1
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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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2
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Sultana A, Geethakumari AM, Islam Z, Kolatkar PR, Biswas KH. BRET-based biosensors for SARS-CoV-2 oligonucleotide detection. Front Bioeng Biotechnol 2024; 12:1353479. [PMID: 38887615 PMCID: PMC11181354 DOI: 10.3389/fbioe.2024.1353479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The need for the early detection of emerging pathogenic viruses and their newer variants has driven the urgent demand for developing point-of-care diagnostic tools. Although nucleic acid-based methods such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and loop-mediated isothermal amplification (LAMP) have been developed, a more facile and robust platform is still required. To address this need, as a proof-of-principle study, we engineered a prototype-the versatile, sensitive, rapid, and cost-effective bioluminescence resonance energy transfer (BRET)-based biosensor for oligonucleotide detection (BioOD). Specifically, we designed BioODs against the SARS-CoV-2 parental (Wuhan strain) and B.1.617.2 Delta variant through the conjugation of specific, fluorescently modified molecular beacons (sensor module) through a complementary oligonucleotide handle DNA functionalized with the NanoLuc (NLuc) luciferase protein such that the dissolution of the molecular beacon loop upon the binding of the viral oligonucleotide will result in a decrease in BRET efficiency and, thus, a change in the bioluminescence spectra. Following the assembly of the BioODs, we determined their kinetics response, affinity for variant-specific oligonucleotides, and specificity, and found them to be rapid and highly specific. Furthermore, the decrease in BRET efficiency of the BioODs in the presence of viral oligonucleotides can be detected as a change in color in cell phone camera images. We envisage that the BioODs developed here will find application in detecting viral infections with variant specificity in a point-of-care-testing format, thus aiding in large-scale viral infection surveillance.
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Affiliation(s)
- Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Prasanna R. Kolatkar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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3
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Terrazas M, Eritja R, Montesarchio D. Special Issue "Frontiers in Nucleic Acid Chemistry-In Memory of Professor Enrique Pedroso for His Outstanding Contributions to Nucleic Acid Chemistry". Molecules 2023; 28:7278. [PMID: 37959697 PMCID: PMC10648547 DOI: 10.3390/molecules28217278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
This Special issue is dedicated to the memory of Enrique Pedroso, Professor Emeritus of Organic Chemistry at University of Barcelona, who passed away at the age of 72 in September 2020 [...].
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Affiliation(s)
- Montserrat Terrazas
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, 08034 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, I-80126 Napoli, Italy
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4
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Basran K, Bujalska A, Karimi A, Luedtke NW. Formal [4 + 2] Cycloadditions of Maleimides on Duplex DNA. Bioconjug Chem 2023; 34:977-982. [PMID: 37290129 DOI: 10.1021/acs.bioconjchem.3c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2'-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU-maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2'-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels-Alder cycloaddition. VdU-maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.
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Affiliation(s)
- Kaleena Basran
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ashkan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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5
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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:pharmaceutics15020320. [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] [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
- Correspondence: ; Tel.: +34-934006145
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6
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Ting CY, Kolbeck PT, Colombo R, Chakiath C, Rice M, Marelli M, Christie RJ. Cyclopentadiene as a Multifunctional Reagent for Normal- and Inverse-Electron Demand Diels-Alder Bioconjugation. Bioconjug Chem 2022; 33:1609-1619. [PMID: 35943835 DOI: 10.1021/acs.bioconjchem.2c00222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Optimizing the Diels-Alder (DA) reaction for aqueous coupling has resulted in practical methods to link molecules such as drugs and diagnostic agents to proteins. Both normal electron demand (NED) and inverse electron demand (IED) DA coupling schemes have been employed, but neither mechanism entails a common multipurpose reactive group. This report focuses on expanding the bioconjugation toolbox for cyclopentadiene through the identification of reactive groups that couple through NED or IED mechanisms in aqueous solution. Dienophiles and tetrazine derivatives were screened for reactivity and selectivity toward antibodies bearing cyclopentadiene amino acids to yield bioconjugates. Twelve NED dienophiles and four tetrazine-based IED substrates were identified as capable of practical biocoupling. Furthermore, tetrazine ligation to cyclopentadiene occurred at a rate of 3.3 ± 0.5 M-1 s-1 and was capable of bioorthogonal transformations, as evidenced by the selective protein labeling in serum. Finally, an antibody-drug conjugate (ADC)-bearing monomethyl auristatin E was prepared via tetrazine conjugation to cyclopentadiene. The resulting ADC was stable and demonstrated potent activity in vitro. These findings expand the utility of cyclopentadiene as a tool to couple entities to proteins via dual DA addition mechanisms.
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Affiliation(s)
- Cheng-Yueh Ting
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Paul T Kolbeck
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Raffaele Colombo
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Chacko Chakiath
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Megan Rice
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Marcello Marelli
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - R James Christie
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
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7
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Oligonucleotide conjugation by tyrosine‐click reaction. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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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: 37] [Impact Index Per Article: 12.3] [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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9
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Liu R, Zuo R, Hudalla GA. Harnessing molecular recognition for localized drug delivery. Adv Drug Deliv Rev 2021; 170:238-260. [PMID: 33484737 PMCID: PMC8274479 DOI: 10.1016/j.addr.2021.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022]
Abstract
A grand challenge in drug delivery is providing the right dose, at the right anatomic location, for the right duration of time to maximize therapeutic efficacy while minimizing off-target toxicity and other deleterious side-effects. Two general modalities are receiving broad attention for localized drug delivery. In the first, referred to as "targeted accumulation", drugs or drug carriers are engineered to have targeting moieties that promote their accumulation at a specific tissue site from circulation. In the second, referred to as "local anchoring", drugs or drug carriers are inserted directly into the tissue site of interest where they persist for a specified duration of time. This review surveys recent advances in harnessing molecular recognition between proteins, peptides, nucleic acids, lipids, and carbohydrates to mediate targeted accumulation and local anchoring of drugs and drug carriers.
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Affiliation(s)
- Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Ran Zuo
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA.
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10
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Hill SA, Steinfort R, Hartmann L. Progress, challenges and future directions of heterocycles as building blocks in iterative methodologies towards sequence-defined oligomers and polymers. Polym Chem 2021. [DOI: 10.1039/d1py00425e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Heterocyclic building blocks for iterative methodologies leading to sequence-defined oligomers and polymers are reviewed. Solid- as well as solution-phase methods, challenges surrounding these systems and potential future directions are presented.
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Affiliation(s)
- Stephen A. Hill
- Institute of Organic and Macromolecular Chemistry
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Robert Steinfort
- Institute of Organic and Macromolecular Chemistry
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
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11
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Patil NA. Conjugation Approaches for Peptide-Mediated Delivery of Oligonucleotides Therapeutics. Aust J Chem 2021. [DOI: 10.1071/ch21131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Clavé G, Dursun E, Vasseur JJ, Smietana M. An Entry of the Chemoselective Sulfo-Click Reaction into the Sphere of Nucleic Acids. Org Lett 2020; 22:1914-1918. [DOI: 10.1021/acs.orglett.0c00265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillaume Clavé
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Enes Dursun
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
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13
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Lossouarn A, Renault K, Bailly L, Frisby A, Le Nahenec-Martel P, Renard PY, Sabot C. Maleimide-based metal-free ligation with dienes: a comparative study. Org Biomol Chem 2020; 18:3874-3887. [DOI: 10.1039/d0ob00403k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Maleimide-based Diels–Alder strategies for bioconjugation are compared in terms of dienes accessibility and stability, reactions rates, as well as products isolation and stability.
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Affiliation(s)
| | | | | | - Axel Frisby
- Normandie Univ
- CNRS
- UNIROUEN
- INSA Rouen
- 76000 Rouen
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14
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Noël M, Clément-Blanc C, Meyer A, Vasseur JJ, Morvan F. Solid Supports for the Synthesis of 3'-Aminooxy Deoxy- or Ribo-oligonucleotides and Their 3'-Conjugation by Oxime Ligation. J Org Chem 2019; 84:14854-14860. [PMID: 31615211 DOI: 10.1021/acs.joc.9b00848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mono- and triethylene glycol aminooxy derivatives were reacted with levulinic acid, protected with dimethoxytrityl, and immobilized on solid support. The resulting solid supports were used for elongation of oligonucleotides. Then, a mild ammonia treatment was applied to remove the oligonucleotide protecting groups, followed by a treatment with 50 mM methoxyamine at pH 4.2, releasing the 3'-aminooxy oligonucleotides by an oxime exchange reaction. The resulting 3'-aminooxy deoxy- or ribo-oligonucleotides were conjugated to various ketones and aldehydes with high efficiency by oxime ligation.
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Affiliation(s)
- Mathieu Noël
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Céline Clément-Blanc
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - François Morvan
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
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15
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Pagel M. Inverse electron demand Diels-Alder (IEDDA) reactions in peptide chemistry. J Pept Sci 2019; 25:e3141. [PMID: 30585397 DOI: 10.1002/psc.3141] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 01/05/2023]
Abstract
Click chemistry is applied to selectively modify, lable and ligate peptides for their use as therapeutics, in biomaterials or analytical investigations. The inverse electron demand Diels-Alder (IEDDA) reaction is a catalyst-free click reaction with pronounced chemoselectivity and fast reaction rates. Applications and achievements of the IEDDA reaction in peptide chemistry since 2008 are described in this review.
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Affiliation(s)
- Mareen Pagel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Leipzig, Germany
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16
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Renault K, Fredy JW, Renard PY, Sabot C. Covalent Modification of Biomolecules through Maleimide-Based Labeling Strategies. Bioconjug Chem 2018; 29:2497-2513. [PMID: 29954169 DOI: 10.1021/acs.bioconjchem.8b00252] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since their first use in bioconjugation more than 50 years ago, maleimides have become privileged chemical partners for the site-selective modification of proteins via thio-Michael addition of biothiols and, to a lesser extent, via Diels-Alder (DA) reactions with biocompatible dienes. Prominent examples include immunotoxins and marketed maleimide-based antibody-drug conjugates (ADCs) such as Adcetris, which are used in cancer therapies. Among the key factors in the success of these groups is the availability of several maleimides that can be N-functionalized by fluorophores, affinity tags, spin labels, and pharmacophores, as well as their unique reactivities in terms of selectivity and kinetics. However, maleimide conjugate reactions have long been considered irreversible, and only recently have systematic studies regarding their reversibility and stability toward hydrolysis been reported. This review provides an overview of the diverse applications for maleimides in bioconjugation, highlighting their strengths and weaknesses, which are being overcome by recent strategies. Finally, the fluorescence quenching ability of maleimides was leveraged for the preparation of fluorogenic probes, which are mainly used for the specific detection of thiol analytes. A summary of the reported structures, their photophysical features, and their relative efficiencies is discussed in the last part of the review.
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Affiliation(s)
- Kévin Renault
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) , 76000 Rouen , France
| | - Jean Wilfried Fredy
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) , 76000 Rouen , France
| | - Pierre-Yves Renard
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) , 76000 Rouen , France
| | - Cyrille Sabot
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) , 76000 Rouen , France
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17
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St. Amant AH, Lemen D, Florinas S, Mao S, Fazenbaker C, Zhong H, Wu H, Gao C, Christie RJ, Read de Alaniz J. Tuning the Diels–Alder Reaction for Bioconjugation to Maleimide Drug-Linkers. Bioconjug Chem 2018; 29:2406-2414. [DOI: 10.1021/acs.bioconjchem.8b00320] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andre H. St. Amant
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Daniel Lemen
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, Maryland 20878, United States
| | - Stelios Florinas
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, Maryland 20878, United States
| | - Shenlan Mao
- Oncology Research, MedImmune, Gaithersburg, Maryland 20878, United States
| | | | - Haihong Zhong
- Oncology Research, MedImmune, Gaithersburg, Maryland 20878, United States
| | - Herren Wu
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, Maryland 20878, United States
| | - Changshou Gao
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, Maryland 20878, United States
| | - R. James Christie
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, Maryland 20878, United States
| | - Javier Read de Alaniz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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18
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Bain RM, Sathyamoorthi S, Zare RN. “On‐Droplet” Chemistry: The Cycloaddition of Diethyl Azodicarboxylate and Quadricyclane. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan M. Bain
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Richard N. Zare
- Department of Chemistry Stanford University Stanford CA 94305 USA
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19
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Bain RM, Sathyamoorthi S, Zare RN. “On‐Droplet” Chemistry: The Cycloaddition of Diethyl Azodicarboxylate and Quadricyclane. Angew Chem Int Ed Engl 2017; 56:15083-15087. [DOI: 10.1002/anie.201708413] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan M. Bain
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Richard N. Zare
- Department of Chemistry Stanford University Stanford CA 94305 USA
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20
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Martens S, Holloway JO, Du Prez FE. Click and Click-Inspired Chemistry for the Design of Sequence-Controlled Polymers. Macromol Rapid Commun 2017; 38. [PMID: 28990247 DOI: 10.1002/marc.201700469] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/18/2017] [Indexed: 01/09/2023]
Abstract
During the previous decade, many popular chemical reactions used in the area of "click" chemistry and similarly efficient "click-inspired" reactions have been applied for the design of sequence-defined and, more generally, sequence-controlled structures. This combination of topics has already made quite a significant impact on scientific research to date and has enabled the synthesis of highly functionalized and complex oligomeric and polymeric structures, which offer the prospect of many exciting further developments and applications in the near future. This minireview highlights the fruitful combination of these two topics for the preparation of sequence-controlled oligomeric and macromolecular structures and showcases the vast number of publications in this field within a relatively short span of time. It is divided into three sections according to the click-(inspired) reaction that has been applied: copper-catalyzed azide-alkyne cycloaddition, thiol-X, and related thiolactone-based reactions, and finally Diels-Alder-chemistry-based routes are outlined, respectively.
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Affiliation(s)
- Steven Martens
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
| | - Joshua O Holloway
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
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21
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Fisher SA, Baker AEG, Shoichet MS. Designing Peptide and Protein Modified Hydrogels: Selecting the Optimal Conjugation Strategy. J Am Chem Soc 2017; 139:7416-7427. [PMID: 28481537 DOI: 10.1021/jacs.7b00513] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hydrogels are used in a wide variety of biomedical applications including tissue engineering, biomolecule delivery, cell delivery, and cell culture. These hydrogels are often designed with a specific biological function in mind, requiring the chemical incorporation of bioactive factors to either mimic extracellular matrix or to deliver a payload to diseased tissue. Appropriate synthetic techniques to ligate bioactive factors, such as peptides and proteins, onto hydrogels are critical in designing materials with biological function. Here, we outline strategies for peptide and protein immobilization. We specifically focus on click chemistry, enzymatic ligation, and affinity binding for transient immobilization. Protein modification strategies have shifted toward site-specific modification using unnatural amino acids and engineered site-selective amino acid sequences to preserve both activity and structure. The selection of appropriate protein immobilization strategies is vital to engineering functional hydrogels. We provide insight into chemistry that balances the need for facile reactions while maintaining protein bioactivity or desired release.
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Affiliation(s)
- Stephanie A Fisher
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Alexander E G Baker
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Molly S Shoichet
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
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22
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Bioorthogonal Chemistry—Introduction and Overview [corrected]. Top Curr Chem (Cham) 2016; 374:9. [PMID: 27572992 DOI: 10.1007/s41061-016-0010-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/15/2016] [Indexed: 01/25/2023]
Abstract
Bioorthogonal chemistry has emerged as a new powerful tool that facilitates the study of structure and function of biomolecules in their native environment. A wide variety of bioorthogonal reactions that can proceed selectively and efficiently under physiologically relevant conditions are now available. The common features of these chemical reactions include: fast kinetics, tolerance to aqueous environment, high selectivity and compatibility with naturally occurring functional groups. The design and development of new chemical transformations in this direction is an important step to meet the growing demands of chemical biology. This chapter aims to introduce the reader to the field by providing an overview on general principles and strategies used in bioorthogonal chemistry. Special emphasis is given to cycloaddition reactions, namely to 1,3-dipolar cycloadditions and Diels-Alder reactions, as chemical transformations that play a predominant role in modern bioconjugation chemistry. The recent advances have established these reactions as an invaluable tool in modern bioorthogonal chemistry. The key aspects of the methodology as well as future outlooks in the field are discussed.
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The Diels–Alder reaction: A powerful tool for the design of drug delivery systems and biomaterials. Eur J Pharm Biopharm 2015; 97:438-53. [DOI: 10.1016/j.ejpb.2015.06.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 01/06/2023]
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Brun O, Elduque X, Pedroso E, Grandas A. On-Resin Conjugation of Diene-Polyamides and Maleimides via Diels-Alder Cycloaddition. J Org Chem 2015; 80:6093-101. [PMID: 25985351 DOI: 10.1021/acs.joc.5b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The reaction between maleimides and resin-linked diene-polyamides allows the latter to be used in the preparation of conjugates. Conjugation takes place by reacting the insoluble, hydrophobic diene component either with water-soluble dienophiles or with dienophiles requiring mixtures of water and organic solvents. Experimental conditions can be adjusted to furnish the target conjugate in good yield with no need of adding large excesses of soluble reagent. In case protected maleimides are used, maleimide deprotection and Diels-Alder cycloaddition can be simultaneously carried out to render conjugates with different linking positions. On-resin conjugation is followed by an acidic treatment that removes the polyamide protecting groups with no harm to the cycloadduct, in contrast with the unreacted diene that is indeed degraded under these conditions. Cycloadducts incorporating suitable functional groups can undergo subsequent additional conjugation reactions in solution to furnish double conjugates.
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Affiliation(s)
- Omar Brun
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Xavier Elduque
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Enrique Pedroso
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Anna Grandas
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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Cobo I, Li M, Sumerlin BS, Perrier S. Smart hybrid materials by conjugation of responsive polymers to biomacromolecules. NATURE MATERIALS 2015; 14:143-59. [PMID: 25401924 DOI: 10.1038/nmat4106] [Citation(s) in RCA: 428] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 09/04/2014] [Indexed: 05/18/2023]
Abstract
The chemical structure and function of biomacromolecules has evolved to fill many essential roles in biological systems. More specifically, proteins, peptides, nucleic acids and polysaccharides serve as vital structural components, and mediate chemical transformations and energy/information storage processes required to sustain life. In many cases, the properties and applications of biological macromolecules can be further expanded by attaching synthetic macromolecules. The modification of biomacromolecules by attaching a polymer that changes its properties in response to environmental variations, thus affecting the properties of the biomacromolecule, has led to the emergence of a new family of polymeric biomaterials. Here, we summarize techniques for conjugating responsive polymers to biomacromolecules and highlight applications of these bioconjugates reported so far. In doing so, we aim to show how advances in synthetic tools could lead to rapid expansion in the variety and uses of responsive bioconjugates.
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Affiliation(s)
- Isidro Cobo
- Key Centre for Polymers &Colloids, School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| | - Ming Li
- Tyco Fire Protection Products, Mansfield, Texas 76063, USA
| | - Brent S Sumerlin
- George &Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science &Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
| | - Sébastien Perrier
- 1] Department of Chemistry, The University of Warwick, Coventry CV4 7AL, UK [2] Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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Elduque X, Pedroso E, Grandas A. Orthogonal protection of peptides and peptoids for cyclization by the thiol-ene reaction and conjugation. J Org Chem 2014; 79:2843-53. [PMID: 24617567 DOI: 10.1021/jo500427c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclic peptides and peptoids were prepared using the thiol-ene Michael-type reaction. The linear precursors were provided with additional functional groups allowing for subsequent conjugation: an orthogonally protected thiol, a protected maleimide, or an alkyne. The functional group for conjugation was placed either within the cycle or in an external position. The click reactions employed for conjugation with suitably derivatized nucleoside or oligonucleotides were either cycloadditions (Diels-Alder, Cu(I)-catalyzed azide-alkyne) or the same Michael-type reaction as for cyclization.
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Affiliation(s)
- Xavier Elduque
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain
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Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors. Chem Cent J 2013; 7:171. [PMID: 24171724 PMCID: PMC4176756 DOI: 10.1186/1752-153x-7-171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/23/2013] [Indexed: 11/22/2022] Open
Abstract
Background In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Results Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. Conclusions A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.
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Cheng Y, Peng H, Chen W, Ni N, Ke B, Dai C, Wang B. Rapid and specific post-synthesis modification of DNA through a biocompatible condensation of 1,2-aminothiols with 2-cyanobenzothiazole. Chemistry 2013; 19:4036-4042. [PMID: 23447494 PMCID: PMC3918485 DOI: 10.1002/chem.201201677] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 11/27/2012] [Indexed: 11/08/2022]
Abstract
Post-synthesis modification of DNA is an important way of functionalizing DNA molecules. Herein, we describe a method that first enzymatically incorporates a cyanobenzothiazole (CBT)-modified thymidine. The side-chain handle CBT can undergo a rapid and site-specific cyclization reaction with 1,2-aminothiols to afford DNA functionalization in aqueous solution. Another key advantage of this method is the formation of a single stereo/regioisomer in the process, which allows for precise control of DNA modification to yield a single component for aptamer selection work and other applications.
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Affiliation(s)
- Yunfeng Cheng
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Hanjing Peng
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Weixuan Chen
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Nanting Ni
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Bowen Ke
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Chaofeng Dai
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
| | - Binghe Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design Georgia State University, P.O. Box 4098, Atlanta, GA 30302-4098
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29
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Hoogewijs K, Buyst D, Winne JM, Martins JC, Madder A. Exploiting furan's versatile reactivity in reversible and irreversible orthogonal peptide labeling. Chem Commun (Camb) 2013; 49:2927-9. [DOI: 10.1039/c3cc40588e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Palomo JM. Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes. Org Biomol Chem 2012; 10:9309-18. [PMID: 23023600 DOI: 10.1039/c2ob26409a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.
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Affiliation(s)
- Jose M Palomo
- Departamento de Biocatálisis. Instituto de Catálisis (CSIC). C/ Marie Curie 2. Cantoblanco. Campus UAM, 28049 Madrid, Spain.
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31
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Sánchez A, Pedroso E, Grandas A. Conjugation reactions involving maleimides and phosphorothioate oligonucleotides. Bioconjug Chem 2012; 23:300-7. [PMID: 22243598 DOI: 10.1021/bc200598g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phosphorothioate diester oligonucleotides proved to be fully compatible with maleimides in the context of two different conjugation reactions: (a) reaction of (5')diene-[phosphorothioate oligonucleotides] with maleimido-containing compounds to afford the Diels-Alder cycloadduct; (b) conjugation of (5')maleimido-[phosphorothioate oligonucleotides] with thiol-containing compounds. No evidence of reaction between phosphorothioate diesters and maleimides was found in any of these processes. Importantly, in the preparation of (5')maleimido-[phosphorothioate oligonucleotides] from [protected maleimido]-[phosphorothioate oligonucleotides], which requires the maleimide to be deprotected by retro-Diels-Alder reaction (heating for 3-4 h in toluene at 90 °C), no addition of phosphorothioate diester to the maleimide was found either. Finally, maleimide-[phosphorothioate monoester] conjugation was also explored for comparison purposes.
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Affiliation(s)
- Albert Sánchez
- Departament de Química Orgànica and IBUB, Facultat de Química, Universitat de Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain
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32
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Tang SY, Shi J, Guo QX. Accurate prediction of rate constants of Diels–Alder reactions and application to design of Diels–Alder ligation. Org Biomol Chem 2012; 10:2673-82. [DOI: 10.1039/c2ob07079k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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Sánchez A, Pedroso E, Grandas A. Maleimide-dimethylfuran exo adducts: effective maleimide protection in the synthesis of oligonucleotide conjugates. Org Lett 2011; 13:4364-7. [PMID: 21790151 DOI: 10.1021/ol201690b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reaction of maleimide-containing compounds with 2,5-dimethylfuran gives a mixture of exo and endo isomers from which the exo cycloadduct can be easily isolated taking advantage of its stability in concentrated aqueous ammonia. Bifunctional compounds incorporating a dimethylfuran-protected maleimide (exo adduct) have been attached to resin-linked oligonucleotide chains. Removal of protecting groups masking oligonucleotide functionalities followed by retro-Diels-Alder maleimide deprotection affords maleimido-oligonucleotides suitable for conjugation, as assessed by their reaction with different thiols.
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Affiliation(s)
- Albert Sánchez
- Departament de Química Orgànica and IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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35
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36
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El-Sagheer AH, Cheong VV, Brown T. Rapid chemical ligation of oligonucleotides by the Diels-Alder reaction. Org Biomol Chem 2010; 9:232-5. [PMID: 21072410 DOI: 10.1039/c0ob00451k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Extremely fast and efficient Diels-Alder chemical ligation of furan and maleimide oligonucleotides has been carried out in aqueous buffer. It was possible to ligate three oligonucleotides simultaneously in a controlled manner with the aid of a complementary splint. The templated reactions proceeded within 1 min at room temperature whereas non-templated reactions were slow and incomplete. Rapid and clean methods of DNA ligation such as the one demonstrated here have potential uses in biology and nanotechnology.
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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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37
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van Delft P, Meeuwenoord NJ, Hoogendoorn S, Dinkelaar J, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of Oligoribonucleic Acid Conjugates Using a Cyclooctyne Phosphoramidite. Org Lett 2010; 12:5486-9. [DOI: 10.1021/ol102357u] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pieter van Delft
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Sascha Hoogendoorn
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jasper Dinkelaar
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Affiliation(s)
- Jose M. Palomo
- Departamento de Biocatálisis, Instituto de Catálisis (CSIC), c/ Marie Curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain, Fax: +34‐91‐585‐4760
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39
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Willems LI, Verdoes M, Florea BI, van der Marel GA, Overkleeft HS. Two-Step Labeling of Endogenous Enzymatic Activities by Diels-Alder Ligation. Chembiochem 2010; 11:1769-81. [DOI: 10.1002/cbic.201000280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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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: 74] [Impact Index Per Article: 5.3] [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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41
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Tiefenbrunn TK, Dawson PE. Chemoselective ligation techniques: modern applications of time-honored chemistry. Biopolymers 2010; 94:95-106. [PMID: 20091876 DOI: 10.1002/bip.21337] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chemoselective ligation techniques enable the selective modification of proteins and other biomolecules in dilute aqueous solution. Importantly, these reactions occur at or near physiological pH and are compatible with the complex array of functional groups commonly found in biological macromolecules including proteins, nucleotides, and carbohydrates, allowing conjugation reactions to be carried out on unprotected substrates. Recently, a growing number of reactions with established utility in synthetic organic chemistry have been shown to have surprising utility in the context of biological molecules in aqueous media. In this review we highlight several promising reactions that may have widespread applicability in the generation of new materials based on biological macromolecules.
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Affiliation(s)
- Theresa K Tiefenbrunn
- Department of Cell Biology, 10550 N. Torrey Pines Road, The Scripps Research Institute, La Jolla, CA 92037, USA
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Franc G, Kakkar AK. "Click" methodologies: efficient, simple and greener routes to design dendrimers. Chem Soc Rev 2010; 39:1536-44. [PMID: 20419208 DOI: 10.1039/b913281n] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Designing dendrimers that are monodisperse hyperbranched macromolecules and offer significant potential in numerous scientific fields, is becoming a major topical area in modern research. Among the challenges of the 21st century, synthetic methodologies that increase efficiency of conversion and a greener chemistry approach, are expected to lead the way in the quest to build novel nanomaterials. The recent entry of so-called "click" reactions that include Diels-Alder, Cu(I)-catalyzed Huisgen cycloaddition and thiol-ene coupling, have generated real stimulus not only in developing elegant materials of choice, but also in making the leap to industrial scale build-up of dendritic macromolecules. This tutorial review takes on the task of demonstrating the simplicity of these "click" reactions and the advantages they offer from a synthetic view point in developing mono- to multifunctional dendrimers. A brief introduction to "click" chemistry is followed by a chronological survey of developments in the field, and the impact these have had in designing novel dendritic macromolecules. The review is intended to introduce scientists to these highly efficient methodologies with demonstrated potential, and provide impetus for further growth of the area.
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Affiliation(s)
- Grégory Franc
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, Canada H3A 2K6
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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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Diels-Alder reaction with cyclopentadiene and electronic structures of (η5-cyclopentadienyl)M(CO)x(η1-N-maleimidato) (M=Fe, Mo, W, x=2 or 3). J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2008.12.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Borsenberger V, Howorka S. Diene-modified nucleotides for the Diels-Alder-mediated functional tagging of DNA. Nucleic Acids Res 2009; 37:1477-85. [PMID: 19139071 PMCID: PMC2655660 DOI: 10.1093/nar/gkn1066] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We explore the potential of the Diels-Alder cycloaddition for the functional tagging of DNA strands. A deoxyuridine triphosphate derivative carrying a diene at position 5 of the pyrimidine base was synthesized using a two-step procedure. The derivative was efficiently accepted as substrate in enzymatic polymerization assays. Diene carrying strands underwent successful cycloaddition with maleimide-terminated fluorescence dyes and a polymeric reagent. Furthermore, a nucleotide carrying a peptide via a Diels-Alder cyclohexene linkage was prepared and sequence-specifically incorporated into DNA. The Diels-Alder reaction presents a number of positive attributes such as good chemoselectivity, water compatibility, high-yield under mild conditions and no additional reagents apart from a diene and a dienophile. Furthermore, suitable dienophiles are commercially available in the form of maleimide-derivatives of fluorescent dyes and bioaffinity tags. Based on these advantages, diene- and cyclohexene-based nucleotide triphosphates are expected to find wider use in the area of nucleic acid chemistry.
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Affiliation(s)
- Vinciane Borsenberger
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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Shi M, Lu J, Shoichet MS. Organic nanoscale drug carriers coupled with ligands for targeted drug delivery in cancer. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b822319j] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Weisbrod SH, Marx A. Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 2008:5675-85. [PMID: 19009049 DOI: 10.1039/b809528k] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.
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Affiliation(s)
- Samuel H Weisbrod
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457, Konstanz, Germany
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Steven V, Graham D. Oligonucleotide conjugation to a cell-penetrating (TAT) peptide by Diels-Alder cycloaddition. Org Biomol Chem 2008; 6:3781-7. [PMID: 18843408 DOI: 10.1039/b807843b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Modifed oligonucleotides are routinely employed as analytical probes for use in diagnostics, e.g. in the examination of specific RNA sequences for infectious diseases, however, a major limiting factor in oligonucleotide-based diagnostics is poor cellular uptake of naked oligonucleotides. This problem can be overcome by covalent attachment of a so-called 'cell-penetrating peptide' to form an oligonucleotide peptide conjugate. Stepwise solid phase synthesis of such a conjugate is difficult and expensive due to the conflicting chemistries of oligonucleotides and peptides. A simple approach to overcome this is post-synthetic conjugation. Diels-Alder cycloaddition is an attractive methodology for oligonucleotide peptide conjugation; the reaction is fast, chemoselective and the reaction rate is greatly enhanced in aqueous media - ideal conditions for biological moieties. An oligodeoxyribonucleotide sequence has been derivatised with a series of dienes at the 5'-terminus, using a series of unique dienyl-modified phosphoramidites, and investigation into the effect of diene type on the efficiency of conjugation, using Diels-Alder cycloaddition with a maleimido-derivatised cell-penetrating (TAT) peptide, has been performed. This led to the observation that the optimal diene for conjugation was cyclohexadiene, allowing conjugation of oligodeoxyribonucleotides to a cell-penetrating peptide by Diels-Alder cycloaddition for the first time.
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Affiliation(s)
- Victoria Steven
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK
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Pulido D, López-Alonso JP, Marchán V, González C, Grandas A, Laurents DV. Preparation of ribonuclease S domain-swapped dimers conjugated with DNA and PNA: modulating the activity of ribonucleases. Bioconjug Chem 2007; 19:263-70. [PMID: 18163547 DOI: 10.1021/bc700374q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Obtaining highly specific and active ribonuclease activities is an important goal with numerous medical and biochemical applications. As a step toward more active and specific ribonucleases, we describe the preparation and the enzymatic and structural properties of RNase S monomers and dimers conjugated to DNA and PNA molecules. Poly(dT)n (2'-oligodeoxyribonucleotides, n = 8, 15) and t8 peptide nucleic acid (PNA) chains have been conjugated to the S-peptide of ribonuclease S. Monomers and dimers of the conjugated enzyme have been obtained and characterized by 1H NMR spectroscopy, showing that DNA or PNA conjugation does not alter the native structure of ribonuclease S. The oligonucleotide-conjugated RNase S monomer and dimer show significant activity against single-stranded RNA and very low/negligible hydrolysis of double-stranded poly(A).poly(U). In contrast, the t8-conjugated RNase S monomer and dimer show substantial activity against both ssRNA and dsRNA. These results highlight the importance of positive charges near but not in the active site in enhancing activity against dsRNA and reveal the promise of PNA-RNase conjugates for modulating RNase activity.
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Affiliation(s)
- Daniel Pulido
- Department de Química Orgànica, Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
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Gogoi K, Mane MV, Kunte SS, Kumar VA. A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water. Nucleic Acids Res 2007; 35:e139. [PMID: 17981837 PMCID: PMC2175367 DOI: 10.1093/nar/gkm935] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The specific 1,3 dipolar Hüisgen cycloaddition reaction known as 'click-reaction' between azide and alkyne groups is employed for the synthesis of peptide-oligonucleotide conjugates. The peptide nucleic acids (PNA)/DNA and peptides may be appended either by azide or alkyne groups. The cycloaddition reaction between the azide and alkyne appended substrates allows the synthesis of the desired conjugates in high purity and yields irrespective of the sequence and functional groups on either of the two substrates. The versatile approach could also be employed to generate the conjugates of peptides with thioacetamido nucleic acid (TANA) analog. The click reaction is catalyzed by Cu (I) in either water or in organic medium. In water, approximately 3-fold excess of the peptide-alkyne/azide drives the reaction to completion in 2 h with no side products.
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Affiliation(s)
- Khirud Gogoi
- Division of Organic Chemistry, National Chemical Laboratory, Pune, India
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