DOI: 10.1021/acs.bioconjchem.0c00717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Oligonucleotide conjugates are widely used as therapeutic drugs, gene analysis, and diagnostic tools. A critical step in the biologically relevant oligonucleotide conjugates is the design and synthesis of functional molecules that connect oligonucleotide with ligands. Here, we report the synthesis and application for oligonucleotide functionalization of novel tethers based on aminomethyl and mercaptomethyl sugar derivatives. Starting from a common cyano sugar precursor, three novel phosphoramidites have been prepared in the two α- and β-anomeric forms. The mercaptomethyl sugar was protected with the S-acetyl group, while two different protecting groups have been developed for the aminomethyl sugar. These two protecting groups are orthogonal, as they can be removed independently using photolysis or ammonolysis. This combination allowed the introduction of two different ligands in a single oligonucleotide.
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Affiliation(s)
- Virginia Martín-Nieves
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Carme Fàbrega
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Marc Guasch
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Ramon Eritja
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
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15
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Honcharenko D, Druceikaite K, Honcharenko M, Bollmark M, Tedebark U, Strömberg R. New Alkyne and Amine Linkers for Versatile Multiple Conjugation of Oligonucleotides. ACS OMEGA 2021; 6:579-593. [PMID: 33458510 PMCID: PMC7807750 DOI: 10.1021/acsomega.0c05075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/08/2020] [Indexed: 05/08/2023]
Abstract
Oligonucleotide (ON) conjugates are increasingly important tools for various molecular diagnostics, nanotechnological applications, and for the development of nucleic acid-based therapies. Multiple labeling of ONs can further equip ON-conjugates and provide improved or additional tailored properties. Typically, the preparation of ON multiconjugates involves additional synthetic steps and/or manipulations in post-ON assembly. This report describes the simplified methodology allowing for multiple labeling of ONs on a solid support and is compatible with phosphodiester as well as phosphorothioate (PS) ONs. The current approach utilizes two novel alkyne- and amino-functionalized linker phosphoramidites that can be readily synthesized from a common aminodiol intermediate in three steps. The combination of new linkers provides orthogonal functionalities, which allow for multiple attachments of similar or varied moieties. The linkers are incorporated into ONs during automated solid-phase ON synthesis, and the conjugation with functional entities is achieved by either amide bond formation or by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The versatility of the approach is demonstrated by the synthesis of 5'-site ON multiconjugates with small molecules, peptides, and fatty acids as well as in the preparation of an internal peptide-ON conjugate.
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Affiliation(s)
- Dmytro Honcharenko
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
| | - Kristina Druceikaite
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | | | - Martin Bollmark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Ulf Tedebark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Roger Strömberg
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
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16
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Abstract
The preparation and applications of DNA containing polymers are comprehensively reviewed, and they are in the form of DNA−polymer covalent conjugators, supramolecular assemblies and hydrogels for advanced materials with promising features.
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Affiliation(s)
- Zeqi Min
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Biyi Xu
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Wen Li
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Afang Zhang
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
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17
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Hawner M, Ducho C. Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules. Molecules 2020; 25:E5963. [PMID: 33339365 PMCID: PMC7766908 DOI: 10.3390/molecules25245963] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular 'targeting', i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.
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Affiliation(s)
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66 123 Saarbrücken, Germany;
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18
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Räuchle M, Leveau G, Richert C. Synthesis of Peptido RNAs from Unprotected Peptides and Oligoribonucleotides via Coupling in Aqueous Solution. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Maximilian Räuchle
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Gabrielle Leveau
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
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19
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Li X, Feng K, Li L, Yang L, Pan X, Yazd HS, Cui C, Li J, Moroz L, Sun Y, Wang B, Li X, Huang T, Tan W. Lipid-oligonucleotide conjugates for bioapplications. Natl Sci Rev 2020; 7:1933-1953. [PMID: 34691533 PMCID: PMC8290939 DOI: 10.1093/nsr/nwaa161] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/28/2019] [Accepted: 07/08/2020] [Indexed: 11/12/2022] Open
Abstract
Lipid-oligonucleotide conjugates (LONs) are powerful molecular-engineering materials for various applications ranging from biosensors to biomedicine. Their unique amphiphilic structures enable the self-assembly and the conveyance of information with high fidelity. In particular, LONs present remarkable potential in measuring cellular mechanical forces and monitoring cell behaviors. LONs are also essential sensing tools for intracellular imaging and have been employed in developing cell-surface-anchored DNA nanostructures for biomimetic-engineering studies. When incorporating therapeutic oligonucleotides or small-molecule drugs, LONs hold promise for targeted therapy. Moreover, LONs mediate the controllable assembly and fusion of vesicles based on DNA-strand displacements, contributing to nanoreactor construction and macromolecule delivery. In this review, we will summarize the general synthesis strategies of LONs, provide some characterization analysis and emphasize recent advances in bioanalytical and biomedical applications. We will also consider the relevant challenges and suggest future directions for building better functional LONs in nanotechnology and materials-science applications.
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Affiliation(s)
- Xiaowei Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Kejun Feng
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
- School of Chemistry and Materials Engineering, Huizhou University, Huizhou 516007, China
| | - Long Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Lu Yang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Xiaoshu Pan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Hoda Safari Yazd
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Cheng Cui
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China
| | - Juan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Leonid Moroz
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Yujia Sun
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Bang Wang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Xiang Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Tong Huang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611–7200, USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China
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20
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Shang W, Su SN, Shi R, Mou ZD, Yu GQ, Zhang X, Niu D. Generation of Glycosyl Radicals from Glycosyl Sulfoxides and Its Use in the Synthesis of C-linked Glycoconjugates. Angew Chem Int Ed Engl 2020; 60:385-390. [PMID: 32935426 DOI: 10.1002/anie.202009828] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/08/2020] [Indexed: 02/05/2023]
Abstract
We here report glycosyl sulfoxides appended with an aryl iodide moiety as readily available, air and moisture stable precursors to glycosyl radicals. These glycosyl sulfoxides could be converted to glycosyl radicals by way of a rapid and efficient intramolecular radical substitution event. The use of this type of precursors enabled the synthesis of various complex C-linked glycoconjugates under mild conditions. This reaction could be performed in aqueous media and is amenable to the synthesis of glycopeptidomimetics and carbohydrate-DNA conjugates.
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Affiliation(s)
- Weidong Shang
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Sheng-Nan Su
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Rong Shi
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Ze-Dong Mou
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Guo-Qiang Yu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, China
| | - Xia Zhang
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
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21
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Shang W, Su S, Shi R, Mou Z, Yu G, Zhang X, Niu D. Generation of Glycosyl Radicals from Glycosyl Sulfoxides and Its Use in the Synthesis of
C
‐linked Glycoconjugates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009828] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Weidong Shang
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Sheng‐Nan Su
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Rong Shi
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Ze‐Dong Mou
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Guo‐Qiang Yu
- Discovery Chemistry Unit HitGen Inc. Building 6, No. Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District Chengdu 610200 China
| | - Xia Zhang
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Dawen Niu
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
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22
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Stepwise electrochemical deposition and single-molecule conductance of nucleic acid analogues. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Saito Y, Cho SM, Danieli LA, Kobayashi S. Zinc-Catalyzed Phosphonylation of Alcohols with Alkyl Phosphites. Org Lett 2020; 22:3171-3175. [PMID: 32251599 DOI: 10.1021/acs.orglett.0c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the presence of a catalytic amount of either Zn(acac)2 or bis(2,2,6,6-tetramethyl-3,5-heptanedionato)zinc(II) (Zn(TMHD)2), primary, secondary, and tertiary alcohol substituents on a wide range of substrates, including acyclic and cyclic structures, carbohydrates, steroids, and amino acids, reacted with dimethyl phosphite to afford the corresponding H-phosphonate diesters in high to excellent yields.
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Affiliation(s)
- Yuki Saito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Soo Min Cho
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Luca Alessandro Danieli
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shu Kobayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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24
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Goyon A, Yehl P, Zhang K. Characterization of therapeutic oligonucleotides by liquid chromatography. J Pharm Biomed Anal 2020; 182:113105. [PMID: 32004766 DOI: 10.1016/j.jpba.2020.113105] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/21/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022]
Abstract
Marketed therapies in the pharmaceutical landscape are rapidly evolving and getting more diverse. Small molecule medicines have dominated in the past while antibodies have grown dramatically in recent years. However, the failure of traditional small and large molecules in accessing certain targets has led to increased R&D efforts to develop alternative modalities. Therapeutic oligonucleotides (ONs) can accurately be directed against their ribonucleic acid (RNA) target and represent a promising approach in previously untreated diseases. Established automated synthesis of ONs coupled with chemical improvements and the advance of new drug delivery technologies has recently brought ONs to a heightened level of interest. The first part of the present review describes the different classes of oligonucleotides, namely antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA), aptamer and immunostimulatory ON, with a focus on their delivery systems relevant for future analytical characterization. The second part reviews the typical impurities in therapeutic ON products. The third part discusses the use of historical methods anion exchange chromatography (AEX), ion-pair reversed phase liquid chromatography (IP-RP), mixed-mode chromatography (MMC) and recent analytical methodologies of hydrophilic interaction liquid chromatography (HILIC), two-dimensional liquid chromatography (2D-LC) mass spectrometry for the characterization of ASO and siRNA modalities. The effects of physicochemical properties of RPLC columns and ion-pair agents on ON separation are specifically addressed with possible future directions for method development provided. Finally, some innovative analytical developments for the analysis of siRNAs and their delivery materials to pave the way toward the use of multi-attribute methods in the near future are discussed.
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Affiliation(s)
- Alexandre Goyon
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Peter Yehl
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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25
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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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26
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Ivancová I, Leone DL, Hocek M. Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking. Curr Opin Chem Biol 2019; 52:136-144. [DOI: 10.1016/j.cbpa.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
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27
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Gauthier F, Malher A, Vasseur JJ, Dupouy C, Debart F. Conjugation of Small Molecules to RNA Using a Reducible Disulfide Linker Attached at the 2′-OH Position through a Carbamate Function. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Florian Gauthier
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Astrid Malher
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
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28
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Covalent Fluorophore Labeling of Oligonucleotides and Generation of Other Oligonucleotide Bioconjugates. Methods Mol Biol 2019; 1943:61-72. [PMID: 30838609 DOI: 10.1007/978-1-4939-9092-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Oligonucleotide conjugates have already reached considerable importance in life science research and oligonucleotide drug development. Since the preparation of oligonucleotide conjugates depends critically on the chemical nature of the used ligand and linker, there is no general and universal procedure. Here, we present a detailed, quick, and facile protocol for attaching fluorescent dyes or cross-linkers of variable chemical stability to oligonucleotides at 3'- or 5'-aminoalkyl handles. Purification and removal of educts and side-products and structural verification by gel electrophoresis and mass spectrometry are presented. Aspects for adapting this protocol for other reaction sites at the oligonucleotide are discussed. We highlight important issues for generating oligonucleotide conjugates with other molecules, including peptide, proteins, and small molecules for receptor-targeting applications. The methodology is suitable for oligonucleotides with various modifications, including stabilized antisense, siRNAs, and miRNAs.
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29
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MacCulloch T, Buchberger A, Stephanopoulos N. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials. Org Biomol Chem 2019; 17:1668-1682. [PMID: 30483688 DOI: 10.1039/c8ob02436g] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe AZ, USA.
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30
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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31
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Sharma VK, Osborn MF, Hassler MR, Echeverria D, Ly S, Ulashchik EA, Martynenko-Makaev YV, Shmanai VV, Zatsepin TS, Khvorova A, Watts JK. Novel Cluster and Monomer-Based GalNAc Structures Induce Effective Uptake of siRNAs in Vitro and in Vivo. Bioconjug Chem 2018; 29:2478-2488. [PMID: 29898368 DOI: 10.1021/acs.bioconjchem.8b00365] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
GalNAc conjugation is emerging as a dominant strategy for delivery of therapeutic oligonucleotides to hepatocytes. The structure and valency of the GalNAc ligand contributes to the potency of the conjugates. Here we present a panel of multivalent GalNAc variants using two different synthetic strategies. Specifically, we present a novel conjugate based on a support-bound trivalent GalNAc cluster, and four others using a GalNAc phosphoramidite monomer that was readily assembled into tri- or tetravalent designs during solid phase oligonucleotide synthesis. We compared these compounds to a clinically used trivalent GalNAc cluster both in vitro and in vivo. In vitro, cluster-based and phosphoramidite-based scaffolds show a similar rate of internalization in primary hepatocytes, with membrane binding observed as early as 5 min. All tested compounds provided potent, dose-dependent silencing, with 2-4% of injected dose recoverable from liver after 1 week. The two preassembled trivalent GalNAc clusters showed higher tissue accumulation and gene silencing relative to di-, tri-, or tetravalent GalNAc conjugates assembled via phosphoramidite chemistry.
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Affiliation(s)
| | | | | | | | | | - Egor A Ulashchik
- Institute of Physical Organic Chemistry , National Academy of Sciences of Belarus , Surganova 13 , 220072 Minsk , Belarus
| | - Yury V Martynenko-Makaev
- Institute of Physical Organic Chemistry , National Academy of Sciences of Belarus , Surganova 13 , 220072 Minsk , Belarus
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry , National Academy of Sciences of Belarus , Surganova 13 , 220072 Minsk , Belarus
| | - Timofei S Zatsepin
- Center for Translational Biomedicine , Skolkovo Institute of Science and Technology , Skolkovo , 143026 Moscow , Russia.,Department of Chemistry , Lomonosov Moscow State University , Leninskie gory 1-3 , 119992 Moscow , Russia
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32
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Winkler J. Extrahepatic Targeting of Oligonucleotides with Receptor-Binding Non-Immunoglobulin Scaffold Proteins. Nucleic Acid Ther 2018; 28:137-145. [PMID: 29733239 DOI: 10.1089/nat.2017.0713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although recent clinical successes of antisense, splice-switching, and siRNA oligonucleotides have established the therapeutic utility of this novel class of medicines, the efficient systemic application for non-liver targets remains elusive. Exploitation of active receptor-mediated targeting followed by efficient and productive cellular uptake is required for enabling the therapy of extrahepatic diseases on the expressional level. Evasion of liver accumulation and organ-specific targeting and also efficient cytosolic delivery after endosomal internalization are currently insufficiently solved issues. Lipid and polymer-based nanoparticles can be engineered for efficient cellular uptake and enhancement of endosomal escape, but are characterized by preferential liver accumulation based on biodistribution largely determined by particle size and biophysical properties. Oligonucleotide bioconjugates with receptor-binding ligands have been evolved for highly efficient targeting, but frequently result in a large extent of endosomal entrapment and consequently a lack of sufficient cytosolic concentrations. Non-immunoglobulin protein-based receptor recognition affords high cell-type selectivity and is promising for achieving nonhepatic oligonucleotide targeting. The use of such novel protein scaffolds, including designed ankyrin repeat proteins (DARPins), for oligonucleotide delivery is attractive for achieving effective tissue targeting. Issues for further development and optimization to advance approaches for extrahepatic oligonucleotide delivery by nanoparticles or bioconjugates are discussed.
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Affiliation(s)
- Johannes Winkler
- Department of Cardiology, Medical University of Vienna , Vienna, Austria
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33
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Tomassi S, Ieranò C, Mercurio ME, Nigro E, Daniele A, Russo R, Chambery A, Baglivo I, Pedone PV, Rea G, Napolitano M, Scala S, Cosconati S, Marinelli L, Novellino E, Messere A, Di Maro S. Cationic nucleopeptides as novel non-covalent carriers for the delivery of peptide nucleic acid (PNA) and RNA oligomers. Bioorg Med Chem 2018; 26:2539-2550. [PMID: 29656988 DOI: 10.1016/j.bmc.2018.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
Cationic nucleopeptides belong to a family of synthetic oligomers composed by amino acids and nucleobases. Their capability to recognize nucleic acid targets and to cross cellular membranes provided the basis for considering them as novel non-covalent delivery agents for nucleic acid pharmaceuticals. Herein, starting from a 12-mer nucleopeptide model, the number of cationic residues was modulated in order to obtain new nucleopeptides endowed with high solubility in acqueous medium, acceptable bio-stability, low cytotoxicity and good capability to bind nucleic acid. Two candidates were selected to further investigate their potential as nucleic acid carriers, showing higher efficiency to deliver PNA in comparison with RNA. Noteworthy, this study encourages the development of nucleopeptides as new carriers to extend the known strategies for those nucleic acid analogues, especially PNA, that still remain difficult to drive into the cells.
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Affiliation(s)
- Stefano Tomassi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Caterina Ieranò
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS-Napoli, 80131 Naples, Italy
| | - Maria Emilia Mercurio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ersilia Nigro
- Department of Cardiothoracic and Respiratory Sciences, University of Campania "Luigi Vanvitelli", Via Leonardo Bianchi c/o Ospedale Monaldi, 80131 Naples, Italy
| | - Aurora Daniele
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy; Ceinge-Biotecnologie Avanzate S.c.a r.l., Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Giuseppina Rea
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS-Napoli, 80131 Naples, Italy
| | - Maria Napolitano
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS-Napoli, 80131 Naples, Italy
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS-Napoli, 80131 Naples, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy.
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy.
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34
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Kapadiya K, Jadeja Y, Khunt R. Synthesis of Purine-based Triazoles by Copper (I)-catalyzed Huisgen Azide-Alkyne Cycloaddition Reaction. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.3025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Khushal Kapadiya
- School of Science, Department of Chemistry; RK University; Rajkot Gujarat India
| | - Yashwantsinh Jadeja
- Center of Excellence, NFDD Center; Saurashtra University; Rajkot Gujarat India
| | - Ranjan Khunt
- Chemical Research Laboratory, Department of Chemistry; Saurashtra University; Rajkot Gujarat India
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35
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Farzan VM, Ulashchik EA, Martynenko-Makaev YV, Kvach MV, Aparin IO, Brylev VA, Prikazchikova TA, Maklakova SY, Majouga AG, Ustinov AV, Shipulin GA, Shmanai VV, Korshun VA, Zatsepin TS. Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Bioconjug Chem 2017; 28:2599-2607. [PMID: 28921968 DOI: 10.1021/acs.bioconjchem.7b00462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a novel technique for the efficient conjugation of oligonucleotides with various alkyl azides such as fluorescent dyes, biotin, cholesterol, N-acetylgalactosamine (GalNAc), etc. using copper-catalysed alkyne-azide cycloaddition on the solid phase and CuI·P(OEt)3 as a catalyst. Conjugation is carried out in an oligonucleotide synthesizer in fully automated mode and is coupled to oligonucleotide synthesis and on-column deprotection. We also suggest a set of reagents for the construction of diverse conjugates. The sequential double-click procedure using a pentaerythritol-derived tetraazide followed by the addition of a GalNAc or Tris-GalNAc alkyne gives oligonucleotide-GalNAc dendrimer conjugates in good yields with minimal excess of sophisticated alkyne reagents. The approach is suitable for high-throughput synthesis of oligonucleotide conjugates ranging from fluorescent DNA probes to various multi-GalNAc derivatives of 2'-modified siRNA.
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Affiliation(s)
- Valentina M Farzan
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Yury V Martynenko-Makaev
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Maksim V Kvach
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Tatiana A Prikazchikova
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Svetlana Yu Maklakova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia
| | - Alexander G Majouga
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,National University of Science and Technology "MISiS" , Leninskiy Prospect 4, Moscow 119991, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Gause Institute of New Antibiotics , Bolshaya Pirogovskaya 11, Moscow 119021, Russia
| | - Timofei S Zatsepin
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia.,Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
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36
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Synthesis of 5'-GalNAc-Conjugated Oligonucleotides: A Comparison of Solid and Solution-Phase Conjugation Strategies. Molecules 2017; 22:molecules22081356. [PMID: 28809818 PMCID: PMC6152335 DOI: 10.3390/molecules22081356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022] Open
Abstract
Antisense oligonucleotides (ASOs) conjugated to triantennary N-acetyl galactosamine (GalNAc) ligands represent an emerging approach to antisense therapy. Our current generation of GalNAc-ASO conjugates link the GalNAc to the 5′-terminus of the ASO. The conjugation reaction can be accomplished using solution-phase or solid-phase techniques. Here we show a direct comparison of a solution-phase and a solid-phase conjugation strategy. The solution-phase approach, using amine-pentafluorophenyl (PFP) ester coupling, is higher yielding and gives material of slightly higher purity, but requires several additional unit operations and longer production time. The solid-phase approach, using a protected GalNAc ligand phosphoramidite, is more expedient, but results in lower yield and purity. Both strategies efficiently deliver conjugated material in excellent purity.
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37
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Cao W, Hu N, Yuan Y, Cheng J, Guo X, Wang Y, Wang X, Hu P. Effects of Tilianin on Proliferation, Migration and TGF-β/Smad Signaling in Rat Vascular Smooth Muscle Cells Induced with Angiotensin II. Phytother Res 2017. [PMID: 28620995 DOI: 10.1002/ptr.5846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Wenjiang Cao
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
| | - Na Hu
- College of Medicine; Shihezi University; Xinjiang 832002 China
| | - Yong Yuan
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
| | - Jiang Cheng
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
| | - Xinhong Guo
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
| | - Yanfang Wang
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
- College of Medicine; Shihezi University; Xinjiang 832002 China
| | - Xinchun Wang
- First Affiliated Hospital of the Medical College; Shihezi University; Xinjiang 832008 China
- College of Medicine; Shihezi University; Xinjiang 832002 China
| | - Ping Hu
- College of Pharmaceutical Sciences and Innovative Drug Research Centre; Chongqing University; 55 South Daxuecheng Road Chongqing 401331 China
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38
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Kumar R, Ries A, Wengel J. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units. Molecules 2017; 22:molecules22050852. [PMID: 28531137 PMCID: PMC6153924 DOI: 10.3390/molecules22050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2′-N-alkyne 2′-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.
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Affiliation(s)
- Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
- Department of Chemistry, University of Delhi, Delhi 110007, India.
| | - Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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39
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Saneyoshi H, Yamamoto Y, Kondo K, Hiyoshi Y, Ono A. Conjugatable and Bioreduction Cleavable Linker for the 5'-Functionalization of Oligonucleotides. J Org Chem 2017; 82:1796-1802. [PMID: 28112510 DOI: 10.1021/acs.joc.6b02527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient conjugatable and bioreduction cleavable linker was designed and synthesized for the 5'-terminal ends of oligonucleotides. A phosphoramidite reagent bearing this linker was successfully applied to solid phase synthesis and incorporated at the 5'-terminal ends of oligonucleotides. The controlled pore glass (CPG)-supported oligonucleotides were subsequently conjugated to a diverse range of functional molecules using a CuAAC reaction. The synthesized oligonucleotide conjugates were then cleaved using a nitroreductase/NADH bioreduction system to release the naked oligonucleotides.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuta Yamamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Kazuhiko Kondo
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuki Hiyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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40
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Okholm AH, Kjems J. DNA nanovehicles and the biological barriers. Adv Drug Deliv Rev 2016; 106:183-191. [PMID: 27276176 DOI: 10.1016/j.addr.2016.05.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/19/2016] [Accepted: 05/26/2016] [Indexed: 01/10/2023]
Abstract
DNA is emerging as a smart material to construct nanovehicles for targeted drug delivery. The programmability of Watson-Crick base paring enables construction of defined and dynamic DNA nanostructures of almost arbitrary shape and DNA can readily be functionalized with a variety of molecular modules. The applications of DNA nanostructures are still in its infancy, but one of the high expectations are to deliver solutions for targeted therapy. Nucleic acids, however, do not easily enter cells unassisted and biological barriers and harsh nucleolytic conditions in the human body must also be overcome. Here, we highlight recent strategies for DNA nanostructures in drug delivery, DNA nanovehicles, to facilitate targeting and crossing of the biological barriers. In light of this, we discuss future solutions and challenges for DNA nanovehicles to unravel their great potential to facilitate targeted drug delivery.
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Affiliation(s)
- Anders H Okholm
- Department of Molecular Biology and Genetics, University of Aarhus, C. F. Møllers Allé 3, 8000 Aarhus C, Denmark; Center for DNA Nanotechnology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, University of Aarhus, C. F. Møllers Allé 3, 8000 Aarhus C, Denmark; Center for DNA Nanotechnology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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41
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Ries A, Kumar R, Lou C, Kosbar T, Vengut-Climent E, Jørgensen PT, Morales JC, Wengel J. Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2'-Amino-LNA Monomers. J Org Chem 2016; 81:10845-10856. [PMID: 27736097 DOI: 10.1021/acs.joc.6b01917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Galactose-modified thymidine, LNA-T, and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2'-functionalized 2'-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2'-amino-LNA-T derivatives induced remarkable 3'-exonuclease resistance. These results were further investigated using molecular modeling studies.
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Affiliation(s)
- Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Tamer Kosbar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Empar Vengut-Climent
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark.,Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Juan C Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain.,Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine López Neyra , CSIC Avenida del conocimiento 17, 18016 Granada, Spain
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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42
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Olszewska A, Pohl R, Brázdová M, Fojta M, Hocek M. Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins. Bioconjug Chem 2016; 27:2089-94. [PMID: 27479485 DOI: 10.1021/acs.bioconjchem.6b00342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).
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Affiliation(s)
- Agata Olszewska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University , Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Gilead Sciences & IOCB Research Center , Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
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Nothisen M, Bagilet J, Behr JP, Remy JS, Kotera M. Structure Tuning of Cationic Oligospermine-siRNA Conjugates for Carrier-Free Gene Silencing. Mol Pharm 2016; 13:2718-28. [PMID: 27398779 DOI: 10.1021/acs.molpharmaceut.6b00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligospermine-siRNA conjugates are able to induce efficient luciferase gene silencing upon carrier-free transfection. These conjugates are readily accessible by a versatile automated chemistry that we developed using a DMT-spermine phosphoramidite reagent. In this article, we used this chemistry to study a wide range of structural modifications of the oligospermine-siRNA conjugates, i.e., variation of conjugate positions and introduction of chemical modifications to increase nuclease resistance. At first we examined gene silencing activity of a series of siRNA-tris(spermine) conjugates with and without chemical modifications in standard carrier assisted conditions. The three spermine units attached at one of the two ends of the sense strand or at the 3'-end of the antisense strand are compatible with gene silencing activity whereas attachment of spermine units at the 5'-end of the antisense strand abolished the activity. 2'-O-Methylated nucleotides introduced in the sense strand are compatible while not in the antisense strand. Thiophosphate links could be used without activity loss at the 3'-end of both strands and at the 5'-end of the sense strand to conjugate oligospermine. Consequently a series of oligospermine-siRNA conjugates containing 15 to 45 spermines units in various configurations were chosen, prepared, and examined in carrier-free conditions. Attachment of 30 spermine units singly at the 5'-end of the sense strand provides the most potent carrier-free siRNA. Longevity of luciferase gene silencing was studied using oligospermine-siRNA conjugates. Five day long efficiency with more than 80% gene expression knockdown was observed upon transfection without vector. Oligospermine-siRNA conjugates targeting cell-constitutive natural lamin A/C gene were prepared. Efficient gene silencing was observed upon carrier-free transfection of siRNA conjugates containing 20 or 30 spermine residues grafted at the 5'-end of the sense strand.
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Affiliation(s)
- Marc Nothisen
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jérémy Bagilet
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jean-Paul Behr
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Jean-Serge Remy
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
| | - Mitsuharu Kotera
- Laboratoire V-SAT, CAMB, UMR 7199, Université de Strasbourg and CNRS, Faculté de Pharmacie , F-67401 Illkirch, France
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44
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Gampe CM, Hollis-Symynkywicz M, Zécri F. Covalent Chemical 5'-Functionalization of RNA with Diazo Reagents. Angew Chem Int Ed Engl 2016; 55:10283-6. [PMID: 27431506 DOI: 10.1002/anie.201604385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/02/2016] [Indexed: 12/12/2022]
Abstract
Functionalization of RNA at the 5'-terminus is important for analytical and therapeutic purposes. Currently, these RNAs are synthesized de novo starting with a chemically functionalized 5'-nucleotide, which is incorporated into RNA using chemical synthesis or biochemical techniques. Methods for direct chemical modification of native RNA would provide an attractive alternative but are currently underexplored. Herein, we report that diazo compounds can be used to selectively alkylate the 5'-phosphate of ribo(oligo)nucleotides to give RNA labelled through a native phosphate ester bond. We applied this method to functionalize oligonucleotides with biotin and an orthosteric inhibitor of the eukaryotic initiation factor 4E (eIF4E), an enzyme involved in mRNA recognition. The modified RNA binds to eIF4E, demonstrating the utility of this labelling technique to modulate biological activity of RNA. This method complements existing techniques and may be used to chemically introduce a broad range of functional handles at the 5'-end of RNA.
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Affiliation(s)
- Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Micah Hollis-Symynkywicz
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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45
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Gampe CM, Hollis-Symynkywicz M, Zécri F. Covalent Chemical 5′-Functionalization of RNA with Diazo Reagents. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Christian M. Gampe
- Novartis Institutes for BioMedical Research; 181 Massachusetts Avenue Cambridge MA 02139 USA
| | | | - Frédéric Zécri
- Novartis Institutes for BioMedical Research; 181 Massachusetts Avenue Cambridge MA 02139 USA
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Fragment-based solid-phase assembly of oligonucleotide conjugates with peptide and polyethylene glycol ligands. Eur J Med Chem 2016; 121:132-142. [PMID: 27236069 DOI: 10.1016/j.ejmech.2016.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/25/2016] [Accepted: 05/01/2016] [Indexed: 12/26/2022]
Abstract
Ligand conjugation to oligonucleotides is an attractive strategy for enhancing the therapeutic potential of antisense and siRNA agents by inferring properties such as improved cellular uptake or better pharmacokinetic properties. Disulfide linkages enable dissociation of ligands and oligonucleotides in reducing environments found in endosomal compartments after cellular uptake. Solution-phase fragment coupling procedures for producing oligonucleotide conjugates are often tedious, produce moderate yields and reaction byproducts are frequently difficult to remove. We have developed an improved method for solid-phase coupling of ligands to oligonucleotides via disulfides directly after solid-phase synthesis. A 2'-thiol introduced using a modified nucleotide building block was orthogonally deprotected on the controlled pore glass solid support with N-butylphosphine. Oligolysine peptides and a short monodisperse ethylene glycol chain were successfully coupled to the deprotected thiol. Cleavage from the resin and full removal of oligonucleotide protection groups were achieved using methanolic ammonia. After standard desalting, and without further purification, homogenous conjugates were obtained as demonstrated by HPLC, gel electrophoresis, and mass spectrometry. The attachment of both amphiphilic and cationic ligands proves the versatility of the conjugation procedure. An antisense oligonucleotide conjugate with hexalysine showed pronounced gene silencing in a cell culture tumor model in the absence of a transfection reagent and the corresponding ethylene glycol conjugate resulted in down regulation of the target gene to nearly 50% after naked application.
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Juliano RL. The delivery of therapeutic oligonucleotides. Nucleic Acids Res 2016; 44:6518-48. [PMID: 27084936 PMCID: PMC5001581 DOI: 10.1093/nar/gkw236] [Citation(s) in RCA: 580] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/28/2016] [Indexed: 12/14/2022] Open
Abstract
The oligonucleotide therapeutics field has seen remarkable progress over the last few years with the approval of the first antisense drug and with promising developments in late stage clinical trials using siRNA or splice switching oligonucleotides. However, effective delivery of oligonucleotides to their intracellular sites of action remains a major issue. This review will describe the biological basis of oligonucleotide delivery including the nature of various tissue barriers and the mechanisms of cellular uptake and intracellular trafficking of oligonucleotides. It will then examine a variety of current approaches for enhancing the delivery of oligonucleotides. This includes molecular scale targeted ligand-oligonucleotide conjugates, lipid- and polymer-based nanoparticles, antibody conjugates and small molecules that improve oligonucleotide delivery. The merits and liabilities of these approaches will be discussed in the context of the underlying basic biology.
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Affiliation(s)
- Rudolph L Juliano
- UNC Eshelman School of Pharmacy and UNC School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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48
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Polyamine-oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics. Future Med Chem 2015; 7:1733-49. [PMID: 26424049 DOI: 10.4155/fmc.15.90] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chemical modification and/or the conjugation of small functional molecules to oligonucleotides have significantly improved their biological and biophysical properties, addressing issues such as poor cell penetration, stability to nucleases and low affinity for their targets. Here, the authors review the literature reporting on the biophysical, biochemical and biological properties of one particular class of modification - polyamine-oligonucleotide conjugates. Naturally derived and synthetic polyamines have been grafted onto a variety of oligonucleotide formats, including antisense oligonucleotides and siRNAs. In many cases this has had beneficial effects on their properties such as target hybridization, nuclease resistance, cellular uptake and activity. Polyamine-oligonucleotide conjugation, therefore, represents a promising direction for the further development of oligonucleotide-based therapeutics and tools.
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49
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Therapeutic oligonucleotides with polyethylene glycol modifications. Future Med Chem 2015; 7:1721-31. [PMID: 26465713 DOI: 10.4155/fmc.15.94] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the field of oligonucleotide drugs, the attachment of PEG is a well-established strategy to prevent enzymatic degradation and avoid renal elimination. Pegaptanib and other oligonucleotides in clinical development utilize the attachment of linear or branched high molecular weight PEG chains for increase of accumulation and duration of the effect after local or systemic application. The length of PEG chains is decisive for the pharmacokinetic and pharmacodynamic effects. Longer chains increase circulation times, but generally decrease gene-silencing efficiencies for antisense and siRNA agents and binding affinities for aptamers. Shorter chains are less efficient in preventing renal filtration, but have also less impact on the gene-silencing machinery and binding kinetics.
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50
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Concise postsynthetic preparation of oligonucleotide-oligopeptide conjugates through facile disulfide bond formation. Future Med Chem 2015; 7:1657-73. [PMID: 26381134 DOI: 10.4155/fmc.15.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Despite recent advances, major hurdles still need to be cleared for widespread application of therapeutic antisense technologies. In particular, pharmacokinetic properties and efficient cellular uptake need to be improved through chemical derivatization or bioconjugation. RESULTS The 2'-O-thioethylene nucleotide building block affords easy implementation into standard oligonucleotide synthesis protocols and was used to attach oligolysine chains to phosphodiester oligonucleotides by direct reaction with S-sulfonate protected peptides. Efficient gene silencing was induced in a cell culture model after transfection reagent-free application of the conjugates. CONCLUSION A facile optimized procedure for generating oligonucleotide-peptide conjugates was established. The attachment of short basic peptides via a labile linker is sufficient to enhance membrane permeability of oligonucleotides and result in successful gene silencing.
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