1
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Rahman M, Sahoo A, Almalki WH, Almujri SS, Altamimi ASA, Alhamyani A, Akhter S. Peptide spiders are emerging as novel therapeutic interventions for nucleic acid delivery. Drug Discov Today 2024; 29:104021. [PMID: 38750928 DOI: 10.1016/j.drudis.2024.104021] [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: 12/21/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/21/2024]
Abstract
The FDA has approved many nucleic acid (NA)-based products. The presence of charges and biological barriers however affect stability and restrict widespread use. The electrostatic complexation of peptide with polyethylene glycol-nucleic acids (PEG-NAs) via nonreducible and reducible agents lead to three parts at one platform.. The reducible linkage made detachment of siRNA from PEG easy compared with a nonreducible linkage. A peptide spider produces a small hydrodynamic particle size, which can improve drug release and pharmacokinetics. Several examples of peptide spiders that enhance stability, protection and transfection efficiency are discussed. Moreover, this review also covers the challenges, future perspectives and unmet needs of peptide-PEG-NAs conjugates for NAs delivery.
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Affiliation(s)
- Mahfoozur Rahman
- Department of Pharmaceutical Sciences, Shalom Institute of Health & Allied Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad 211007, Uttar Pradesh, India.
| | - Ankit Sahoo
- College of Pharmacy, J.S. University, Shikohabad, Firozabad, Uttar Pradesh 283135, India
| | - Waleed H Almalki
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Asir-Abha 61421, Saudi Arabia
| | | | - Abdurrahman Alhamyani
- Pharmaceuticals Chemistry Department, Faculty of Clinical Pharmacy, Al Baha University, Al Baha 65779, Saudi Arabia
| | - Sohail Akhter
- Senior Principal Scientist, Global R&D, Pfizer, Sandwich, UK
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2
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Del Bene A, D'Aniello A, Tomassi S, Merlino F, Mazzarella V, Russo R, Chambery A, Cosconati S, Di Maro S, Messere A. Ultrasound-assisted Peptide Nucleic Acids synthesis (US-PNAS). ULTRASONICS SONOCHEMISTRY 2023; 95:106360. [PMID: 36913782 PMCID: PMC10024050 DOI: 10.1016/j.ultsonch.2023.106360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Herein, we developed an innovative and easily accessible solid-phase synthetic protocol for Peptide Nucleic Acid (PNA) oligomers by systematically investigating the ultrasonication effects in all steps of the PNA synthesis (US-PNAS). When compared with standard protocols, the application of the so-obtained US-PNAS approach succeeded in improving the crude product purities and the isolated yields of different PNA, including small or medium-sized oligomers (5-mer and 9-mer), complex purine-rich sequences (like a 5-mer Guanine homoligomer and the telomeric sequence TEL-13) and longer oligomers (such as the 18-mer anti-IVS2-654 PNA and the 23-mer anti-mRNA 155 PNA). Noteworthy, our ultrasound-assisted strategy is compatible with the commercially available PNA monomers and well-established coupling reagents and only requires the use of an ultrasonic bath, which is a simple equipment generally available in most synthetic laboratories.
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Affiliation(s)
- Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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3
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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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4
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Zhang X, Zhang Z, Xue X, Fan T, Tan C, Liu F, Tan Y, Jiang Y. PROTAC Degrader of Estrogen Receptor α Targeting DNA-Binding Domain in Breast Cancer. ACS Pharmacol Transl Sci 2022; 5:1109-1118. [PMID: 36407946 PMCID: PMC9667539 DOI: 10.1021/acsptsci.2c00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 12/24/2022]
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) are a powerful class of drugs that selectively degrade the proteins of interest (POIs) through cellular ubiquitination mechanisms. Estrogen receptor α (ERα) plays a vital role in the pathogenesis and treatment of breast cancer. In this work, the DNA-binding domain (DBD) of ERα was selected as the target to avoid drug resistance caused by the ligand-binding domain (LBD) of ERα. The estrogen response element (ERE), a natural DNA sequence binding with DBD of ERα, was chosen as a recognized unit of PROTAC. Therefore, we designed a nucleic acid-conjugated PROTAC, ERE-PROTAC, via a click reaction, in which the ERE sequence recruits ERα and the typical small molecule VH032 recruits the von Hippel-Lindau (VHL) E3 ligase. The proposed ERE-PROTAC showed to efficiently and reversibly degrade ERα in different breast cancer cells by targeting the DBD, indicating its potential to overcome the current resistance caused by LBD mutations.
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Affiliation(s)
| | | | - Xiaoqi Xue
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Tingting Fan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Feng Liu
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Ying Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
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5
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Li C, Callahan AJ, Phadke KS, Bellaire B, Farquhar CE, Zhang G, Schissel CK, Mijalis AJ, Hartrampf N, Loas A, Verhoeven DE, Pentelute BL. Automated Flow Synthesis of Peptide-PNA Conjugates. ACS CENTRAL SCIENCE 2022; 8:205-213. [PMID: 35233452 PMCID: PMC8874765 DOI: 10.1021/acscentsci.1c01019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/04/2023]
Abstract
Antisense peptide nucleic acids (PNAs) have yet to translate to the clinic because of poor cellular uptake, limited solubility, and rapid elimination. Cell-penetrating peptides (CPPs) covalently attached to PNAs may facilitate clinical development by improving uptake into cells. We report an efficient technology that utilizes a fully automated fast-flow instrument to manufacture CPP-conjugated PNAs (PPNAs) in a single shot. The machine is rapid, with each amide bond being formed in 10 s. Anti-IVS2-654 PPNA synthesized with this instrument presented threefold activity compared to transfected PNA in a splice-correction assay. We demonstrated the utility of this approach by chemically synthesizing eight anti-SARS-CoV-2 PPNAs in 1 day. A PPNA targeting the 5' untranslated region of SARS-CoV-2 genomic RNA reduced the viral titer by over 95% in a live virus infection assay (IC50 = 0.8 μM). Our technology can deliver PPNA candidates to further investigate their potential as antiviral agents.
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Affiliation(s)
- Chengxi Li
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alex J. Callahan
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kruttika S. Phadke
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Bryan Bellaire
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Charlotte E. Farquhar
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Genwei Zhang
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carly K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander J. Mijalis
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David E. Verhoeven
- Department
of Veterinary Microbiology and Preventive Medicine, College of Veterinary
Medicine, Iowa State University, Ames, Iowa 50011 United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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6
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Liczner C, Hanna CC, Payne RJ, Wilds CJ. Generation of oligonucleotide conjugates via one-pot diselenide-selenoester ligation-deselenization/alkylation. Chem Sci 2022; 13:410-420. [PMID: 35126973 PMCID: PMC8729807 DOI: 10.1039/d1sc04937b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
A breadth of strategies are needed to efficiently modify oligonucleotides with peptides or lipids to capitalize on their therapeutic and diagnostic potential, including the modulation of in vivo chemical stability and for applications in cell-targeting and cell-permeability. The chemical linkages typically used in peptide oligonucleotide conjugates (POCs) have limitations in terms of stability and/or ease of synthesis. Herein, we report an efficient method for POC synthesis using a diselenide-selenoester ligation (DSL)-deselenization strategy that rapidly generates a stable amide linkage between the two biomolecules. This conjugation strategy is underpinned by a novel selenide phosphoramidite building block that can be incorporated into an oligonucleotide by solid-phase synthesis to generate diselenide dimer molecules. These can be rapidly ligated with peptide selenoesters and, following in situ deselenization, lead to the efficient generation of POCs. The diselenide within the oligonucleotide also serves as a flexible functionalisation handle that can be leveraged for fluorescent labelling, as well as for alkylation to generate micelles.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University 7141 Rue Sherbrooke Ouest Montréal Québec H4B 1R6 Canada
| | - Cameron C Hanna
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University 7141 Rue Sherbrooke Ouest Montréal Québec H4B 1R6 Canada
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7
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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8
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RNA-Peptide Conjugation through an Efficient Covalent Bond Formation. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10248920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many methods for modification of an oligonucleotide with a peptide have been developed to apply for the therapeutic and diagnostic applications or for the assembly of nanostructure. We have developed a method for the construction of receptor-based fluorescent sensors and catalysts using the ribonucleopeptide (RNP) as a scaffold. Formation of a covalent linkage between the RNA and the peptide subunit of RNP improved its stability, thereby expanding the application of functional RNPs. A representative method was applied for the formation of Schiff base or dihydroxy-morpholino linkage between a dialdehyde group at the 3′-end of sugar-oxidized RNA and a hydrazide group introduced at the C-terminal of a peptide subunit through a flexible peptide linker. In this report, we investigated effects of the solution pH and contribution of the RNA and peptide subunits to the conjugation reaction by using RNA and peptide mutants. The reaction yield reached 90% at a wide range of solution pH with reaction within 3 h. The efficient reaction was mainly supported by the electrostatic interaction between the RNA subunit and the cationic peptide subunit of the RNP scaffold. Formation of the RNP complex was verified to efficiently promote the reaction for construction of the RNA-peptide conjugate.
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9
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Sabale P, Ambi UB, Srivatsan SG. Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs. ACS OMEGA 2018; 3:15343-15352. [PMID: 30556003 PMCID: PMC6289544 DOI: 10.1021/acsomega.8b02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
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10
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Wierzba AJ, Maximova K, Wincenciuk A, Równicki M, Wojciechowska M, Nexø E, Trylska J, Gryko D. Does a Conjugation Site Affect Transport of Vitamin B 12 -Peptide Nucleic Acid Conjugates into Bacterial Cells? Chemistry 2018; 24:18772-18778. [PMID: 30286265 DOI: 10.1002/chem.201804304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Indexed: 12/14/2022]
Abstract
Gram-negative bacteria develop specific systems for the uptake of scarce nutrients, including vitamin B12 . These uptake pathways may be utilized for the delivery of biologically relevant molecules into cells. Indeed, it was recently reported that vitamin B12 transported an antisense peptide nucleic acid (PNA) into Escherichia coli and Salmonella Typhimurium cells. The present studies indicate that the conjugation site of PNA to vitamin B12 has an impact on PNA transport into bacterial cells. Toward this end, a specifically designed PNA oligomer has been tethered at various positions of vitamin B12 (central Co, R5' -OH, c and e amide chains, meso position, and at the hydroxy group of cobinamide) by using known or newly developed methodologies and tested for the uptake of the synthesized conjugates by E. coli. Compounds in which the PNA oligonucleotide was anchored at the R5' -OH position were transported more efficiently than that of other compounds tethered at the peripheral positions around the corrin ring. Of importance is the fact that, contrary to mammalian organisms, E. coli also takes up cobinamide, which is an incomplete corrinoid. This selectivity opens up ways to fight bacterial infections.
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Affiliation(s)
- Aleksandra J Wierzba
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Ksenia Maximova
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Aleksandra Wincenciuk
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics, and Natural Sciences, Banacha 2c, 02-097, Warsaw, Poland
| | - Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Ebba Nexø
- Department of Clinical Biochemistry, Aarhus University Hospital, PalleJuul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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11
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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12
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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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13
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Toh DFK, Patil KM, Chen G. Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids. J Vis Exp 2017:56221. [PMID: 28994801 PMCID: PMC5752312 DOI: 10.3791/56221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNAs are emerging as important biomarkers and therapeutic targets. Thus, there is great potential in developing chemical probes and therapeutic ligands for the recognition of RNA sequence and structure. Chemically modified Peptide Nucleic Acid (PNA) oligomers have been recently developed that can recognize RNA duplexes in a sequence-specific manner. PNAs are chemically stable with a neutral peptide-like backbone. PNAs can be synthesized relatively easily by the manual Boc-chemistry solid-phase peptide synthesis method. PNAs are purified by reverse-phase HPLC, followed by molecular weight characterization by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Non-denaturing polyacrylamide gel electrophoresis (PAGE) technique facilitates the imaging of the triplex formation, because carefully designed free RNA duplex constructs and PNA bound triplexes often show different migration rates. Non-denaturing PAGE with ethidium bromide post staining is often an easy and informative technique for characterizing the binding affinities and specificities of PNA oligomers. Typically, multiple RNA hairpins or duplexes with single base pair mutations can be used to characterize PNA binding properties, such as binding affinities and specificities. 2-Aminopurine is an isomer of adenine (6-aminopurine); the 2-aminopurine fluorescence intensity is sensitive to local structural environment changes, and is suitable for the monitoring of triplex formation with the 2-aminopurine residue incorporated near the PNA binding site. 2-Aminopurine fluorescence titration can also be used to confirm the binding selectivity of modified PNAs towards targeted double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). UV-absorbance-detected thermal melting experiments allow the measurement of the thermal stability of PNA-RNA duplexes and PNA·RNA2 triplexes. Here, we describe the synthesis and purification of PNA oligomers incorporating modified residues, and describe biochemical and biophysical methods for characterization of the recognition of RNA duplexes by the modified PNAs.
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Affiliation(s)
- Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University;
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14
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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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15
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Flett FJ, Walton JGA, Mackay CL, Interthal H. Click chemistry generated model DNA-peptide heteroconjugates as tools for mass spectrometry. Anal Chem 2016; 87:9595-9. [PMID: 26335278 DOI: 10.1021/acs.analchem.5b02047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
UV cross-linking of nucleic acids to proteins in combination with mass spectrometry is a powerful technique to identify proteins, peptides, and the amino acids involved in intermolecular interactions within nucleic acid-protein complexes. However, the mass spectrometric identification of cross-linked nucleic acid-protein heteroconjugates in complex mixtures and MS/MS characterization of the specific sites of cross-linking is extremely challenging. As a tool for the optimization of sample preparation, ionization, fragmentation, and detection by mass spectrometry, novel synthetic DNA-peptide heteroconjugates were generated to act as mimics of UV cross-linked heteroconjugates. Click chemistry was employed to cross-link peptides to DNA oligonucleotides. These heteroconjugates were fully characterized by high resolution FTICR mass spectrometry and by collision-induced dissociation (CID) following nuclease P1 digestion of the DNA moiety to a single nucleotide monophosphate. This allowed the exact site of the cross-linking within the peptide to be unambiguously assigned. These synthetic DNA-peptide heteroconjugates have the potential to be of use for a variety of applications that involve DNA-peptide heteroconjugates.
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Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, United Kingdom
| | - Jeffrey G A Walton
- School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - C Logan Mackay
- School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, United Kingdom
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16
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Duan Q, Lu K, Ma L, Zhao D. Concise Synthesis of Triazole-Linked 5'-Peptide-Oligonucleotide Conjugates by Click Chemistry. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:579-89. [PMID: 26167666 DOI: 10.1080/15257770.2015.1037455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A concise synthesis of oligonucleotide 5'-peptide-conjugates via copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition in aqueous solution is described. Synthesis of reagents was accomplished by on-column derivatization of corresponding peptides and oligonucleotides. This method is well suited for the preparation of peptide-oligonucleotide conjugates containing 1,2,3-triazole linkage between the 5'-position of an oligonucleotide and the N-terminus of a peptide.
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Affiliation(s)
- Qunpeng Duan
- a School of Material and Chemical Engineering, Henan Institute of Engineering , Zhengzhou , China
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17
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Kath-Schorr S. Cycloadditions for Studying Nucleic Acids. Top Curr Chem (Cham) 2015; 374:4. [PMID: 27572987 DOI: 10.1007/s41061-015-0004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.
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Affiliation(s)
- Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, University of Bonn, Bonn, Germany.
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18
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Boisguérin P, Deshayes S, Gait MJ, O'Donovan L, Godfrey C, Betts CA, Wood MJA, Lebleu B. Delivery of therapeutic oligonucleotides with cell penetrating peptides. Adv Drug Deliv Rev 2015; 87:52-67. [PMID: 25747758 PMCID: PMC7102600 DOI: 10.1016/j.addr.2015.02.008] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/15/2022]
Abstract
Oligonucleotide-based drugs have received considerable attention for their capacity to modulate gene expression very specifically and as a consequence they have found applications in the treatment of many human acquired or genetic diseases. Clinical translation has been often hampered by poor biodistribution, however. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular delivery of non-permeant biomolecules such as nucleic acids. This review focuses on CPP-delivery of several classes of oligonucleotides (ONs), namely antisense oligonucleotides, splice switching oligonucleotides (SSOs) and siRNAs. Two main strategies have been used to transport ONs with CPPs: covalent conjugation (which is more appropriate for charge-neutral ON analogues) and non-covalent complexation (which has been used for siRNA delivery essentially). Chemical synthesis, mechanisms of cellular internalization and various applications will be reviewed. A comprehensive coverage of the enormous amount of published data was not possible. Instead, emphasis has been put on strategies that have proven to be effective in animal models of important human diseases and on examples taken from the authors' own expertise.
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Affiliation(s)
- Prisca Boisguérin
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France.
| | - Sébastien Deshayes
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Michael J Gait
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Liz O'Donovan
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Caroline Godfrey
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Corinne A Betts
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Bernard Lebleu
- UMR 5235 CNRS, Université Montpellier 2, Place Eugene Bataillon, Montpellier 34095, France
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19
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Serva S, Lagunavičius A. Direct conjugation of peptides and 5-hydroxymethylcytosine in DNA. Bioconjug Chem 2015; 26:1008-12. [PMID: 25982286 DOI: 10.1021/acs.bioconjchem.5b00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent discovery of functional 5-hydroxymethylcytosine in vertebrate genomes prompted for elaboration of methods to localize this modification at the nucleotide resolution level. Among several covalent modification-based approaches, atypical activity of cytosine-5 DNA methyltransferases to couple small molecules to 5-hydroxymethylcytosine stands out for acceptance of broad range of ligands. We went further to explore the possibility for methyltransferase-maintained coupling of compounds possessing autonomous functions. Functionalization of DNA was achieved by direct conjugation of chemically synthesized peptides of regular structure. Sequence, residue, and position-specific coupling of DNA containing 5-hydroxymethylcytosine and different peptides has been demonstrated, with the nature of the resulting conjugates confirmed by protease treatment and mass spectrometry. Coupling products were compatible with affinity-driven separation from the unmodified DNA. This approach highlights an emerging avenue toward the enzymatic, sequence-specific DNA functionalization, enabling a single step merge of the DNA and peptide moieties into a bifunctional entity.
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Affiliation(s)
- Saulius Serva
- †Thermo Fisher Scientific Baltics, Graičiu̅no 8, Vilnius LT-02241, Lithuania.,‡Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Vilnius University, MK Čiurlionio 21/27, LT-03101 Vilnius, Lithuania
| | - Arūnas Lagunavičius
- †Thermo Fisher Scientific Baltics, Graičiu̅no 8, Vilnius LT-02241, Lithuania
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20
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Devi G, Ganesh KN. 1,4-linked 1,2,3-Triazole des-peptidic analogues of PNA (TzNA): Synthesis of TzNA oligomers by "click" reaction on solid phase and stabilization of derived triplexes with DNA. ARTIFICIAL DNA, PNA & XNA 2014; 1:68-75. [PMID: 21686241 DOI: 10.4161/adna.1.2.13185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Revised: 07/01/2010] [Accepted: 07/27/2010] [Indexed: 11/19/2022]
Abstract
1,2,3-triazole analogues of PNA (TzNA) in which the amide link in backbone is replaced by triazole ring is synthesized on solid phase by 'click' chemistry and such triazolothymine PNA chimeric oligomers are shown to significantly stabilize the derived PNA(2):DNA triplexes. With increasing number of triazole units in the backbone, single stranded PNA oligomers exhibit enhanced self-ordering.
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Affiliation(s)
- Gitali Devi
- Division of Organic Chemistry; National Chemical Laboratory; Pune, India
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21
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Astakhova IK, Hansen LH, Vester B, Wengel J. Peptide-LNA oligonucleotide conjugates. Org Biomol Chem 2013; 11:4240-9. [PMID: 23681061 DOI: 10.1039/c3ob40786a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although peptide-oligonucleotide conjugates (POCs) are well-known for nucleic acids delivery and therapy, reports on internal attachment of peptides to oligonucleotides are limited in number. To develop a convenient route for preparation of internally labeled POCs with improved biomedical properties, peptides were introduced into oligonucleotides via a 2'-alkyne-2'-amino-LNA scaffold. Derivatives of methionine- and leucine-enkephalins were chosen as model peptides of mixed amino acid content, which were singly and doubly incorporated into LNA/DNA strands using highly efficient copper(i)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry. DNA/RNA target binding affinity and selectivity of the resulting POCs were improved in comparison to LNA/DNA mixmers and unmodified DNA controls. This clearly demonstrates that internal attachment of peptides to oligonucleotides can significantly improve biomolecular recognition by synthetic nucleic acid analogues. Circular dichroism (CD) measurements showed no distortion of the duplex structure by the incorporated peptide chains while studies in human serum indicated superior stability of the POCs compared to LNA/DNA mixmers and unmodified DNA references. Molecular modeling suggests strong interactions between positively charged regions of the peptides and the negative oligonucleotide backbones which leads to clamping of the peptides in a fixed orientation along the duplexes.
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center and the Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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22
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Lin F, Yu J, Tang W, Zheng J, Xie S, Becker ML. Postelectrospinning “Click” Modification of Degradable Amino Acid-Based Poly(ester urea) Nanofibers. Macromolecules 2013. [DOI: 10.1021/ma401964e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Fei Lin
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Jiayi Yu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Wen Tang
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Jukuan Zheng
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Sibai Xie
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Matthew L. Becker
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
- Austen Bioinnovation Institute in Akron, Akron, Ohio 44308, United States
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23
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Deuss PJ, Arzumanov AA, Williams DL, Gait MJ. Parallel synthesis and splicing redirection activity of cell-penetrating peptide conjugate libraries of a PNA cargo. Org Biomol Chem 2013; 11:7621-30. [PMID: 24105028 PMCID: PMC4002126 DOI: 10.1039/c3ob41659c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/01/2013] [Indexed: 11/21/2022]
Abstract
A novel method for the parallel synthesis of peptide-biocargo conjugates was developed that utilizes affinity purification for fast isolation of the conjugates in order to avoid time consuming HPLC purification. The methodology was applied to create two libraries of cell-penetrating peptide (CPP)-PNA705 conjugates from parallel-synthesized peptide libraries. The conjugates were tested for their ability to induce splicing redirection in HeLa pLuc705 cells. The results demonstrate how the novel methodology can be applied for screening purposes in order to find suitable CPP-biocargo combinations and further optimization of CPPs.
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Affiliation(s)
- Peter J. Deuss
- Medical Research Council , Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge , CB2 0QH , UK .
| | - Andrey A. Arzumanov
- Medical Research Council , Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge , CB2 0QH , UK .
| | - Donna L. Williams
- Medical Research Council , Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge , CB2 0QH , UK .
| | - Michael J. Gait
- Medical Research Council , Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge , CB2 0QH , UK .
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24
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Kotikam V, Kumar VA. Synthesis and properties of 2′-O-[R- and S-(2-amino-3-methoxy)propyl] (R-AMP and S-AMP) nucleic acids. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.05.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Soni K, Gupta S, Gokhale SS, Dey R, Gunjal AD, Kumar VA, Pillai B. Detection and knockdown of microRNA-34a using thioacetamido nucleic acid. Nucleic Acid Ther 2013; 23:195-202. [PMID: 23647235 DOI: 10.1089/nat.2012.0411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Thioacetamido nucleic acids (TANA) contain a backbone modification of dinucleotides consisting of a 5-atom amide linker N3'-COCH2-S-CH2 at thymidine or thymidine-cytidine dimer blocks. Here, the chemical synthesis of the TANA linked 5-methyl-cytidine-cytidine ((Me)cc) dimer block and its incorporation into the DNA sequence, complementary to human microRNA 34 (miR-34) is described. Further, for the first time, we demonstrate the biological applications of TANA modified oligonucleotides in detection and intracellular knockdown of a cancer related microRNA in comparison with DNA containing locked nucleic acid (LNA) and 2'-O-methyl modifications. The human microRNA miR-34 is a pro-apoptotic microRNA under the transcriptional control of protein 53 (p53). It gets expressed in response to DNA damage and regulates several cell cycle and apoptosis related targets. Here, we show that the TANA modified antisense oligonucleotide binds specifically to miR-34a, allowing its detection using primer extension. We also show that, using the TANA modified antisense oligonucleotide against miR-34a, intracellular levels of miR-34 can be reduced, and consequently, the expression of its target oncogene V-myc myelocytomatosis viral related oncogene, neuroblastoma derived (MYCN) is enhanced. Further, we assessed the toxicity and serum stability of the oligonucleotide to conclude that it is suitable for detection and modulation of the vital biomarker and tumor suppressor microRNA.
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Affiliation(s)
- Kartik Soni
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
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26
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St. Amant AH, Engbers C, Hudson RH. A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates. ARTIFICIAL DNA, PNA & XNA 2013; 4:4-10. [PMID: 23422048 PMCID: PMC3654728 DOI: 10.4161/adna.23982] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 11/19/2022]
Abstract
The synthesis of an azide containing PNA monomer is described. The monomer was incorporated into two PNA sequences for the purpose of synthesizing an intercalating fluorophore-labeled PNA and a metal binding hairpin using a solid phase copper catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Click chemistry was performed using 2-ethynylfluorene or 1-ethynylpyrene to add a fluorophore to the PNA, which were tested for their ability to recognize an abasic site on a DNA target. A PNA hairpin possessing azide monomers at each termini was synthesized and reacted with 2-ethynylpyridine to form a hairpin that is stabilized by Ni²⁺.
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Affiliation(s)
- André H. St. Amant
- Department of Chemistry; The University of Western Ontario; London, ON Canada
| | - Christopher Engbers
- Department of Chemistry; The University of Western Ontario; London, ON Canada
| | - Robert H.E. Hudson
- Department of Chemistry; The University of Western Ontario; London, ON Canada
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27
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Ghosh PS, Hamilton AD. Noncovalent template-assisted mimicry of multiloop protein surfaces: assembling discontinuous and functional domains. J Am Chem Soc 2012; 134:13208-11. [PMID: 22839643 DOI: 10.1021/ja305360q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report here a novel noncovalent synthetic strategy for template-assembled de novo protein design. In this approach, a peptide was first conjugated with two oligoguanosine strands via click chemistry and the conjugates were then self-assembled in the presence of metal ions. G-quadruplex formation directs two peptide strands to assemble on one face of the scaffold and form an adjacent two loop surface. This approach can be used to rapidly prepare multiple two-loop structures with both homo- and heterosequences.
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Affiliation(s)
- Partha S Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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28
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Krishna H, Caruthers MH. Alkynyl phosphonate DNA: a versatile "click"able backbone for DNA-based biological applications. J Am Chem Soc 2012; 134:11618-31. [PMID: 22612466 DOI: 10.1021/ja3026714] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Major hurdles associated with DNA-based biological applications include, among others, targeted cell delivery, undesirable nonspecific effects, toxicity associated with various analogues or the reagents used to deliver oligonucleotides to cells, and stability toward intracellular enzymes. Although a plethora of diverse analogues have been investigated, a versatile methodology that can systematically address these challenges has not been developed. In this contribution, we present a new, Clickable, and versatile chemistry that can be used to rapidly introduce diverse functionality for studying these various problems. As a demonstration of the approach, we synthesized the core analogue, which is useful for introducing additional functionality, the triazolylphosphonate, and present preliminary data on its biological properties. We have developed a new phosphoramidite synthon--the alkynyl phosphinoamidite, which is compatible with conventional solid-phase oligonucleotide synthesis. Postsynthesis, the alkynylphosphonate can be functionalized via "Click" chemistry to generate the 1,2,3-triazolyl or substituted 1,2,3-triazolyl phosphonate-2'-deoxyribonucleotide internucleotide linkage. This manuscript describes the automated, solid-phase synthesis of mixed backbone oligodeoxyribonucleotides (ODNs) having 1,2,3-triazolylphosphonate (TP) as well as phosphate or thiophosphate internucleotide linkages and also 2'-OMe ribonucleotides and locked nucleic acids (LNAs) at selected sites. Nuclease stability assays demonstrate that the TP linkage is highly resistant toward 5'- and 3'-exonucleases, whereas melting studies indicate a slight destabilization when a TP-modified ODN is hybridized to its complementary RNA. A fluorescently labeled 16-mer ODN modified with two TP linkages shows efficient cellular uptake during passive transfection. Of particular interest, the subcellular distribution of TP-modified ODNs is highly dependent on cell type; a significant nuclear uptake is observed in HeLa cells, whereas diffuse cytoplasmic fluorescence is found in the WM-239A cell line. Cytoplasmic distribution is also present in human neuroblastoma cells (SK-N-F1), but Jurkat cells show both diffuse and punctate cytoplasmic uptake. Our results demonstrate that triazolylphosphonate ODNs are versatile additions to the oligonucleotide chemist's toolbox relative to designing new biological research reagents.
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Affiliation(s)
- Heera Krishna
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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29
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Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Crumpton JB, Santos WL. Site-specific incorporation of diamondoids on DNA using click chemistry. Chem Commun (Camb) 2012; 48:2018-20. [PMID: 22237385 DOI: 10.1039/c2cc16860j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and robust solid phase synthetic method for the ligation of diamondoids on the phosphate backbone of DNA with "click" chemistry using [Cu(CH(3)CN)(4)]PF(6) without a stabilizing ligand is reported. It was found that as the size of dimondoid increased, a corresponding increase in melting temperature was observed.
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Affiliation(s)
- Jason B Crumpton
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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31
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Howarth NM, Ricci (née Goujon) J. Synthesis of N-propynyl analogues of peptide nucleic acid (PNA) monomers and their use in the click reaction to prepare N-functionalized PNAs. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.09.124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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32
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Le Quement ST, Ishoey M, Petersen MT, Thastrup J, Hagel G, Nielsen TE. Solid-phase synthesis of smac peptidomimetics incorporating triazoloprolines and biarylalanines. ACS COMBINATORIAL SCIENCE 2011; 13:667-75. [PMID: 21905744 DOI: 10.1021/co200078u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Apoptotic induction mechanisms are of crucial importance for the general homeostasis of multicellular organisms. In cancer the apoptotic pathways are downregulated, which, at least partly, is due to an abundance of inhibitors of apoptosis proteins (IAPs) that block the apoptotic cascade by deactivating proteolytic caspases. The Smac protein has an antagonistic effect on IAPs, thus providing structural clues for the synthesis of new pro-apoptotic compounds. Herein, we report a solid-phase approach for the synthesis of Smac-derived tetrapeptide libraries. On the basis of a common (N-Me)AVPF sequence, peptides incorporating triazoloprolines and biarylalanines were synthesized by means of Cu(I)-catalyzed azide-alkyne cycloaddition and Pd-catalyzed Suzuki cross-coupling reactions. Solid-phase procedures were optimized to high efficiency, thus accessing all products in excellent crude purities and yields (both typically above 90%). The peptides were subjected to biological evaluation in a live/dead cellular assay which revealed that structural decorations on the AVPF sequence indeed are highly important for cytotoxicity toward HeLa cells.
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Affiliation(s)
| | - Mette Ishoey
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Mette T. Petersen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jacob Thastrup
- 2CureX, Department of Surgery, K, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400 Copenhagen NV, Denmark
| | - Grith Hagel
- 2CureX, Department of Surgery, K, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400 Copenhagen NV, Denmark
| | - Thomas E. Nielsen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Wenska M, Alvira M, Steunenberg P, Stenberg Å, Murtola M, Strömberg R. An activated triple bond linker enables 'click' attachment of peptides to oligonucleotides on solid support. Nucleic Acids Res 2011; 39:9047-59. [PMID: 21795380 PMCID: PMC3203603 DOI: 10.1093/nar/gkr603] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 07/05/2011] [Accepted: 07/06/2011] [Indexed: 11/13/2022] Open
Abstract
A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the use of a readily attachable activated triple bond linker enhances the Cu(I) catalyzed 1,3-dipolar cycloaddition ('click' reaction). The preferred scheme for conjugate preparation involves sequential conjugation to oligonucleotides on solid support of (i) an H-phosphonate-based aminolinker; (ii) the triple bond donor p-(N-propynoylamino)toluic acid (PATA); and (iii) azido-functionalized peptides. The method gives conversion of oligonucleotide to the POC on solid support, and only involves a single purification step after complete assembly. The synthesis is flexible and can be carried out without the need for specific automated synthesizers since it has been designed to utilize commercially available oligonucleotide and peptide derivatives on solid support or in solution. Methodology for the ready conversion of peptides into 'clickable' azidopeptides with the possibility of selecting either N-terminus or C-terminus connection also adds to the flexibility and usability of the method. Examples of synthesis of POCs include conjugates of oligonucleotides with peptides known to be membrane penetrating and nuclear localization signals.
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Affiliation(s)
- Malgorzata Wenska
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-141 83 Huddinge, Sweden
| | | | | | | | | | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-141 83 Huddinge, Sweden
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34
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Uhlig N, Li CJ. Alkynes as an eco-compatible “on-call” functionality orthogonal to biological conditions in water. Chem Sci 2011. [DOI: 10.1039/c1sc00164g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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35
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Abstract
Integrins have become key targets for molecular imaging and for selective delivery of anti-cancer agents. Here we review recent work concerning the targeted delivery of antisense and siRNA oligonucleotides via integrins. A variety of approaches have been used to link oligonucleotides to ligands capable of binding integrins with high specificity and affinity. This includes direct chemical conjugation, incorporating oligonucleotides into lipoplexes, and use of various polymeric nanocarriers including dendrimers. The ligand-oligonucleotide conjugate or complex associates selectively with the integrin, followed by internalization into endosomes and trafficking through subcellular compartments. Escape of antisense or siRNA from the endosome to the cytosol and nucleus may come about through endogenous trafficking mechanisms, or because of membrane disrupting capabilities built into the conjugate or complex. Thus a variety of useful strategies are available for using integrins to enhance the pharmacological efficacy of therapeutic oligonucleotides.
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Yamada T, Peng CG, Matsuda S, Addepalli H, Jayaprakash KN, Alam MR, Mills K, Maier MA, Charisse K, Sekine M, Manoharan M, Rajeev KG. Versatile site-specific conjugation of small molecules to siRNA using click chemistry. J Org Chem 2011; 76:1198-211. [PMID: 21299239 DOI: 10.1021/jo101761g] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have previously demonstrated that conjugation of small molecule ligands to small interfering RNAs (siRNAs) and anti-microRNAs results in functional siRNAs and antagomirs in vivo. Here we report on the development of an efficient chemical strategy to make oligoribonucleotide-ligand conjugates using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) or click reaction. Three click reaction approaches were evaluated for their feasibility and suitability for high-throughput synthesis: the CuAAC reaction at the monomer level prior to oligonucleotide synthesis, the solution-phase postsynthetic "click conjugation", and the "click conjugation" on an immobilized and completely protected alkyne-oligonucleotide scaffold. Nucleosides bearing 5'-alkyne moieties were used for conjugation to the 5'-end of the oligonucleotide. Previously described 2'- and 3'-O-propargylated nucleosides were prepared to introduce the alkyne moiety to the 3' and 5' termini and to the internal positions of the scaffold. Azido-functionalized ligands bearing lipophilic long chain alkyls, cholesterol, oligoamine, and carbohydrate were utilized to study the effect of physicochemical characteristics of the incoming azide on click conjugation to the alkyne-oligonucleotide scaffold in solution and on immobilized solid support. We found that microwave-assisted click conjugation of azido-functionalized ligands to a fully protected solid-support bound alkyne-oligonucleotide prior to deprotection was the most efficient "click conjugation" strategy for site-specific, high-throughput oligonucleotide conjugate synthesis tested. The siRNA conjugates synthesized using this approach effectively silenced expression of a luciferase gene in a stably transformed HeLa cell line.
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Affiliation(s)
- Takeshi Yamada
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, USA
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Meyer A, Pourceau G, Vasseur JJ, Morvan F. 5'-Bis-conjugation of oligonucleotides by amidative oxidation and click chemistry. J Org Chem 2011; 75:6689-92. [PMID: 20795720 DOI: 10.1021/jo101134z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A pent-4-ynyl tert-butyl N,N-diisopropyl phosphoramidite was coupled at the 5'-end of oligonucleotides to give a phosphite triester linkage, which forms an H-phosphonate diester linkage during treatment with dichloroacetic acid. Then an amidative oxidation with CCl(4) in the presence of an amine and a 1,3-dipolar cycloaddition with an azide under copper(I) catalysis afforded the bis-conjugated oligonucleotides with high efficiency. The introduction of a bromoalkyl group as a precursor of azidoalkyl by amidative oxidation allowed the performance of two selective 1,3-dipolar cycloadditions.
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Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS Université Montpellier 1, Université Montpellier 2, CC1704, Place E. Bataillon, 34095 Montpellier Cedex 5, France
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38
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Mercier F, Paris J, Kaisin G, Thonon D, Flagothier J, Teller N, Lemaire C, Luxen A. General method for labeling siRNA by click chemistry with fluorine-18 for the purpose of PET imaging. Bioconjug Chem 2010; 22:108-14. [PMID: 21174402 DOI: 10.1021/bc100263y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The alkyne-azide Cu(I)-catalyzed Huisgen cycloaddition, a click-type reaction, was used to label a double-stranded oligonucleotide (siRNA) with fluorine-18. An alkyne solid support CPG for the preparation of monostranded oligonucleotides functionalized with alkyne has been developed. Two complementary azide labeling agents (1-(azidomethyl)-4-[(18)F]fluorobenzene) and 1-azido-4-(3-[(18)F]fluoropropoxy)benzene have been produced with 41% and 35% radiochemical yields (decay-corrected), respectively. After annealing with the complementary strand, the siRNA was directly labeled by click chemistry with [(18)F]fluoroazide to produce the [(18)F]-radiolabeled siRNA with excellent radiochemical yield and purity.
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Affiliation(s)
- Frédéric Mercier
- Cyclotron Research Center, Université de Liège, Sart-Tilman B.30, B-4000 Liège, Belgium
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39
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Jayaprakash KN, Peng CG, Butler D, Varghese JP, Maier MA, Rajeev KG, Manoharan M. Non-Nucleoside Building Blocks for Copper-Assisted and Copper-Free Click Chemistry for the Efficient Synthesis of RNA Conjugates. Org Lett 2010; 12:5410-3. [DOI: 10.1021/ol102205j] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- K. N. Jayaprakash
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - Chang Geng Peng
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - David Butler
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - Jos P. Varghese
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - Martin A. Maier
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - Kallanthottathil G. Rajeev
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
| | - Muthiah Manoharan
- Drug Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States, and Sanmar Speciality Chemicals Ltd., Chennai, Tamil Nadu, India
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Diezmann F, Eberhard H, Seitz O. Native chemical ligation in the synthesis of internally modified oligonucleotide-peptide conjugates. Biopolymers 2010; 94:397-404. [PMID: 20593471 DOI: 10.1002/bip.21440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Peptide-oligonucleotide conjugates have frequently been synthesized to improve cellular delivery of antisense or antigene compounds, to allow the immobilization of peptide and protein conjugates on DNA arrays, or to decorate nucleic acid architectures with peptide functions. In such applications, the site of conjugation is of little importance, and peptides have predominantly been appended to one of the terminal ends of the oligonucleotide by using an oxime-, thioether-, or disulfide-linkage or native chemical ligation. We, herein, demonstrate the first coupling of peptides to sequence internal sites. This attachment mode provides better control of the spatial arrangement of peptides presented by self-assembled nucleic acid scaffolds. Internal modification requires special phosphoramidite building blocks that can be used in automated DNA synthesis. For this purpose, Fmoc/StBu-protected cysteine was attached via an aminopropargyl linker to the C5-position of uridine. The rigid triple bond conferred a high reactivity in native chemical ligation reactions of 5-6mer peptide thioesters with up to 15 nucleotides long oligonucleotides. The desired peptide-oligonucleotide conjugates were obtained in high yields after purification. UV melt experiments revealed that the peptide modification does not hamper nucleic acid hybridization. This finding marked an important step in our research program devoted to studies of multivalent presentation of peptides via modular assembly of nucleic acid complexes.
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Affiliation(s)
- Franziska Diezmann
- Institute of Chemistry, Humboldt-University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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41
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Abstract
Targeted drug delivery to specific group of cells offers an attractive strategy to minimize the undesirable side effects and achieve the therapeutic effect with a lower dose. Both linear and cyclic peptides have been explored as trafficking moiety due to ease of synthesis, structural simplicity, and low probability of undesirable immunogenicity. Peptides derived from sequence of cell surface proteins, such as intercellular adhesion molecule-1 (ICAM-1), LHRH, Bombesin, and LFA-1, have shown potent binding affinity to the target cell surface receptors. Moreover, peptides derived from ICAM-1 receptor can be internalized by the leukemic T-cells along with the conjugated moiety offering the promise to selectively treat cancers and autoimmune diseases. Systematic analyses have revealed that physicochemical properties of the drug-peptide conjugates and their mechanism of receptor-mediated cellular internalization are important controlling factors for developing a successful targeting system. This review is focused on understanding the factors involved in the development of an effective drug-peptide conjugate with an emphasis on the chemistry and biology of the conjugates. Reported results on several promising drug-peptide conjugates have been critically evaluated. The approaches and results presented here will serve as a guide to systematically approach targeted delivery of cytotoxic drug molecules using peptides for treatment of several diseases.
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Affiliation(s)
- Sumit Majumdar
- Department of Pharmaceutical Chemistry, The University of Kansas, Simons Research Laboratories, 2095 Constant Ave., Lawrence, Kansas, 66047, USA
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42
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Brown SD, Graham D. Conjugation of an oligonucleotide to Tat, a cell-penetrating peptide, via click chemistry. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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43
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Ustinov AV, Stepanova IA, Dubnyakova VV, Zatsepin TS, Nozhevnikova EV, Korshun VA. Modification of nucleic acids using [3 + 2]-dipolar cycloaddition of azides and alkynes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:437-81. [DOI: 10.1134/s1068162010040011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Avitabile C, Moggio L, D’Andrea LD, Pedone C, Romanelli A. Development of an efficient and low-cost protocol for the manual PNA synthesis by Fmoc chemistry. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.05.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Lu K, Duan QP, Ma L, Zhao DX. Chemical strategies for the synthesis of peptide-oligonucleotide conjugates. Bioconjug Chem 2010; 21:187-202. [PMID: 19856957 DOI: 10.1021/bc900158s] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The use of synthetic oligonucleotides and their mimics to inhibit gene expression by hybridizing with their target sequences has been hindered by their poor cellular uptake and inability to reach the nucleus. Covalent postsynthesis or solid-phase conjugation of peptides to oligonucleotides offers a possible solution to these problems. As feasible chemistry is a prerequisite for biological studies, development of efficient and reproducible approaches for convenient preparation of peptide-oligonucleotide conjugates has become a subject of considerable importance. The present review gives an account of the main synthetic methods available to prepare covalent conjugation of peptides to oligonucleotides.
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Affiliation(s)
- Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China.
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46
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Synthesis and ‘double click’ density functionalization of 8-aza-7-deazaguanine DNA bearing branched side chains with terminal triple bonds. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Schneggenburger PE, Worbs B, Diederichsen U. Azide reduction during peptide cleavage from solid support-the choice of thioscavenger? J Pept Sci 2010; 16:10-4. [PMID: 19950105 DOI: 10.1002/psc.1202] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peptide azides acquired growing impact because of application in bioconjugation via 'click chemistry' or Staudinger ligation. Furthermore, there are many methods established in organic synthesis addressing the reduction of azides to amines, but no observation of a reductive transformation of peptide azides during SPPS cleavage was yet reported. In the present study, the reduction of peptide azides during SPPS cleavage was investigated depending on the choice of thioscavenger, reacting as reductive species. First observed for short PNA/peptide conjugates the occurring extensive side reaction was also validated for one of the applied azide amino acid building blocks and was further investigated by applying different cleavage cocktails to a series of peptides varying in hydrophobicity and position of the azide moiety in the oligomer sequence.
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Affiliation(s)
- Philipp E Schneggenburger
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
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48
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Abstract
The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne-azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbones. In this critical review we describe some of the pioneering work that has been carried out in this area (78 references).
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Affiliation(s)
- Afaf H El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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49
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Nwe K, Brechbiel MW. Growing applications of "click chemistry" for bioconjugation in contemporary biomedical research. Cancer Biother Radiopharm 2009; 24:289-302. [PMID: 19538051 PMCID: PMC2811415 DOI: 10.1089/cbr.2008.0626] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This update summarizes the growing application of "click" chemistry in diverse areas such as bioconjugation, drug discovery, materials science, and radiochemistry. This update also discusses click chemistry reactions that proceed rapidly with high selectivity, specificity, and yield. Two important characteristics make click chemistry so attractive for assembling compounds, reagents, and biomolecules for preclinical and clinical applications. First, click reactions are bio-orthogonal; neither the reactants nor their product's functional groups interact with functionalized biomolecules. Second, the reactions proceed with ease under mild nontoxic conditions, such as at room temperature and, usually, in water. The copper-catalyzed Huisgen cycloaddition, azide-alkyne [3 + 2] dipolar cycloaddition, Staudinger ligation, and azide-phosphine ligation each possess these unique qualities. These reactions can be used to modify one cellular component while leaving others unharmed or untouched. Click chemistry has found increasing applications in all aspects of drug discovery in medicinal chemistry, such as for generating lead compounds through combinatorial methods. Bioconjugation via click chemistry is rigorously employed in proteomics and nucleic research. In radiochemistry, selective radiolabeling of biomolecules in cells and living organisms for imaging and therapy has been realized by this technology. Bifunctional chelating agents for several radionuclides useful for positron emission tomography and single-photon emission computed tomography imaging have also been prepared by using click chemistry. This review concludes that click chemistry is not the perfect conjugation and assembly technology for all applications, but provides a powerful, attractive alternative to conventional chemistry. This chemistry has proven itself to be superior in satisfying many criteria (e.g., biocompatibility, selectivity, yield, stereospecificity, and so forth); thus, one can expect it will consequently become a more routine strategy in the near future for a wide range of applications.
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Affiliation(s)
- Kido Nwe
- Radioimmune and Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1002, USA
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50
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Gramlich P, Wirges C, Manetto A, Carell T. Postsynthetische DNA-Modifizierung mithilfe der kupferkatalysierten Azid-Alkin-Cycloaddition. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802077] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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