1
|
Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
Collapse
Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| |
Collapse
|
2
|
Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [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: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
Collapse
Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
3
|
Singh MK, Kenney LJ. Visualizing the invisible: novel approaches to visualizing bacterial proteins and host-pathogen interactions. Front Bioeng Biotechnol 2024; 12:1334503. [PMID: 38415188 PMCID: PMC10898356 DOI: 10.3389/fbioe.2024.1334503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Host-pathogen interactions play a critical role in infectious diseases, and understanding the underlying mechanisms is vital for developing effective therapeutic strategies. The visualization and characterization of bacterial proteins within host cells is key to unraveling the dynamics of these interactions. Various protein labeling strategies have emerged as powerful tools for studying host-pathogen interactions, enabling the tracking, localization, and functional analysis of bacterial proteins in real-time. However, the labeling and localization of Salmonella secreted type III secretion system (T3SS) effectors in host cells poses technical challenges. Conventional methods disrupt effector stoichiometry and often result in non-specific staining. Bulky fluorescent protein fusions interfere with effector secretion, while other tagging systems such as 4Cys-FLaSH/Split-GFP suffer from low labeling specificity and a poor signal-to-noise ratio. Recent advances in state-of-the-art techniques have augmented the existing toolkit for monitoring the translocation and dynamics of bacterial effectors. This comprehensive review delves into the bacterial protein labeling strategies and their application in imaging host-pathogen interactions. Lastly, we explore the obstacles faced and potential pathways forward in the realm of protein labeling strategies for visualizing interactions between hosts and pathogens.
Collapse
Affiliation(s)
- Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| |
Collapse
|
4
|
Wang Y, Zhang Y, Li M, Gao X, Su D. An Efficient Strategy for Constructing Fluorescent Nanoprobes for Prolonged and Accurate Tumor Imaging. Anal Chem 2024; 96:2481-2490. [PMID: 38293931 DOI: 10.1021/acs.analchem.3c04495] [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: 02/01/2024]
Abstract
Activatable near-infrared (NIR) fluorescent probes possess advantages of high selectivity, sensitivity, and deep imaging depth, holding great potential in the early diagnosis and prognosis assessment of tumors. However, small-molecule fluorescent probes are largely limited due to the rapid diffusion and metabolic clearance of activated fluorophores in vivo. Herein, we propose an efficient and reproducible novel strategy to construct activatable fluorescent nanoprobes through bioorthogonal reactions and the strong gold-sulfur (Au-S) interactions to achieve an enhanced permeability and retention (EPR) effect, thereby achieving prolonged and high-contrast tumor imaging in vivo. To demonstrate the merits of this strategy, we prepared an activatable nanoprobe, hCy-ALP@AuNP, for imaging alkaline phosphatase (ALP) activity in vivo, whose nanoscale properties facilitate accumulation and long-term retention in tumor lesions. Tumor-overexpressed ALP significantly increased the fluorescence signal of hCy-ALP@AuNP in the NIR region. More importantly, compared with the small-molecule probe hCy-ALP-N3, the nanoprobe hCy-ALP@AuNP significantly improved the distribution and retention time in the tumor, thus improving the imaging window and accuracy. Therefore, this nanoprobe platform has great potential in the efficient construction of biomarker-responsive fluorescent nanoprobes to realize precise tumor diagnosis in vivo.
Collapse
Affiliation(s)
- Yaling Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, 100124 Beijing, P. R. China
| | - Yong Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, 100124 Beijing, P. R. China
| | - Mingrui Li
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, 100124 Beijing, P. R. China
| | - Xueyun Gao
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, 100124 Beijing, P. R. China
| | - Dongdong Su
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, 100124 Beijing, P. R. China
| |
Collapse
|
5
|
Wang W, Mo W, Hang Z, Huang Y, Yi H, Sun Z, Lei A. Cuproptosis: Harnessing Transition Metal for Cancer Therapy. ACS NANO 2023; 17:19581-19599. [PMID: 37820312 DOI: 10.1021/acsnano.3c07775] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Transition metal elements, such as copper, play diverse and pivotal roles in oncology. They act as constituents of metalloenzymes involved in cellular metabolism, function as signaling molecules to regulate the proliferation and metastasis of tumors, and are integral components of metal-based anticancer drugs. Notably, recent research reveals that excessive copper can also modulate the occurrence of programmed cell death (PCD), known as cuprotosis, in cancer cells. This modulation occurs through the disruption of tumor cell metabolism and the induction of proteotoxic stress. This discovery uncovers a mode of interaction between transition metals and proteins, emphasizing the intricate link between copper homeostasis and tumor metabolism. Moreover, they provide innovative therapeutic strategies for the precise diagnosis and treatment of malignant tumors. At the crossroads of chemistry and oncology, we undertake a comprehensive review of copper homeostasis in tumors, elucidating the molecular mechanisms underpinning cuproptosis. Additionally, we summarize current nanotherapeutic approaches that target cuproptosis and provide an overview of the available laboratory and clinical methods for monitoring this process. In the context of emerging concepts, challenges, and opportunities, we emphasize the significant potential of nanotechnology in the advancement of this field.
Collapse
Affiliation(s)
- Wuyin Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
| | - Wentao Mo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
| | - Zishan Hang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
| | - Yueying Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
| | - Hong Yi
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, P. R. China
| | - Zhijun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, P. R. China
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, P. R. China
| | - Aiwen Lei
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, P. R. China
| |
Collapse
|
6
|
Nørgård MØ, Svenningsen P. Acute Kidney Injury by Ischemia/Reperfusion and Extracellular Vesicles. Int J Mol Sci 2023; 24:15312. [PMID: 37894994 PMCID: PMC10607034 DOI: 10.3390/ijms242015312] [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: 09/26/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Acute kidney injury (AKI) is often caused by ischemia-reperfusion injury (IRI). IRI significantly affects kidney metabolism, which elicits pro-inflammatory responses and kidney injury. The ischemia/reperfusion of the kidney is associated with transient high mitochondrial-derived reactive oxygen species (ROS) production rates. Excessive mitochondrial-derived ROS damages cellular components and, together with other pathogenic mechanisms, elicits a range of acute injury mechanisms that impair kidney function. Mitochondrial-derived ROS production also stimulates epithelial cell secretion of extracellular vesicles (EVs) containing RNAs, lipids, and proteins, suggesting that EVs are involved in AKI pathogenesis. This literature review focuses on how EV secretion is stimulated during ischemia/reperfusion and how cell-specific EVs and their molecular cargo may modify the IRI process. Moreover, critical pitfalls in the analysis of kidney epithelial-derived EVs are described. In particular, we will focus on how the release of kidney epithelial EVs is affected during tissue analyses and how this may confound data on cell-to-cell signaling. By increasing awareness of methodological pitfalls in renal EV research, the risk of false negatives can be mitigated. This will improve future EV data interpretation regarding EVs contribution to AKI pathogenesis and their potential as biomarkers or treatments for AKI.
Collapse
Affiliation(s)
| | - Per Svenningsen
- Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark;
| |
Collapse
|
7
|
Lin J, Selicharová I, Mitrová K, Fabre B, Miriyala VM, Lepšík M, Jiráček J, Hernández MSG. Targeting the insulin receptor with hormone and peptide dimers. J Pept Sci 2023; 29:e3461. [PMID: 36336650 DOI: 10.1002/psc.3461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Insulin is a key hormone involved in the regulation of overall energetic homeostasis of the organism. The dimeric character of the receptor for insulin evokes ideas about its activation or inhibition with peptide dimers that could either trigger or block the structural transition of the insulin receptor, leading to its activation. Herewith, we present the chemical engineering and biological characterization of several series of insulin dimers or dimers of specific peptides that should be able to bind receptors for insulin or insulin growth factor 1. The hormones or peptides in the dimers were interconnected with different linkers, consisting of triazole moieties and 3, 6, 8, 11, or 23 polyethylene glycol units. The prepared dimers were weaker in binding to insulin receptors than human insulin. However, some of the insulin dimers showed preferential binding specificity toward the isoform A of the insulin receptor, and the insulin dimers also stimulated the insulin receptor more strongly than would be consistent with their binding affinities. Our results suggest that designing insulin dimers may be a promising strategy for modulating the ability of the hormone to activate the receptor or to alter its specificity toward insulin receptor isoforms.
Collapse
Affiliation(s)
- Jingjing Lin
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Katarína Mitrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Benjamin Fabre
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | | |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Zhang N, Bessel P, Wu C. Copper-Containing Artificial Polyenzymes as a Clickase for Bioorthogonal Chemistry. Bioconjug Chem 2022; 33:1892-1899. [PMID: 36194410 DOI: 10.1021/acs.bioconjchem.2c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial polyenzymes (ArPoly) are tailored combinations of universal protein scaffolds and polymers newly proposed as promising alternatives to natural enzymes to expand the biocatalyst toolbox. The concept of ArPoly has been continuously extended to metal-containing ArPoly to overcome the drawbacks faced by conventional artificial metalloenzymes. Herein, we present a sustainable route to synthesize a novel water-soluble metalloenzyme for copper-catalyzed azide-alkyne cycloadditions in water with remarkable selectivity. In this case, synthetic l-proline monomers were polymerized onto bovine serum albumen in an aqueous medium via copper-mediated "grafting-from" atom-transfer radical polymerization, resulting in protein-polymer-copper conjugates named ArPolyclickase. The copper in ArPolyclickase plays pivotal bifunctional roles, not only as the catalyst for polymerization but also as the coordinated active site for alkyne-azide click catalysis. ArPolyclickase showcases high efficiency, substrate generality, regioselectivity, and ease of product separation for "click chemistry" in water. Notably, ArPolyclickase displays good biocompatibility without imposing copper toxicity on living cells, which offers the prospect for the upcoming bioorthogonal chemistry.
Collapse
Affiliation(s)
- Ningning Zhang
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany.,Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Patrick Bessel
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.,Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| |
Collapse
|
10
|
Partipilo G, Graham AJ, Belardi B, Keitz BK. Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition. ACS CENTRAL SCIENCE 2022; 8:246-257. [PMID: 35233456 PMCID: PMC8875427 DOI: 10.1021/acscentsci.1c01208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Indexed: 05/03/2023]
Abstract
Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.
Collapse
Affiliation(s)
- Gina Partipilo
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Austin J. Graham
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K. Keitz
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
11
|
Lee S, Kim J, Koh M. Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids. J Mol Biol 2021; 434:167248. [PMID: 34547330 DOI: 10.1016/j.jmb.2021.167248] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/09/2023]
Abstract
Technical innovations in protein labeling with a fluorophore at the specific residue have played a significant role in studying protein dynamics. The genetic code expansion (GCE) strategy enabled the precise installation of fluorophores at the tailored site of proteins in live cells with minimal perturbation of native functions. Considerable advances have been achieved over the past decades in fluorescent imaging using GCE strategies along with bioorthogonal chemistries. In this review, we discuss advances in the GCE-based strategies to site-specifically introduce fluorophore at a defined position of the protein and their bio-imaging applications.
Collapse
Affiliation(s)
- Sanghee Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Minseob Koh
- Department of Chemistry, Pusan National University, Busan 46241, Republic of Korea.
| |
Collapse
|
12
|
Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| |
Collapse
|
13
|
Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
Collapse
Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| |
Collapse
|
14
|
Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
Collapse
Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| |
Collapse
|
15
|
Gao Z, Li Y, Liu Z, Zhang Y, Chen F, An P, Lu W, Hu J, You C, Xu J, Zhang X, Sun B. Small-Molecule-Selective Organosilica Nanoreactors for Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions in Cellular and Living Systems. NANO LETTERS 2021; 21:3401-3409. [PMID: 33843242 DOI: 10.1021/acs.nanolett.0c04930] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We reported the synthesis of a tris(triazolylmethyl)amine (TTA)-bridged organosilane, functioning as Cu(I)-stabilizing ligands, and the installation of this building block into the backbone of mesoporous organosilica nanoparticles (TTASi) by a sol-gel way. Upon coordinating with Cu(I), the mesoporous CuI-TTASi, with a restricted metal active center inside the pore, functions as a molecular-sieve-typed nanoreactor to efficiently perform Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions on small-molecule substrates but fails to work on macromolecules larger than the pore diameter. As a proof of concept, we witnessed the advantages of selective nanoreactors in screening protein substrates for small molecules. Also, the robust CuI-TTASi could be implanted into the body of animal models including zebrafish and mice as biorthogonal catalysts without apparent toxicity, extending its utilization in vivo ranging from fluorescent labeling to in situ drug synthesis.
Collapse
Affiliation(s)
- Zhiguo Gao
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yaojia Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Zhikun Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yu Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Fanghui Chen
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Peijing An
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Wenjun Lu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Jinzhong Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Chaoqun You
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jun Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Baiwang Sun
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| |
Collapse
|
16
|
Pandey S, Mandal T. Discrete Benzotriazole‐Copper(II) Complexes in Chelated and Non‐Chelated Coordination Modes: Structural Analysis and Catalytic Application in Click and A
3
Coupling Reactions. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sharmila Pandey
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Bhopal Bhopal 462 066 India
- School of Sciences SAGE University Bhopal Bhopal 462 022 India
| | - Tanmoy Mandal
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Bhopal Bhopal 462 066 India
| |
Collapse
|
17
|
Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
Collapse
Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| |
Collapse
|
18
|
Kiranmye T, Vadivelu M, Magadevan D, Sampath S, Parthasarathy K, Aman N, Karthikeyan K. Sunlight‐Assisted Photocatalytic Sustainable Synthesis of 1,4‐Disubstituted 1,2,3‐Triazoles and Benzimidazoles Using TiO
2
−Cu
2
(OH)PO
4
Under Solvent‐Free Condition. ChemistrySelect 2021. [DOI: 10.1002/slct.202004427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tayyala Kiranmye
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
| | - Murugan Vadivelu
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
| | - Deviga Magadevan
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
| | - Sugirdha Sampath
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
- Department of Metallurgical & Materials Engineering Indian Institute of Technology, Madras Chennai 600036 India
| | - Kannabiran Parthasarathy
- Animal & Mineral Origin Drug Research Laboratory (AMDRL) Siddha Central Research Institute Central Council for Research in Siddha, Arignar Anna Hospital Campus, Arumbakkam Chennai 600 106 India
| | - Noor Aman
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
| | - Kesavan Karthikeyan
- Department of Chemistry B. S. Abdur Rahman Crescent Institute of Science and Technology Vandalur Chennai 600048 India
| |
Collapse
|
19
|
Hadar D, Gelkop S, Vaserman L, Amiram M. Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria. Chembiochem 2021; 22:1379-1384. [PMID: 33350556 DOI: 10.1002/cbic.202000663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/22/2020] [Indexed: 11/09/2022]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment - typically at a single site or at a few sites per protein - of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l-phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production - using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain - of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.
Collapse
Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Sigal Gelkop
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| |
Collapse
|
20
|
Yuan D, Wang S, Zhu G, Zhu A, Li L. Efficient copper-catalyzed tandem oxidative iodination and alkyne-azide cycloaddition in the presence of glycine-type ligands. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
21
|
Yao J, Huang X, Ren J. Selective analysis of newly synthesized proteins by combining fluorescence correlation spectroscopy with bioorthogonal non-canonical amino acid tagging. Analyst 2021; 146:478-486. [DOI: 10.1039/d0an01697g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
FCS with the BONCAT strategy is a promising approach for analysis of newly synthesized proteins and also be extended to further application for studying physiological or pathological processes related to proteins or other metabolic molecular changes.
Collapse
Affiliation(s)
- Jun Yao
- School of Chemistry and Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Xiangyi Huang
- School of Chemistry and Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Jicun Ren
- School of Chemistry and Chemical Engineering
- Frontiers Science Center for Transformative Molecules
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai 200240
| |
Collapse
|
22
|
Wang X, Zhang X, Huang Z, Fan X, Chen PR. Recent Progress of Bioorthogonal Chemistry in China. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20110530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
23
|
Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
Collapse
Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
24
|
Kaur J, Bhardwaj A, Wuest F. In Cellulo Generation of Fluorescent Probes for Live-Cell Imaging of Cylooxygenase-2. Chemistry 2020; 27:3326-3337. [PMID: 32786126 DOI: 10.1002/chem.202003315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Indexed: 02/01/2023]
Abstract
Live-cell imaging with fluorescent probes is an essential tool in chemical biology to visualize the dynamics of biological processes in real-time. Intracellular disease biomarker imaging remains a formidable challenge due to the intrinsic limitations of conventional fluorescent probes and the complex nature of cells. This work reports the in cellulo assembly of a fluorescent probe to image cyclooxygenase-2 (COX-2). We developed celecoxib-azide derivative 14, possessing favorable biophysical properties and excellent COX-2 selectivity profile. In cellulo strain-promoted fluorogenic click chemistry of COX-2-engaged compound 14 with non/weakly-fluorescent compounds 11 and 17 formed fluorescent probes 15 and 18 for the detection of COX-2 in living cells. Competitive binding studies, biophysical, and comprehensive computational analyses were used to describe protein-ligand interactions. The reported new chemical toolbox enables precise visualization and tracking of COX-2 in live cells with superior sensitivity in the visible range.
Collapse
Affiliation(s)
- Jatinder Kaur
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Atul Bhardwaj
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank Wuest
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
25
|
Rivera SL, Espaillat A, Aditham AK, Shieh P, Muriel-Mundo C, Kim J, Cava F, Siegrist MS. Chemically Induced Cell Wall Stapling in Bacteria. Cell Chem Biol 2020; 28:213-220.e4. [PMID: 33238158 DOI: 10.1016/j.chembiol.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/09/2020] [Accepted: 11/06/2020] [Indexed: 12/16/2022]
Abstract
Transpeptidation reinforces the structure of cell-wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell-wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many species makes it challenging to determine cross-link function. Here, we present a technique to link peptide strands by chemical rather than enzymatic reaction. We employ biocompatible click chemistry to induce triazole formation between azido- and alkynyl-d-alanine residues that are metabolically installed in the peptidoglycan of Gram-positive or Gram-negative bacteria. Synthetic triazole cross-links can be visualized using azidocoumarin-d-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell-wall stapling protects Escherichia coli from treatment with the broad-spectrum β-lactams ampicillin and carbenicillin. Chemical control of cell-wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.
Collapse
Affiliation(s)
- Sylvia L Rivera
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine, Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, CA 94305, USA
| | - Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Chris Muriel-Mundo
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine, Department of Molecular Biology, Umeå University, Umeå 90187, Sweden.
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA.
| |
Collapse
|
26
|
Xiao CD, He ZY, Guo CX, Shen XC, Xu Y. Conformation of G-quadruplex Controlled by Click Reaction. Molecules 2020; 25:molecules25184339. [PMID: 32971833 PMCID: PMC7570587 DOI: 10.3390/molecules25184339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are non-canonical four stranded secondary structures possessing great biological importance. Controlling G-quadruplex conformation for further regulating biological processes is both exciting and challenging. In this study, we described a method for regulating G-quadruplex conformation by click chemistry for the first time. 8-ethynyl-2'-deoxyguanosine was synthesized and incorporated into a 12-nt telomere DNA sequence. Such a sequence, at first, formed mixed parallel/anti-parallel G-quadruplexes, while it changed to anti-parallel after reaction with azidobenzene. Meanwhile, the click reaction can give the sequence intense fluorescence.
Collapse
Affiliation(s)
- Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China;
- Correspondence: (C.-D.X.); (Y.X.); Tel.: +86-0851-88416160 (C.-D.X.); +81-985-85-0993 (Y.X.)
| | - Zhi-Yong He
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan;
| | - Chuan-Xin Guo
- Nucleic Acid Division, Shanghai Cell Therapy Group Co. Ltd., Jiading, Shanghai 201805, China;
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China;
| | - Yan Xu
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan;
- Correspondence: (C.-D.X.); (Y.X.); Tel.: +86-0851-88416160 (C.-D.X.); +81-985-85-0993 (Y.X.)
| |
Collapse
|
27
|
Deciphering the Mechanism of Silver Catalysis of “Click” Chemistry in Water by Combining Experimental and MEDT Studies. Catalysts 2020. [DOI: 10.3390/catal10090956] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A combined experimental study and molecular electron density theory (MEDT) analysis was carried out to investigate the click of 1,2,3-triazole derivatives by Ag(I)-catalyzed azide-alkyne cycloaddition (AgAAC) reaction as well as its corresponding mechanistic pathway. Such a synthetic protocol leads to the regioselective formation of 1,4-disubstituted-1,2,3-triazoles in the presence of AgCl as catalyst and water as reaction solvent at room temperature and pressure. The MEDT was performed by applying Density Functional Theory (DFT) calculations at both B3LYP/6-31G(d,p) (LANL2DZ for Ag) and ωB97XD/6-311G(d,p) (LANL2DZ for Ag) levels with a view to decipher the observed regioselectivity in AgAAC reactions, and so to set out the number of silver(I) species and their roles in the formation of 1,4-disubstituted-1,2,3-triazoles. The comparison of the values of the energy barriers for the mono- and dinuclear Ag(I)-acetylide in the AgAAC reaction paths shows that the calculated energy barriers of dinuclear processes are smaller than those of the mononuclear one. The type of intramolecular interactions in the investigated AgAAC click chemistry reaction accounts for the regioselective formation of the 1,4-regiosisomeric triazole isomer. The ionic character of the starting compounds, namely Ag-acetylide, is revealed for the first time. This finding rules out any type of covalent interaction, involving the silver(I) complexes, along the reaction pathway. Electron localization function (ELF) topological analysis of the electronic structure of the stationary points reaffirmed the zw-type (zwitterionic-type) mechanism of the AgAAC reactions.
Collapse
|
28
|
Use of a Fluorescence-Based Assay To Measure Escherichia coli Membrane Potential Changes in High Throughput. Antimicrob Agents Chemother 2020; 64:AAC.00910-20. [PMID: 32631824 DOI: 10.1128/aac.00910-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Bacterial membrane potential is difficult to measure using classical electrophysiology techniques due to the small cell size and the presence of the peptidoglycan cell wall. Instead, chemical probes are often used to study membrane potential changes under conditions of interest. Many of these probes are fluorescent molecules that accumulate in a charge-dependent manner, and the resulting fluorescence change can be analyzed via flow cytometry or using a fluorescence microplate reader. Although this technique works well in many Gram-positive bacteria, it generates fairly low signal-to-noise ratios in Gram-negative bacteria due to dye exclusion by the outer membrane. We detail an optimized workflow that uses the membrane potential probe, 3,3'-diethyloxacarbocyanine iodide [DiOC2(3)], to measure Escherichia coli membrane potential changes in high throughput and describe the assay conditions that generate significant signal-to-noise ratios to detect membrane potential changes using a fluorescence microplate reader. A valinomycin calibration curve demonstrates this approach can robustly report membrane potentials over at least an ∼144-mV range with an accuracy of ∼12 mV. As a proof of concept, we used this approach to characterize the effects of some commercially available small molecules known to elicit membrane potential changes in other systems, increasing the repertoire of compounds known to perturb E. coli membrane energetics. One compound, the eukaryotic Ca2+ channel blocker amlodipine, was found to alter E. coli membrane potential and decrease the MIC of kanamycin, further supporting the value of this screening approach. This detailed methodology permits studying E. coli membrane potential changes quickly and reliably at the population level.
Collapse
|
29
|
Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
Collapse
Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
| |
Collapse
|
30
|
Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.
Collapse
Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| |
Collapse
|
31
|
Palanisamy N, Öztürk MA, Akmeriç EB, Di Ventura B. C-terminal eYFP fusion impairs Escherichia coli MinE function. Open Biol 2020; 10:200010. [PMID: 32456552 PMCID: PMC7276532 DOI: 10.1098/rsob.200010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Escherichia coli Min system plays an important role in the proper placement of the septum ring at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator with the membrane-bound ATPase MinD, resulting in MinD concentration being the lowest at mid-cell. MinC, the direct inhibitor of the septum initiator protein FtsZ, forms a complex with MinD at the membrane, mirroring its polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. Min oscillations are often studied in living cells by time-lapse microscopy using fluorescently labelled Min proteins. Here, we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo, in vitro and in silico approaches, we demonstrate that eYFP compromises the ability of MinE to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. In silico analyses predict that other fluorescent proteins are also likely to compromise several functionalities of MinE, suggesting that the results presented here are not specific to eYFP.
Collapse
Affiliation(s)
- Navaneethan Palanisamy
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Mehmet Ali Öztürk
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Emir Bora Akmeriç
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Faculty of Biology, Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| |
Collapse
|
32
|
Gao L, Lin X, Zheng A, Shuang E, Wang J, Chen X. Real-time monitoring of intracellular pH in live cells with fluorescent ionic liquid. Anal Chim Acta 2020; 1111:132-138. [PMID: 32312389 DOI: 10.1016/j.aca.2020.03.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
Real-time monitoring of intracellular pH is of great significance due to its essential role in physiological and pathological processes. In present work, the ionic liquid (IL) N-methyl-6-hydroxyquinolinium bis(trifluoromethylsulfonyl) imide ([6MQc][NTf2]) is proposed as a fluorescence probe for the quantitative imaging of intracellular pH in response to external stimuli. The fluorescence of the IL [6MQc][NTf2] exhibits a sensitive response to pH variations, as the deprotonation of [6MQc][NTf2] generates the highly fluorescent zwitterionic product [6MQz]. pH fluctuations in the range of 6.0-7.5 can be accurately sensed by monitoring the fluorescence change at 555 nm. Moreover, this IL probe exhibits favorable biocompatibility, excellent anti-photobleaching properties, and high tolerance to ionic strength. Using the IL probe, real-time sensing of hypoxia- and drug-induced intracellular pH changes in MCF-7 cells is achieved.
Collapse
Affiliation(s)
- Lifang Gao
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - Xin Lin
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - Anqi Zheng
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - E Shuang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - Jianhua Wang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China
| | - Xuwei Chen
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China.
| |
Collapse
|
33
|
Widder P, Schuck J, Summerer D, Drescher M. Combining site-directed spin labeling in vivo and in-cell EPR distance determination. Phys Chem Chem Phys 2020; 22:4875-4879. [DOI: 10.1039/c9cp05584c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Non-canonical amino acid incorporation via amber stop codon suppression and in vivo site-directed spin labeling allow in-cell EPR distance determination in E. coli.
Collapse
Affiliation(s)
- Pia Widder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Julian Schuck
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| |
Collapse
|
34
|
Guo YY, Zhang B, Wang L, Huang S, Wang S, You Y, Zhu G, Zhu A, Geng M, Li L. An efficient and easily-accessible ligand for Cu(i)-catalyzed azide–alkyne cycloaddition bioconjugation. Chem Commun (Camb) 2020; 56:14401-14403. [DOI: 10.1039/d0cc06348g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel ligand (6) for copper-catalyzed azide–alkyne cycloaddition (CuAAC) in bioconjugation has been developed.
Collapse
Affiliation(s)
- Yuan-Yang Guo
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Bo Zhang
- Department of Medical Research Center
- Peking Union Medical College Hospital
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100730
- China
| | - Luying Wang
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Shenlong Huang
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Shilei Wang
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Yanbo You
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Gongming Zhu
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Anlian Zhu
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Mingwei Geng
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Lingjun Li
- School of Chemistry and Chemical engineering
- Henan Normal University
- Xinxiang 453007
- China
| |
Collapse
|
35
|
Liu HS, Ishizuka T, Kawaguchi M, Nishii R, Kataoka H, Xu Y. A Nucleoside Derivative 5-Vinyluridine (VrU) for Imaging RNA in Cells and Animals. Bioconjug Chem 2019; 30:2958-2966. [DOI: 10.1021/acs.bioconjchem.9b00643] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong-shan Liu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makiko Kawaguchi
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Ryuichi Nishii
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Hiroaki Kataoka
- Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| |
Collapse
|
36
|
Neumann S, Biewend M, Rana S, Binder WH. The CuAAC: Principles, Homogeneous and Heterogeneous Catalysts, and Novel Developments and Applications. Macromol Rapid Commun 2019; 41:e1900359. [PMID: 31631449 DOI: 10.1002/marc.201900359] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/06/2019] [Indexed: 01/08/2023]
Abstract
The copper-catalyzed azide/alkyne cycloaddition reaction (CuAAC) has emerged as the most useful "click" chemistry. Polymer science has profited enormously from CuAAC by its simplicity, ease, scope, applicability and efficiency. Basic principles of the CuAAC are reviewed with a focus on homogeneous and heterogeneous catalysts, ligands, anchimeric assistance, and basic chemical principles. Recent developments of ligand design and acceleration are discussed.
Collapse
Affiliation(s)
- Steve Neumann
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
| | - Michel Biewend
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
| | - Sravendra Rana
- School of Engineering University of Petroleum and Energy Studies (UPES), Dehradun, Uttarakhand, 248007, India
| | - Wolfgang H Binder
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
| |
Collapse
|
37
|
Wang X, Liu Y, Fan X, Wang J, Ngai WSC, Zhang H, Li J, Zhang G, Lin J, Chen PR. Copper-Triggered Bioorthogonal Cleavage Reactions for Reversible Protein and Cell Surface Modifications. J Am Chem Soc 2019; 141:17133-17141. [DOI: 10.1021/jacs.9b05833] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Xin Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yanjun Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - William Shu Ching Ngai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaofeng Li
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gong Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
38
|
Ben El Ayouchia H, ElMouli H, Bahsis L, Anane H, Laamari R, Gómez-García CJ, Julve M, Stiriba SE. Hyperbranched polyethylenimine-supported copper(II) ions as a macroliganted homogenous catalyst for strict click reactions of azides and alkynes in water. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.120881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
39
|
Bahsis L, Ben El Ayouchia H, Anane H, Pascual-Álvarez A, De Munno G, Julve M, Stiriba SE. A reusable polymer-supported copper(I) catalyst for triazole click reaction on water: An experimental and computational study. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4669] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lahoucine Bahsis
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi; Université Cadi Ayyad; Safi Morocco
| | - Hicham Ben El Ayouchia
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi; Université Cadi Ayyad; Safi Morocco
| | - Hafid Anane
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi; Université Cadi Ayyad; Safi Morocco
| | - Alejandro Pascual-Álvarez
- Instituto de Ciencia Molecular/ICMol, Universidad de Valencia; C/Catedrático José Beltrán 2 46980 Valencia Spain
| | - Giovanni De Munno
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Rende, Cosenza Italy
| | - Miguel Julve
- Instituto de Ciencia Molecular/ICMol, Universidad de Valencia; C/Catedrático José Beltrán 2 46980 Valencia Spain
| | - Salah-Eddine Stiriba
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi; Université Cadi Ayyad; Safi Morocco
- Instituto de Ciencia Molecular/ICMol, Universidad de Valencia; C/Catedrático José Beltrán 2 46980 Valencia Spain
| |
Collapse
|
40
|
Aflak N, Ben El Ayouchia H, Bahsis L, El Mouchtari EM, Julve M, Rafqah S, Anane H, Stiriba SE. Sustainable Construction of Heterocyclic 1,2,3-Triazoles by Strict Click [3+2] Cycloaddition Reactions Between Azides and Alkynes on Copper/Carbon in Water. Front Chem 2019; 7:81. [PMID: 30838201 PMCID: PMC6389623 DOI: 10.3389/fchem.2019.00081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 11/16/2022] Open
Abstract
1,4-Disubstituted-1,2,3-triazoles, considered as an important and useful class of heterocycles with potential applications in material science and biology, have been prepared in an efficient and selective manner by copper on carbon-catalyzed [3+2] cycloaddition reactions of azides and alkynes (CuAAC) in water under strict click chemistry conditions. Copper(I) catalysts heterogenized onto commercially activated carbon materials (Cu-CC) and on another carbon material produced from vegetable biomass using Argan nut shells (Cu-CANS) were found to be versatile catalytic sources for sustainable CuAAC. These copper on carbon supports were prepared and fully characterized by using two types of activated carbons that exhibit different porosity and specific surface. The delineation of the nature of the catalytic copper species and the role of the carbon support in the CuAAC were addressed. These heterogeneous copper on carbon catalysts were recovered and reused until ten catalytic runs without any noticeable loss of activity.
Collapse
Affiliation(s)
- Noura Aflak
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Hicham Ben El Ayouchia
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Lahoucine Bahsis
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - El Mountassir El Mouchtari
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Miguel Julve
- Instituto de Ciencia Molecular/ICMol, Universidad de Valencia, Valencia, Spain
| | - Salah Rafqah
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Hafid Anane
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Salah-Eddine Stiriba
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
- Instituto de Ciencia Molecular/ICMol, Universidad de Valencia, Valencia, Spain
| |
Collapse
|
41
|
Karlikova M, Cermakova V, Demuth J, Valer V, Miletin M, Novakova V, Zimcik P. Magnesium tetrapyrazinoporphyrazines: tuning of the pKa of red-fluorescent pH indicators. Dalton Trans 2019; 48:6162-6173. [DOI: 10.1039/c9dt00381a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence of Mg(ii) complexes of tetrapyrazinoporphyrazines can be switched off and on depending on pH.
Collapse
Affiliation(s)
- Martina Karlikova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Veronika Cermakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Vojtech Valer
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove
- Czech Republic
| |
Collapse
|
42
|
Li L, Huang S, Shang T, Zhang B, Guo Y, Zhu G, Zhou D, Zhang G, Zhu A, Zhang L. Medium Rings Bearing Bitriazolyls: Easily Accessible Structures with Superior Performance as Cu Catalyst Ligands. J Org Chem 2018; 83:13166-13177. [PMID: 30354127 DOI: 10.1021/acs.joc.8b01899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benefiting from their unique properties, the development of structurally novel and easily accessible medium rings is of significant interest in the pharmaceutical industry and academic research. However, synthetic access to medium-ring scaffolds is very difficult due to their rigid skeleton and large-angle strains. In this paper, a new class of medium rings bearing bitriazolyls (MRBTs) was designed, synthesized, identified as a promising new skeleton ligand for the Cu(I)-catalyzed click reaction, and used in site-special modification of protein. One of the MRBTs, 3aa, exhibited a turnover number (TON) as high as 55 000 and dramatic accelerating effects ( kobs = 1.95 M-1 s-1) and ranked among the most efficient ligands for copper-catalyzed alkyne and azide cycloaddition. Unlike the difficult access to other known medium rings, these 7-12-membered MRBTs can be prepared in straightforward, one-step manner from structurally diverse linear terminal diynes and azides. The unique accessibility and intriguing properties therefore imply their broad application perspectives.
Collapse
Affiliation(s)
- Lingjun Li
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Shenlong Huang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Tongpeng Shang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Bo Zhang
- National Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100083 , P. R. China
| | - Yuanyang Guo
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Gongming Zhu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Demin Zhou
- National Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100083 , P. R. China
| | - Guisheng Zhang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Anlian Zhu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , P. R. China
| | - Lihe Zhang
- National Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100083 , P. R. China
| |
Collapse
|
43
|
Fermentative degradation of Patulin by Saccharomyces cerevisiae in aqueous solution. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.07.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
44
|
Stull F, Hipp H, Stockbridge RB, Bardwell JCA. In vivo chloride concentrations surge to proteotoxic levels during acid stress. Nat Chem Biol 2018; 14:1051-1058. [PMID: 30323217 PMCID: PMC6193267 DOI: 10.1038/s41589-018-0143-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/29/2018] [Indexed: 11/23/2022]
Abstract
To successfully colonize the intestine, bacteria must survive passage through the stomach. The permeability of the outer membrane renders the periplasm of Gram-negative bacteria vulnerable to stomach acid, which inactivates proteins. Here we report that the semipermeable nature of the outer membrane allows the development of a strong Donnan equilibrium across this barrier at low pH. As a result, when bacteria are exposed to conditions that mimic gastric juice, periplasmic chloride concentrations rise to levels that exceed 0.6 M. At these chloride concentrations, proteins readily aggregate in vitro. The acid sensitivity of strains lacking acid-protective chaperones is enhanced by chloride, suggesting that these chaperones protect periplasmic proteins both from acidification and from the accompanying accumulation of chloride. These results illustrate how organisms have evolved chaperones to respond to the substantial chemical threat imposed by otherwise innocuous chloride concentrations that are amplified to proteotoxic levels by low-pH-induced Donnan equilibrium effects.
Collapse
Affiliation(s)
- Frederick Stull
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Hannah Hipp
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
45
|
García-Heredia A, Pohane AA, Melzer ES, Carr CR, Fiolek TJ, Rundell SR, Lim HC, Wagner JC, Morita YS, Swarts BM, Siegrist MS. Peptidoglycan precursor synthesis along the sidewall of pole-growing mycobacteria. eLife 2018; 7:37243. [PMID: 30198841 PMCID: PMC6191288 DOI: 10.7554/elife.37243] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 09/09/2018] [Indexed: 12/25/2022] Open
Abstract
Rod-shaped mycobacteria expand from their poles, yet d-amino acid probes label cell wall peptidoglycan in this genus at both the poles and sidewall. We sought to clarify the metabolic fates of these probes. Monopeptide incorporation was decreased by antibiotics that block peptidoglycan synthesis or l,d-transpeptidation and in an l,d-transpeptidase mutant. Dipeptides complemented defects in d-alanine synthesis or ligation and were present in lipid-linked peptidoglycan precursors. Characterizing probe uptake pathways allowed us to localize peptidoglycan metabolism with precision: monopeptide-marked l,d-transpeptidase remodeling and dipeptide-marked synthesis were coincident with mycomembrane metabolism at the poles, septum and sidewall. Fluorescent pencillin-marked d,d-transpeptidation around the cell perimeter further suggested that the mycobacterial sidewall is a site of cell wall assembly. While polar peptidoglycan synthesis was associated with cell elongation, sidewall synthesis responded to cell wall damage. Peptidoglycan editing along the sidewall may support cell wall robustness in pole-growing mycobacteria.
Collapse
Affiliation(s)
- Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
| | - Amol Arunrao Pohane
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Emily S Melzer
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Caleb R Carr
- Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Taylor J Fiolek
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, United States
| | - Sarah R Rundell
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, United States
| | - Hoong Chuin Lim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Jeffrey C Wagner
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Yasu S Morita
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States.,Department of Microbiology, University of Massachusetts, Amherst, United States
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, United States
| | - M Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States.,Department of Microbiology, University of Massachusetts, Amherst, United States
| |
Collapse
|
46
|
Loukopoulos E, Abdul-Sada A, Csire G, Kállay C, Brookfield A, Tizzard GJ, Coles SJ, Lykakis IN, Kostakis GE. Copper(ii)-benzotriazole coordination compounds in click chemistry: a diagnostic reactivity study. Dalton Trans 2018; 47:10491-10508. [PMID: 29796447 DOI: 10.1039/c8dt01256c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This diagnostic study aims to shed light on the catalytic activity of a library of Cu(ii) based coordination compounds with benzotriazole-based ligands. We report herein the synthesis and characterization of five new coordination compounds formulated as [CuII(L4)(MeCN)2(CF3SO3)2] (1), [CuII(L5)2(CF3SO3)2] (2), [CuII(L6)2(MeCN)(CF3SO3)]·(CF3SO3) (3), [CuII(L6)2(H2O)(CF3SO3)]·(CF3SO3)·2(Me2CO) (4), and [Cu(L1)2(L1')2(CF3SO3)2]2·4(CF3SO3)·8(Me2CO) (5), derived from similar nitrogen-based ligands. The homogeneous catalytic activity of these compounds along with our previously reported coordination compounds (6-13), derived from similar ligands, is tested against the well-known Cu(i)-catalysed azide-alkyne cycloaddition reaction. The optimal catalyst [CuII(L1)2(CF3SO3)2] (10) activates the reaction to afford 1,4-disubstituted 1,2,3-triazoles with yields up to 98% and without requiring a reducing agent. Various control experiments are performed to optimize the method and examine parameters such as ligand variation, metal coordination geometry and environment, in order to elucidate the behaviour of the catalytic system.
Collapse
Affiliation(s)
- Edward Loukopoulos
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
| | - Alaa Abdul-Sada
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
| | - Gizella Csire
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Csilla Kállay
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
| | - Adam Brookfield
- School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
| | - Graham J Tizzard
- UK National Crystallography Service, Chemistry, University of Southampton, SO1 71BJ, UK
| | - Simon J Coles
- UK National Crystallography Service, Chemistry, University of Southampton, SO1 71BJ, UK
| | - Ioannis N Lykakis
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - George E Kostakis
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
| |
Collapse
|
47
|
Seifter JL, Chang HY. Extracellular Acid-Base Balance and Ion Transport Between Body Fluid Compartments. Physiology (Bethesda) 2018; 32:367-379. [PMID: 28814497 DOI: 10.1152/physiol.00007.2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 01/18/2023] Open
Abstract
Clinical assessment of acid-base disorders depends on measurements made in the blood, part of the extracellular compartment. Yet much of the metabolic importance of these disorders concerns intracellular events. Intracellular and interstitial compartment acid-base balance is complex and heterogeneous. This review considers the determinants of the extracellular fluid pH related to the ion transport processes at the interface of cells and the interstitial fluid, and between epithelial cells lining the transcellular contents of the gastrointestinal and urinary tracts that open to the external environment. The generation of acid-base disorders and the associated disruption of electrolyte balance are considered in the context of these membrane transporters. This review suggests a process of internal and external balance for pH regulation, similar to that of potassium. The role of secretory gastrointestinal epithelia and renal epithelia with respect to normal pH homeostasis and clinical disorders are considered. Electroneutrality of electrolytes in the ECF is discussed in the context of reciprocal changes in Cl- or non Cl- anions and [Formula: see text].
Collapse
|
48
|
Ngo AH, Bose S, Do LH. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems. Chemistry 2018; 24:10584-10594. [DOI: 10.1002/chem.201800504] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Anh H. Ngo
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Sohini Bose
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| | - Loi H. Do
- Department of Chemistry; University of Houston; 4800 Calhoun Road Houston TX 77004 USA
| |
Collapse
|
49
|
Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides. Proc Natl Acad Sci U S A 2018; 115:E4870-E4879. [PMID: 29735649 PMCID: PMC6003464 DOI: 10.1073/pnas.1801336115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Capsules are critical virulence determinants for bacterial pathogens. They are composed of capsular polysaccharides (CPSs) with diverse structures, whose assembly on the cell surface is often powered by a conserved ABC transporter. Current capsule-assembly models include a contiguous trans-envelope channel directing nascent CPSs from the transporter to the cell surface. This conserved apparatus is an attractive target for antivirulence antimicrobial development. This work describes a CPS depolymerizing lyase enzyme found in the Burkholderiales and unique structural features that define its mechanism, CPS specificity, and evolution to function in the periplasm in a noncatabolic role. The activity of this enzyme provides evidence that CPS assembled in an ABC transporter-dependent system is exposed to periplasm during translocation to the cell surface. Capsules are surface layers of hydrated capsular polysaccharides (CPSs) produced by many bacteria. The human pathogen Salmonella enterica serovar Typhi produces “Vi antigen” CPS, which contributes to virulence. In a conserved strategy used by bacteria with diverse CPS structures, translocation of Vi antigen to the cell surface is driven by an ATP-binding cassette (ABC) transporter. These transporters are engaged in heterooligomeric complexes proposed to form an enclosed translocation conduit to the cell surface, allowing the transporter to power the entire process. We identified Vi antigen biosynthesis genetic loci in genera of the Burkholderiales, which are paradoxically distinguished from S. Typhi by encoding VexL, a predicted pectate lyase homolog. Biochemical analyses demonstrated that VexL is an unusual metal-independent endolyase with an acidic pH optimum that is specific for O-acetylated Vi antigen. A 1.22-Å crystal structure of the VexL-Vi antigen complex revealed features which distinguish common secreted catabolic pectate lyases from periplasmic VexL, which participates in cell-surface assembly. VexL possesses a right-handed parallel β-superhelix, of which one face forms an electropositive glycan-binding groove with an extensive hydrogen bonding network that includes Vi antigen acetyl groups and confers substrate specificity. VexL provided a probe to interrogate conserved features of the ABC transporter-dependent export model. When introduced into S. Typhi, VexL localized to the periplasm and degraded Vi antigen. In contrast, a cytosolic derivative had no effect unless export was disrupted. These data provide evidence that CPS assembled in ABC transporter-dependent systems is actually exposed to the periplasm during envelope translocation.
Collapse
|
50
|
Gilormini PA, Lion C, Vicogne D, Guérardel Y, Foulquier F, Biot C. Chemical glycomics enrichment: imaging the recycling of sialic acid in living cells. J Inherit Metab Dis 2018; 41:515-523. [PMID: 29294191 PMCID: PMC5959963 DOI: 10.1007/s10545-017-0118-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/28/2017] [Accepted: 11/20/2017] [Indexed: 01/10/2023]
Abstract
The development of metabolic oligosaccharide engineering (MOE) over the past two decades enabled the bioimaging studies of glycosylation processes in physio-pathological contexts. Herein, we successfully applied the chemical reporter strategy to image the fate of sialylated glycoconjugates in healthy and sialin-deficient patient fibroblasts. This chemical glycomics enrichment is a powerful tool for tracking sialylated glycoconjugates and probing lysosomal recycling capacities. Thus, such strategies appear fundamental for the characterization of lysosomal storage diseases.
Collapse
Affiliation(s)
- Pierre André Gilormini
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Cédric Lion
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Dorothée Vicogne
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Yann Guérardel
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - François Foulquier
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
| | - Christophe Biot
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
| |
Collapse
|