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Sato F, Alejandra HPL, Takemae H, Inagaki NF, Ito T, Tera M. Enhancing Cell Aggregation and Migration via Double-Click Cross-Linking with Azide-Modified Hyaluronic Acid. Bioconjug Chem 2024. [PMID: 39213494 DOI: 10.1021/acs.bioconjchem.4c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
We present a novel approach to the formation of cell aggregates by employing click chemistry with water-soluble zwitterionic dibenzo cyclooctadiyne (WS-CODY) and azide-modified hyaluronic acid (HA-N3) as a linker to facilitate rapid and stable cell aggregation. By optimizing the concentrations of HA-N3 and WS-CODY, we achieved efficient cross-linking between azide-modified cell surfaces and HA-N3, generating cell aggregates within 10 min, and the resulting aggregates remained stable for up to 5 days, with cell viability maintained at approximately 80%. Systematic experiments revealed that a stoichiometric balance between HA-N3 and WS-CODY is important for effective cross-linking, highlighting the roles of both cell-surface azide modification and HA in the aggregate formation. We also investigated the genetic basis of altered cell behavior within these aggregates. Transcriptome analysis (RNA-seq) of aggregates postcultivation revealed a marked fluctuation of genes associated with 'cell migration' and 'cell adhesion', including notable changes in the expression of HYAL1, ICAM-1, CEACAM5 and RHOB. These findings suggest that HA-N3-mediated cell aggregation can induce intrinsic cellular responses that not only facilitate cell aggregate formation but also modulate cell-matrix interactions. We term this phenomenon 'chemo-resilience', The simplicity and efficacy of this click chemistry-based approach suggest it may have broad applicability for forming cell aggregates and modulating cell-matrix interactions in tissue engineering and regenerative medicine.
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Affiliation(s)
- Fumiya Sato
- Department of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Hernandez Paniagua Liliana Alejandra
- Department of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Hitoshi Takemae
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Natsuko F Inagaki
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taichi Ito
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
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2
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Noël N, Martinez A, Massicot F, Vasse JL, Behr JB. Kinetics of Strain-Promoted Alkyne-Nitrone Cycloadditions (SPANC) with Unprotected Carbohydrate Scaffolded Nitrones. Org Lett 2024; 26:3917-3922. [PMID: 38690807 DOI: 10.1021/acs.orglett.4c01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The use of unprotected carbohydrate-derived nitrones as partners in strain-promoted alkyne-nitrone cycloadditions was investigated as a new tool for bioconjugation. The observed second-order reactions displayed rate constants of 3.4 × 10-4-5.8 × 10-2 M-1 s-1, which is the common order of magnitude of reaction kinetics with other simple aliphatic or aromatic nitrones. Applicability of this method to aqueous media was demonstrated by performing a one-pot protocol, which combines sequential formation of the nitrone and cycloaddition with cyclooctyne in water.
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Affiliation(s)
- Nathan Noël
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Agathe Martinez
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Fabien Massicot
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Luc Vasse
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
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3
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Bilodeau DA, Margison KD, Masoud SS, Nakajima M, Pezacki JP. Mechanistic Analysis of Bioorthogonal Double Strain-Promoted Alkyne-Nitrone Cycloadditions Involving Dibenzocyclooctadiyne. ACS Chem Biol 2023; 18:2430-2438. [PMID: 37852229 DOI: 10.1021/acschembio.3c00491] [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: 10/20/2023]
Abstract
The reactions of nitrones with cyclooctadiynes were studied to establish the relative rates of sequential reactions and to determine the limits and scope of this bioorthogonal chemistry. We have established the second-order rate constants for the consecutive additions of a variety of nitrones onto diyne and studied the structure-activity relationships via Hammett plots. Results show that the addition of the second nitrone to the monointermediate occurs significantly faster than the first, with both reactions being faster than analogous reactions with azides. Computational chemistry supports these observations. The rate of second addition increases with electron-deficient nitrones, as demonstrated by a large rho value of 2.08, suggesting that the reaction rate can be controlled by nitrone selectivity. To further investigate the kinetic parameters of the reaction, dinitrone monomers containing cyclic and diaryl-nitrones were designed for use in oligomerization applications. Oligomerization was used as a probe to test the limits of the reactivity and attempt to isolate monocycloaddition products. The oligomer formed from a cyclic nitrone reacts faster, and detailed MALDI mass spectrometry analysis shows that monoaddition products exist only transiently and are not isolatable. These studies inform on the scope and limits of this chemistry in a variety of applications. We successfully demonstrated bacterial cell wall labeling using heterogeneous dual cycloadditions involving nitrone and azide dipoles, where the nitrone was the faster reacting partner on the bacterial cell surface.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Shadi Sedghi Masoud
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Masaya Nakajima
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
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4
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Zheng Q, Chang PV. Shedding Light on Bacterial Physiology with Click Chemistry. Isr J Chem 2023; 63:e202200064. [PMID: 37841997 PMCID: PMC10569449 DOI: 10.1002/ijch.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 11/11/2022]
Abstract
Bacteria constitute a major lifeform on this planet and play numerous roles in ecology, physiology, and human disease. However, conventional methods to probe their activities are limited in their ability to visualize and identify their functions in these diverse settings. In the last two decades, the application of click chemistry to label these microbes has deepened our understanding of bacterial physiology. With the development of a plethora of chemical tools that target many biological molecules, it is possible to track these microorganisms in real-time and at unprecedented resolution. Here, we review click chemistry, including bioorthogonal reactions, and their applications in imaging bacterial glycans, lipids, proteins, and nucleic acids using chemical reporters. We also highlight significant advances that have enabled biological discoveries that have heretofore remained elusive.
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Affiliation(s)
- Qiuyu Zheng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
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Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
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Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
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Bilodeau DA, Margison KD, Serhan M, Pezacki JP. Bioorthogonal Reactions Utilizing Nitrones as Versatile Dipoles in Cycloaddition Reactions. Chem Rev 2021; 121:6699-6717. [PMID: 33464040 DOI: 10.1021/acs.chemrev.0c00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemical reactions have emerged as convenient and rapid methods for incorporating unnatural functionality into living systems. Different prototype reactions have been optimized for use in biological settings. Optimization of 3 + 2 dipolar cycloadditions involving nitrones has resulted in highly efficient reaction conditions for bioorthogonal chemistry. Through substitution at the nitrone carbon or nitrogen atom, stereoelectronic tuning of the reactivity of the dipole has assisted in optimizing reactivity. Nitrones have been shown to react rapidly with cyclooctynes with bimolecular rate constants approaching k2 = 102 M-1 s-1, which are among the fastest bioorthogonal reactions reported (McKay et al. Org. Biomol. Chem. 2012, 10, 3066-3070). Nitrones have also been shown to react with trans-cyclooctenes (TCO) in strain-promoted TCO-nitrone cycloadditions reactions. Copper catalyzed reactions involving alkynes and nitrones have also been optimized for applications in biology. This review provides a comprehensive accounting of the different bioorthogonal reactions that have been developed using nitrones as versatile reactants, and provides some recent examples of applications for probing biological systems.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Mariam Serhan
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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8
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Smeenk MLWJ, Agramunt J, Bonger KM. Recent developments in bioorthogonal chemistry and the orthogonality within. Curr Opin Chem Biol 2020; 60:79-88. [PMID: 33152604 DOI: 10.1016/j.cbpa.2020.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/09/2023]
Abstract
The emergence of bioorthogonal reactions has greatly advanced research in the fields of biology and medicine. They are not only valuable for labeling, tracking, and understanding biomolecules within living organisms, but also important for constructing advanced bioengineering and drug delivery systems. As the systems studied are increasingly complex, the simultaneous use of multiple bioorthogonal reactions is equally desirable. In this review, we take a look at the different bioorthogonal reactions that have recently been developed, the methods of cellular incorporation and the strategies to create orthogonality within the bioorthogonal landscape.
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Affiliation(s)
- Mike L W J Smeenk
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jordi Agramunt
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Kimberly M Bonger
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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Nakajima M, Bilodeau DA, Pezacki JP. Predicting reactivity for bioorthogonal cycloadditions involving nitrones. RSC Adv 2020; 10:29306-29310. [PMID: 35521144 PMCID: PMC9055992 DOI: 10.1039/d0ra05092j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/23/2020] [Indexed: 01/20/2023] Open
Abstract
Nitrones are useful dipoles in both synthesis and in bioorthogonal transformations to report on biological phenomena. In bioorthogonal reactions, nitrones are both small and relatively easy to incorporate into biomolecules, while providing versatility in their ability to harbor different substituents that tune their reactivity. Herein, we examine the reactivities of some common and useful nitrone cycloadditions using density functional theory (DFT) and the distortion/interaction (D/I) model. The data show that relative reactivities can be predicted using these approaches, and useful insights gained further enchancing reactivities of both nitrones and their dipolarophile reaction partners. We find that D/I is a useful guide to understanding and predicting reactivities of cycloadditions involving nitrones.
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Affiliation(s)
- Masaya Nakajima
- Graduate School of Pharmaceutical Sciences, Chiba University 1-8-1 Inohana Chuo-ku Chiba 260-8675 Japan
| | - Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 150 Louis-Pasteur Ottawa Ontario K1N 6N5 Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 150 Louis-Pasteur Ottawa Ontario K1N 6N5 Canada
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