1
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Paliya BS, Sharma VK, Tuohy MG, Singh HB, Koffas M, Benhida R, Tiwari BK, Kalaskar DM, Singh BN, Gupta VK. Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans. Biotechnol Adv 2023; 67:108180. [PMID: 37236328 DOI: 10.1016/j.biotechadv.2023.108180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023]
Abstract
The recent advancement in the human glycome and progress in the development of an inclusive network of glycosylation pathways allow the incorporation of suitable machinery for protein modification in non-natural hosts and explore novel opportunities for constructing next-generation tailored glycans and glycoconjugates. Fortunately, the emerging field of bacterial metabolic engineering has enabled the production of tailored biopolymers by harnessing living microbial factories (prokaryotes) as whole-cell biocatalysts. Microbial catalysts offer sophisticated means to develop a variety of valuable polysaccharides in bulk quantities for practical clinical applications. Glycans production through this technique is highly efficient and cost-effective, as it does not involve expensive initial materials. Metabolic glycoengineering primarily focuses on utilizing small metabolite molecules to alter biosynthetic pathways, optimization of cellular processes for glycan and glycoconjugate production, characteristic to a specific organism to produce interest tailored glycans in microbes, using preferably cheap and simple substrate. However, metabolic engineering faces one of the unique challenges, such as the need for an enzyme to catalyze desired substrate conversion when natural native substrates are already present. So, in metabolic engineering, such challenges are evaluated, and different strategies have been developed to overcome them. The generation of glycans and glycoconjugates via metabolic intermediate pathways can still be supported by glycol modeling achieved through metabolic engineering. It is evident that modern glycans engineering requires adoption of improved strain engineering strategies for creating competent glycoprotein expression platforms in bacterial hosts, in the future. These strategies include logically designing and introducing orthogonal glycosylation pathways, identifying metabolic engineering targets at the genome level, and strategically improving pathway performance (for example, through genetic modification of pathway enzymes). Here, we highlight current strategies, applications, and recent progress in metabolic engineering for producing high-value tailored glycans and their applications in biotherapeutics and diagnostics.
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Affiliation(s)
- Balwant S Paliya
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Vivek K Sharma
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Maria G Tuohy
- Biochemistry, School of Biological and Chemical Sciences, College of Science & Engineering, University of Galway (Ollscoil na Gaillimhe), University Road, Galway City, Ireland
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rachid Benhida
- Institut de Chimie de Nice, UMR7272, Université Côte d'Azur, Nice, France; Mohamed VI Polytechnic University, Lot 660, Hay Moulay Rachid 43150, Benguerir, Morocco
| | | | - Deepak M Kalaskar
- UCL Division of Surgery and Interventional Science, Royal Free Hospital Campus, University College London, Rowland Hill Street, NW3 2PF, UK
| | - Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India.
| | - Vijai K Gupta
- Biorefining and Advanced Materials Research Centre, SRUC, Barony Campus, Parkgate, Dumfries DG1 3NE, United Kingdom.
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2
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Zhang S, Liu P, Li L, Liu Z, Qian X, Jiang X, Sun W, Wang L, Akkaya EU. Upconverting Nanoparticle-Based Photoactive Probes for Highly Efficient Labeling and Isolation of Target Proteins. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40280-40291. [PMID: 37585283 DOI: 10.1021/acsami.3c08397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Photoaffinity labeling (PAL) has blossomed into a powerful and versatile tool for capture and identification of biomolecular targets. However, low labeling efficiency for specific targets such as lectins, the tedious process for protein purification, inevitable cellular photodamage, and less tissue penetration of UV light are significant challenges. Herein, we reported a near-infrared (NIR) light-driven photoaffinity labeling approach using upconverting nanoparticle (UCNP)-based photoactive probes, which were constructed by assembling photoactive groups and ligands onto NaYF4:Yb,Tm nanoparticles. The novel probes were easily prepared and functionalized, and the labeled proteins can be isolated and purified through simple centrifugation and washing. The advantages of this approach were demonstrated by labeling and isolation of peanut agglutinin (PNA), asialoglycoprotein receptor (ASGPR), and human carbonic anhydrase II (hCAII) from mixed proteins or cell lysates with good selectivity and efficiency, especially for PNA and ASGPR, two lectins that showed low binding affinity to their ligands. More importantly, successful labeling of PNA through pork tissues and ASGPR in mice strongly proved the good tissue penetrating capacity of NIR light and the application potential of UCNP-based photoactive probes for protein labeling in vivo. Biosafety of this approach was experimentally validated by enzyme, cell, and animal work, and we demonstrated that NIR light caused minimal photodamage to enzyme activity compared to UV light, and the UCNP-based photoactive probe presents good biosafety both in vitro and in vivo. We believe that this novel PAL approach will provide a promising tool for study of ligand-protein interactions and identification of biomolecular targets.
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Affiliation(s)
- Shengli Zhang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Peng Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Li Li
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Ziang Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xiao Qian
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xueying Jiang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Engin U Akkaya
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
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3
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Ondrus AE, Zhang T. Structure, Bonding, and Photoaffinity Labeling Applications of Dialkyldiazirines. Synlett 2021. [DOI: 10.1055/a-1437-8202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractDialkyldiazirine photoaffinity probes are unparalleled tools for the study of small molecule–protein interactions. Here we summarize the basic principles of structure, bonding, and photoreactivity of dialkyldiazirines, current methods for their synthesis, and their practical application in photoaffinity labeling experiments. We demonstrate the unique utility of dialkyldiazirine probes in the context of our recent photoaffinity crosslinking-mass spectrometry analysis to reveal a hidden cholesterol binding site in the Hedgehog morphogen proteins.1 Introduction2 Structure, Bonding, and Spectral Properties3 Photoreactivity4 Synthesis5 Application in Photoaffinity Labeling6 Discovery of a Cholesterol–Hedgehog Protein Interface7 Conclusions and Outlook
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4
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Heiss TK, Dorn RS, Prescher JA. Bioorthogonal Reactions of Triarylphosphines and Related Analogues. Chem Rev 2021; 121:6802-6849. [PMID: 34101453 PMCID: PMC10064493 DOI: 10.1021/acs.chemrev.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.
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5
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Saidjalolov S, Braud E, Edoo Z, Iannazzo L, Rusconi F, Riomet M, Sallustrau A, Taran F, Arthur M, Fonvielle M, Etheve-Quelquejeu M. Click and Release Chemistry for Activity-Based Purification of β-Lactam Targets. Chemistry 2021; 27:7687-7695. [PMID: 33792096 DOI: 10.1002/chem.202100653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 12/30/2022]
Abstract
β-Lactams, the cornerstone of antibiotherapy, inhibit multiple and partially redundant targets referred to as transpeptidases or penicillin-binding proteins. These enzymes catalyze the essential cross-linking step of the polymerization of cell wall peptidoglycan. The understanding of the mechanisms of action of β-lactams and of resistance to these drugs requires the development of reliable methods to characterize their targets. Here, we describe an activity-based purification method of β-lactam targets based on click and release chemistry. We synthesized alkyne-carbapenems with suitable properties with respect to the kinetics of acylation of a model target, the Ldtfm L,D-transpeptidase, the stability of the resulting acylenzyme, and the reactivity of the alkyne for the cycloaddition of an azido probe containing a biotin moiety for affinity purification and a bioorthogonal cleavable linker. The probe provided access to the fluorescent target in a single click and release step.
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Affiliation(s)
- Saidbakhrom Saidjalolov
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Zainab Edoo
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Filippo Rusconi
- PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech GQE - Le Moulon, Gif-sur-Yvette, 91190, France
| | - Margaux Riomet
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Antoine Sallustrau
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Frédéric Taran
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
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6
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Congdon MD, Gildersleeve JC. Enhanced Binding and Reduced Immunogenicity of Glycoconjugates Prepared via Solid-State Photoactivation of Aliphatic Diazirine Carbohydrates. Bioconjug Chem 2020; 32:133-142. [PMID: 33325683 DOI: 10.1021/acs.bioconjchem.0c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological conjugation is an important tool employed for many basic research and clinical applications. While useful, common methods of biological conjugation suffer from a variety of limitations, such as (a) requiring the presence of specific surface-exposed residues, such as lysines or cysteines, (b) reducing protein activity, and/or (c) reducing protein stability and solubility. Use of photoreactive moieties including diazirines, azides, and benzophenones provide an alternative, mild approach to conjugation. Upon irradiation with UV and visible light, these functionalities generate highly reactive carbenes, nitrenes, and radical intermediates. Many of these will couple to proteins in a non-amino-acid-specific manner. The main hurdle for photoactivated biological conjugation is very low yield. In this study, we developed a solid-state method to increase conjugation efficiency of diazirine-containing carbohydrates to proteins. Using this methodology, we produced multivalent carbohydrate-protein conjugates with unaltered protein charge and secondary structure. Compared to carbohydrate conjugates prepared with amide linkages to lysine residues using standard NHS conjugation, the photoreactive prepared conjugates displayed up to 100-fold improved binding to lectins and diminished immunogenicity in mice. These results indicate that photoreactive bioconjugation could be especially useful for in vivo applications, such as lectin targeting, where high binding affinity and low immunogenicity are desired.
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Affiliation(s)
- Molly D Congdon
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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7
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O'Brien JGK, Jemas A, Asare-Okai PN, Am Ende CW, Fox JM. Probing the Mechanism of Photoaffinity Labeling by Dialkyldiazirines through Bioorthogonal Capture of Diazoalkanes. Org Lett 2020; 22:9415-9420. [PMID: 33259213 DOI: 10.1021/acs.orglett.0c02714] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dialkyldiazirines have emerged as reagents of choice for biological photoaffinity labeling studies. The mechanism of crosslinking has dramatic consequences for biological applications where instantaneous labeling is desirable, as carbene insertions display different chemoselectivity and are much faster than competing mechanisms involving diazo or ylide intermediates. Here, deuterium labeling and diazo compound trapping experiments are employed to demonstrate that both carbene and diazo mechanisms operate in the reactions of a dialkyldiazirine motif that is commonly utilized for biological applications. For the fraction of intermolecular labeling that does involve a carbene mechanism, direct insertion is not necessarily involved, as products derived from a carbonyl ylide are also observed. We demonstrate that a strained cycloalkyne can intercept diazo compound intermediates and serve as a bioorthogonal probe for studying the contribution of the diazonium mechanism of photoaffinity labeling on a model protein under aqueous conditions.
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Affiliation(s)
- Jessica G K O'Brien
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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8
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Kitoun C, Fonvielle M, Sakkas N, Lefresne M, Djago F, Blancart Remaury Q, Poinot P, Arthur M, Etheve-Quelquejeu M, Iannazzo L. Phosphine-Mediated Bioconjugation of the 3′-End of RNA. Org Lett 2020; 22:8034-8038. [DOI: 10.1021/acs.orglett.0c02982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camélia Kitoun
- UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, F-75006 Paris, France
| | - Matthieu Fonvielle
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006, Paris, France
| | - Nicolas Sakkas
- UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, F-75006 Paris, France
| | - Manon Lefresne
- UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, F-75006 Paris, France
| | - Fabiola Djago
- Institut de Chimie des Milieux et Matériaux de Poitiers IC2MP, Université de Poitiers, UMR 7285, 86073, Poitiers, France
| | - Quentin Blancart Remaury
- Institut de Chimie des Milieux et Matériaux de Poitiers IC2MP, Université de Poitiers, UMR 7285, 86073, Poitiers, France
| | - Pauline Poinot
- Institut de Chimie des Milieux et Matériaux de Poitiers IC2MP, Université de Poitiers, UMR 7285, 86073, Poitiers, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006, Paris, France
| | - Mélanie Etheve-Quelquejeu
- UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, F-75006 Paris, France
| | - Laura Iannazzo
- UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, F-75006 Paris, France
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9
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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10
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Jensen SM, Kimani FW, Jewett JC. Light-Activated Triazabutadienes for the Modification of a Viral Surface. Chembiochem 2016; 17:2216-2219. [PMID: 27647786 PMCID: PMC5170875 DOI: 10.1002/cbic.201600508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Indexed: 11/10/2022]
Abstract
Chemical crosslinking is a versatile tool for the examination of biochemical interactions, in particular host-pathogen interactions. We report the critical first step toward the goal of probing these interactions by the synthesis and use of a new heterobifunctional crosslinker containing a triazabutadiene scaffold. The triazabutadiene is stable to protein conjugation and liberates a reactive aryl diazonium species upon irradiation with 350 nm light. We highlight the use of this technology by modifying the surface of several proteins, including the dengue virus envelope protein.
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Affiliation(s)
- Stephanie M Jensen
- Department of Chemistry and Biochemistry, University of Arizona, Building 41, Room 104, 1306 E University Boulevard, Tucson, AZ, 85721, USA
| | - Flora W Kimani
- Department of Chemistry and Biochemistry, University of Arizona, Building 41, Room 104, 1306 E University Boulevard, Tucson, AZ, 85721, USA
| | - John C Jewett
- Department of Chemistry and Biochemistry, University of Arizona, Building 41, Room 104, 1306 E University Boulevard, Tucson, AZ, 85721, USA
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11
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Sminia TJ, Zuilhof H, Wennekes T. Getting a grip on glycans: A current overview of the metabolic oligosaccharide engineering toolbox. Carbohydr Res 2016; 435:121-141. [PMID: 27750120 DOI: 10.1016/j.carres.2016.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022]
Abstract
This review discusses the advances in metabolic oligosaccharide engineering (MOE) from 2010 to 2016 with a focus on the structure, preparation, and reactivity of its chemical probes. A brief historical overview of MOE is followed by a comprehensive overview of the chemical probes currently available in the MOE molecular toolbox and the bioconjugation techniques they enable. The final part of the review focusses on the synthesis of a selection of probes and finishes with an outlook on recent and potential upcoming advances in the field of MOE.
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Affiliation(s)
- Tjerk J Sminia
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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12
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Cornali BM, Kimani FW, Jewett JC. Cu-Click Compatible Triazabutadienes To Expand the Scope of Aryl Diazonium Ion Chemistry. Org Lett 2016; 18:4948-4950. [PMID: 27619479 DOI: 10.1021/acs.orglett.6b02420] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triazabutadienes can be used to readily generate reactive aryl diazonium ions under mild, physiologically relevant conditions. These conditions are compatible with a range of functionalities that do not tolerate traditional aryl diazonium ion generation. To increase the utility of this aryl diazonium ion releasing chemistry an alkyne-containing triazabutadiene was synthesized. The copper-catalyzed azide-alkyne cycloaddition ("Cu-click") reaction was utilized to modify the alkyne-containing triazabutadiene and shown to be compatible with the nitrogen-rich triazabutadiene. One of the triazole products was tethered to a fluorophore, thus enabling the direct fluorescent labeling of a model protein.
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Affiliation(s)
- Brandon M Cornali
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Flora W Kimani
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - John C Jewett
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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13
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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14
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Fujita A, Kohler JJ. Photocrosslinking Sugars for Capturing Glycan-dependent Interactions (Jpn. Ed.). TRENDS GLYCOSCI GLYC 2015. [DOI: 10.4052/tigg.1439.1j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Akiko Fujita
- Department of Biochemistry, University of Texas Southwestern Medical Center
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center
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15
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Fujita A, Kohler JJ. Photocrosslinking Sugars for Capturing Glycan-dependent Interactions. TRENDS GLYCOSCI GLYC 2015. [DOI: 10.4052/tigg.1439.1e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Akiko Fujita
- Department of Biochemistry, University of Texas Southwestern Medical Center
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center
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16
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Stewart JA, Piligian BF, Rundell SR, Swarts BM. A trifunctional cyclooctyne for modifying azide-labeled biomolecules with photocrosslinking and affinity tags. Chem Commun (Camb) 2015; 51:17600-3. [DOI: 10.1039/c5cc07536j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A trifunctional cyclooctyne-based reagent that harnesses bioorthogonal chemistry to facilitate the probing of biomolecular interactions is described.
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Affiliation(s)
- Jessica A. Stewart
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Brent F. Piligian
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Sarah R. Rundell
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
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MacKenzie DA, Pezacki JP. Kinetics studies of rapid strain-promoted [3+2] cycloadditions of nitrones with bicyclo[6.1.0]nonyne. CAN J CHEM 2014. [DOI: 10.1139/cjc-2013-0577] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strain-promoted alkyne−nitrone cycloaddition (SPANC) reactions represent a bioorthogonal labeling strategy that is both very rapid and at the same time efficient and selective. Nitrones provide increased reaction rates as well as greater susceptibility toward stereoelectronic modification when compared with organic azides. We find that strain-promoted cycloadditions of cyclic nitrones with bicyclo[6.1.0]nonyne react with second-order rate constants as large as 1.49 L mol−1 s−1 at 25 °C. These reactions display rate constants that are up to 37-fold greater than those of the analogous reactions of benzyl azide with bicyclo[6.1.0]nonyne. We observed that reactions of nitrones with bicyclo[6.1.0]nonyne showed a stronger dependence on substituent effect for the reaction, as evidenced by a larger Hammett ρ value, than that for biaryl-aza-cyclooctanone. We demonstrate the ability to stereoelectronically tune the reactivity of nitrones towards different cyclooctynes in SPANC reactions. This ability to introduce selectivity into different SPANC reactions through substituent provides the opportunity to perform multiple SPANC reactions in one reaction vessel and opens up potential applications in multiplex labeling.
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Affiliation(s)
- Douglas A. MacKenzie
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
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Patterson DM, Nazarova LA, Prescher JA. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014; 9:592-605. [PMID: 24437719 DOI: 10.1021/cb400828a] [Citation(s) in RCA: 531] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.
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Affiliation(s)
- David M. Patterson
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Lidia A. Nazarova
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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