51
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Kanagasundaram T, Kramer CS, Boros E, Kopka K. Rhenium and technetium-complexed silicon rhodamines as near-infrared imaging probes for bimodal SPECT- and optical imaging. Dalton Trans 2020; 49:7294-7298. [DOI: 10.1039/d0dt01084g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first technetium-99m tricarbonyl core labelled fluorescent Si-rhodamine and its rhenium analogue for bimodal SPECT- and near-infrared fluorescence imaging is presented.
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Affiliation(s)
- Thines Kanagasundaram
- Division of Radiopharmaceutical Chemistry
- German Cancer Research Center (DKFZ)
- 69120 Heidelberg
- Germany
- Institute of Inorganic Chemistry
| | - Carsten S. Kramer
- Division of Radiopharmaceutical Chemistry
- German Cancer Research Center (DKFZ)
- 69120 Heidelberg
- Germany
| | - Eszter Boros
- Department of Chemistry
- Stony Brook University
- Stony Brook
- USA
| | - Klaus Kopka
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR) e.V
- Institute of Radiopharmaceutical Cancer Research
- 01328 Dresden
- Germany
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52
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Gu L, Renault K, Romieu A, Richard JA, Srinivasan R. Synthesis and spectral properties of 6′-triazolyl-dihydroxanthene-hemicyanine fused near-infrared dyes. NEW J CHEM 2020. [DOI: 10.1039/d0nj01724h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Copper(i)-catalyzed azide alkyne cycloaddition (CuAAC) to explore the fluorogenic potential of near-infrared (NIR) dihydroxanthene (DHX) triazole dyes.
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Affiliation(s)
- Lingyue Gu
- School of Pharmaceutical Science and Technology (SPST)
- Tianjin University
- Tianjin
- P. R. China
| | - Kévin Renault
- ICMUB, UMR 6302, CNRS
- Univ. Bourgogne Franche-Comté 9
- Avenue Alain Savary
- 21000 Dijon
- France
| | - Anthony Romieu
- ICMUB, UMR 6302, CNRS
- Univ. Bourgogne Franche-Comté 9
- Avenue Alain Savary
- 21000 Dijon
- France
| | - Jean-Alexandre Richard
- Functional Molecules and Polymers Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR)
- Neuros, #07-01 138665
- Singapore
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology (SPST)
- Tianjin University
- Tianjin
- P. R. China
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53
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Egyed A, Kormos A, Söveges B, Németh K, Kele P. Bioothogonally applicable, π-extended rhodamines for super-resolution microscopy imaging for intracellular proteins. Bioorg Med Chem 2020; 28:115218. [DOI: 10.1016/j.bmc.2019.115218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/22/2023]
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54
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Zhao M, Guo YS, Xu WN, Zhao YF, Xie HY, Li HJ, Chen XF, Zhao RS, Guo DS. Far-red to near-infrared fluorescent probes based on silicon-substituted xanthene dyes for sensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115704] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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55
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Zhang ZJ, Wang YC, Yang X, Hang HC. Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms. Chembiochem 2019; 21:19-32. [PMID: 31730246 DOI: 10.1002/cbic.201900535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/14/2019] [Indexed: 12/11/2022]
Abstract
The advances made in bioorthogonal chemistry and the development of chemical reporters have afforded new strategies to explore the targets and functions of specific metabolites in biology. These metabolite chemical reporters have been applied to diverse classes of bacteria including Gram-negative, Gram-positive, mycobacteria, and more complex microbiota communities. Herein we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease.
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Affiliation(s)
- Zhenrun J Zhang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Xinglin Yang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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56
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Fleiszig SMJ, Kroken AR, Nieto V, Grosser MR, Wan SJ, Metruccio MME, Evans DJ. Contact lens-related corneal infection: Intrinsic resistance and its compromise. Prog Retin Eye Res 2019; 76:100804. [PMID: 31756497 DOI: 10.1016/j.preteyeres.2019.100804] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022]
Abstract
Contact lenses represent a widely utilized form of vision correction with more than 140 million wearers worldwide. Although generally well-tolerated, contact lenses can cause corneal infection (microbial keratitis), with an approximate annualized incidence ranging from ~2 to ~20 cases per 10,000 wearers, and sometimes resulting in permanent vision loss. Research suggests that the pathogenesis of contact lens-associated microbial keratitis is complex and multifactorial, likely requiring multiple conspiring factors that compromise the intrinsic resistance of a healthy cornea to infection. Here, we outline our perspective of the mechanisms by which contact lens wear sometimes renders the cornea susceptible to infection, focusing primarily on our own research efforts during the past three decades. This has included studies of host factors underlying the constitutive barrier function of the healthy cornea, its response to bacterial challenge when intrinsic resistance is not compromised, pathogen virulence mechanisms, and the effects of contact lens wear that alter the outcome of host-microbe interactions. For almost all of this work, we have utilized the bacterium Pseudomonas aeruginosa because it is the leading cause of lens-related microbial keratitis. While not yet common among corneal isolates, clinical isolates of P. aeruginosa have emerged that are resistant to virtually all currently available antibiotics, leading the United States CDC (Centers for Disease Control) to add P. aeruginosa to its list of most serious threats. Compounding this concern, the development of advanced contact lenses for biosensing and augmented reality, together with the escalating incidence of myopia, could portent an epidemic of vision-threatening corneal infections in the future. Thankfully, technological advances in genomics, proteomics, metabolomics and imaging combined with emerging models of contact lens-associated P. aeruginosa infection hold promise for solving the problem - and possibly life-threatening infections impacting other tissues.
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Affiliation(s)
- Suzanne M J Fleiszig
- School of Optometry, University of California, Berkeley, CA, USA; Graduate Group in Vision Science, University of California, Berkeley, CA, USA; Graduate Groups in Microbiology and Infectious Diseases & Immunity, University of California, Berkeley, CA, USA.
| | - Abby R Kroken
- School of Optometry, University of California, Berkeley, CA, USA
| | - Vincent Nieto
- School of Optometry, University of California, Berkeley, CA, USA
| | | | - Stephanie J Wan
- Graduate Group in Vision Science, University of California, Berkeley, CA, USA
| | | | - David J Evans
- School of Optometry, University of California, Berkeley, CA, USA; College of Pharmacy, Touro University California, Vallejo, CA, USA
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57
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Kanagasundaram T, Timmermann A, Kramer CS, Kopka K. A new approach to silicon rhodamines by Suzuki-Miyaura coupling - scope and limitations. Beilstein J Org Chem 2019; 15:2569-2576. [PMID: 31728171 PMCID: PMC6839552 DOI: 10.3762/bjoc.15.250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022] Open
Abstract
Background: Silicon rhodamines are of particular interest because of their advantageous dye properties (fluorescence- and biostability, quantum efficiency, tolerance to photobleaching). Therefore, silicon rhodamines find frequent application in STED (stimulated emission depletion) microscopy, as sensor molecules for, e.g., ions and as fluorophores for the optical imaging of tumors. Different strategies were already employed for their synthesis. Because of just three known literature examples in which Suzuki–Miyaura cross couplings gave access to silicon rhodamines in poor to moderate yields, we wanted to improve these first valuable experimental results. Results: The preparation of the xanthene triflate was enhanced and several boron sources were screened to find the optimal coupling partner. After optimization of the palladium catalyst, different substituted boroxines were assessed to explore the scope of the Pd-catalyzed cross-coupling reaction. Conclusions: A number of silicon rhodamines were synthesized under the optimized conditions in up to 91% yield without the necessity of HPLC purification. Moreover, silicon rhodamines functionalized with free acid moieties are directly accessible in contrast to previously described methods.
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Affiliation(s)
- Thines Kanagasundaram
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Antje Timmermann
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Carsten S Kramer
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Klaus Kopka
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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58
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Li M, Li Y, Wang X, Cui X, Wang T. Synthesis and application of near-infrared substituted rhodamines. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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59
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Matthias J, Kanagasundaram T, Kopka K, Kramer CS. Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement. Beilstein J Org Chem 2019; 15:2333-2343. [PMID: 31666868 PMCID: PMC6808212 DOI: 10.3762/bjoc.15.226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Since their first synthesis, silicon xanthenes and the subsequently developed silicon rhodamines (SiR) gained a lot of attention as attractive fluorescence dyes offering a broad field of application. We aimed for the synthesis of a fluorinable pyridinyl silicon rhodamine for the use in multimodal (PET/OI) medical imaging of mitochondria in cancerous cells. Results: A dihalogenated fluorinatable pyridinyl rhodamine could be successfully synthesized with the high yield of 85% by application of a halogen dance (HD) rearrangement. The near-infrared dye shows a quantum yield of 0.34, comparable to other organelle targeting SiR derivatives and absorbs at 665 nm (εmax = 34 000 M−1cm−1) and emits at 681 nm (τ = 1.9 ns). Using colocalization experiments with MitoTracker® Green FM, we could prove the intrinsic targeting ability to mitochondria in two human cell lines (Pearson coefficient >0.8). The dye is suitable for live cell STED nanoscopy imaging and shows a nontoxic profile which makes it an appropriate candidate for medical imaging. Conclusions: We present a biocompatible, nontoxic, small molecule near-infrared dye with the option of subsequent radiolabelling and excellent optical properties for medical and bioimaging. As a compound with intrinsic mitochondria targeting ability, the radiolabelled analogue can be applied in multimodal (PET/OI) imaging of mitochondria for diagnostic and therapeutic use in, e.g., cancer patients.
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Affiliation(s)
- Jessica Matthias
- Max Planck Institute for Medical Research, Department of Optical Nanoscopy, Jahnstraße 29, 69120 Heidelberg, Germany.,Helmholtz International Graduate School, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany
| | - Thines Kanagasundaram
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany.,Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Klaus Kopka
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carsten S Kramer
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany
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60
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Ranieri AM, Caporale C, Fiorini V, Hubbard A, Rigby P, Stagni S, Watkin E, Ogden MI, Hackett MJ, Massi M. Complementary Approaches to Imaging Subcellular Lipid Architectures in Live Bacteria Using Phosphorescent Iridium Complexes and Raman Spectroscopy. Chemistry 2019; 25:10566-10570. [DOI: 10.1002/chem.201902023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/11/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Anna Maria Ranieri
- Curtin Institute for Functional Molecules and Interfaces, and School of Molecular and Life SciencesCurtin University Bentley 6102 WA Australia
| | - Chiara Caporale
- Curtin Institute for Functional Molecules and Interfaces, and School of Molecular and Life SciencesCurtin University Bentley 6102 WA Australia
| | - Valentina Fiorini
- Department of Industrial Chemistry “Toso Montanari”University of Bologna, viale del Risorgimento4 40136 Bologna Italy
| | - Alysia Hubbard
- Centre for Microscopy, Characterisation and AnalysisThe University of Western Australia Perth 6009 WA Australia
| | - Paul Rigby
- Centre for Microscopy, Characterisation and AnalysisThe University of Western Australia Perth 6009 WA Australia
| | - Stefano Stagni
- Department of Industrial Chemistry “Toso Montanari”University of Bologna, viale del Risorgimento4 40136 Bologna Italy
| | - Elizabeth Watkin
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research InstituteCurtin University Kent Street Bentley 6102 Australia
| | - Mark I. Ogden
- Curtin Institute for Functional Molecules and Interfaces, and School of Molecular and Life SciencesCurtin University Bentley 6102 WA Australia
| | - Mark J. Hackett
- Curtin Institute for Functional Molecules and Interfaces, and School of Molecular and Life SciencesCurtin University Bentley 6102 WA Australia
| | - Massimiliano Massi
- Curtin Institute for Functional Molecules and Interfaces, and School of Molecular and Life SciencesCurtin University Bentley 6102 WA Australia
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61
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Li W, Zou J, Zhu S, Mao X, Tian H, Wang X. Fluorodibenzocyclooctynes: A Trackable Click Reagent with Enhanced Reactivity. Chemistry 2019; 25:10328-10332. [PMID: 31243812 DOI: 10.1002/chem.201902834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 12/16/2022]
Abstract
Bioorthogonal reactions have widespread applications in biological systems, and development of new bioorthogonal reactions has been of great interest over the past two decades. In this work, the design and synthesis of a family of fluorinated dibenzocyclooctynes (FDIBOs) are reported. The electron-deficient nature of fluorine atoms significantly accelerated the reaction of cyclooctynes in 1,3-dipolar cycloadditions, with either benzyl azide or ethyl diazoacetate, compared to conventional dibenzocyclooctyne (DIBO). In addition, FDIBOs showed unique trackable properties owing to the high NMR sensitivity of the naturally abundant 19 F isotope. Biological molecules, including a monosaccharide, a peptide, and a protein, were tested with FDIBOs, and these reactions could be easily monitored by 19 F NMR spectroscopy to evaluate the progress of the conjugation reactions. In addition, labeling of live cells was also demonstrated with metabolically modified bacteria to expand the possible applications of FDIBOs.
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Affiliation(s)
- Wei Li
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Juan Zou
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Shiyu Zhu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Xianxian Mao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Hongyan Tian
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
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62
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Li B, Zhou X, Yang P, Zhu L, Zhong Y, Cai Z, Jiang B, Cai X, Liu J, Jiang X. Photoactivatable Fluorogenic Labeling via Turn-On "Click-Like" Nitroso-Diene Bioorthogonal Reaction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802039. [PMID: 31380178 PMCID: PMC6662066 DOI: 10.1002/advs.201802039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/27/2019] [Indexed: 06/10/2023]
Abstract
Fluorogenic labeling enables imaging cellular molecules of interest with minimal background. This process is accompanied with the notable increase of the quantum yield of fluorophore, thus minimizing the background signals from unactivated profluorophores. Herein, the development of a highly efficient and bioorthogonal nitroso-based Diels-Alder fluorogenic reaction is presented and its usefulness is validated as effective and controllable in fluorescent probes and live-cell labeling strategies for dynamic cellular imaging. It is demonstrated that nitroso-based cycloaddition is an efficient fluorogenic labeling tool through experiments of further UV-activatable fluorescent labeling on proteins and live cells. The ability of tuning the fluorescence of labeled proteins by UV-irradiation enables selective activation of proteins of interest in a particular cell compartment at a given time point, while leaving the remaining labeled molecules untouched.
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Affiliation(s)
- Bai Li
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Xian‐Hao Zhou
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201210China
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Peng‐Yu Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Liping Zhu
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Yuan Zhong
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Zhengjun Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xiaoqing Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Xianxing Jiang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
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63
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Siegl SJ, Galeta J, Dzijak R, Dračínský M, Vrabel M. Bioorthogonal Fluorescence Turn-On Labeling Based on Bicyclononyne-Tetrazine Cycloaddition Reactions that Form Pyridazine Products. Chempluschem 2019; 84:493-497. [PMID: 31245251 PMCID: PMC6582594 DOI: 10.1002/cplu.201900176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/24/2019] [Indexed: 12/12/2022]
Abstract
Fluorogenic bioorthogonal reactions enable visualization of biomolecules with excellent signal-to-noise ratio. A bicyclononyne-tetrazine ligation that produces fluorescent pyridazine products has been developed. In stark contrast to previous approaches, the formation of the dye is an inherent result of the chemical reaction and no additional fluorophores are needed in the reagents. The crucial structural elements that determine dye formation are electron-donating groups present in the starting tetrazine unit. The newly formed pyridazine fluorophores show interesting photophysical properties the fluorescence intensity increase in the reaction can reach an excellent 900-fold. Model imaging experiments demonstrate the application potential of this new fluorogenic bioorthogonal reaction.
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Affiliation(s)
- Sebastian J. Siegl
- Institute of Organic Chemistry and Biochemistry of theCzech Academy of SciencesFlemingovo nám. 2166 10PragueCzech Republic
| | - Juraj Galeta
- Institute of Organic Chemistry and Biochemistry of theCzech Academy of SciencesFlemingovo nám. 2166 10PragueCzech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of theCzech Academy of SciencesFlemingovo nám. 2166 10PragueCzech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of theCzech Academy of SciencesFlemingovo nám. 2166 10PragueCzech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of theCzech Academy of SciencesFlemingovo nám. 2166 10PragueCzech Republic
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64
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Spangler B, Yang S, Baxter Rath CM, Reck F, Feng BY. A Unified Framework for the Incorporation of Bioorthogonal Compound Exposure Probes within Biological Compartments. ACS Chem Biol 2019; 14:725-734. [PMID: 30908011 DOI: 10.1021/acschembio.9b00008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Compartmentalization is a crucial facet of many biological systems, and key aspects of cellular processes rely on spatial segregation within the cell. While many drug targets reside in specific intracellular compartments, the tools available for assessing compound exposure are generally limited to whole-cell measurements. To address this gap, we recently developed a bioorthogonal chemistry-based method to assess compartment-specific compound exposure and demonstrated its use in Gram-negative bacteria. To expand the applicability of this approach, we report here novel bioorthogonal probe modalities which enable diverse probe incorporation strategies. The probes we developed utilize a cleavable thiocarbamate linker to connect localizing elements such as metabolic substrates to a cyclooctyne moiety which enables the detection of azide-containing molecules. Adducts between the probe and azide-bearing compounds can be recovered and affinity purified after exposure experiments, thus facilitating the mass-spectrometry based analysis used to assess compound exposure. The bioorthogonal system reported here thus provides a valuable new tool for interrogating compartment-specific compound exposure in a variety of biological contexts while retaining a simple and unified sample preparation and analysis workflow.
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Affiliation(s)
- Benjamin Spangler
- Novartis Institutes for BioMedical Research, Emerville, California 94608, United States
| | - Shengtian Yang
- Novartis Institutes for BioMedical Research, Emerville, California 94608, United States
| | | | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emerville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, Emerville, California 94608, United States
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65
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Lazor KM, Zhou J, DeMeester KE, D'Ambrosio EA, Grimes CL. Synthesis and Application of Methyl N,O-Hydroxylamine Muramyl Peptides. Chembiochem 2019; 20:1369-1375. [PMID: 30672111 DOI: 10.1002/cbic.201800731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 01/01/2023]
Abstract
The innate immune system's interaction with bacterial cells plays a pivotal role in a variety of human diseases. Carbohydrate units derived from a component of bacterial cell wall, peptidoglycan (PG), are known to stimulate an immune response. Nonetheless, access to modified late-stage peptidoglycan intermediates is limited due to their synthetic complexity. A method to rapidly functionalize PG fragments is needed to better understand the natural host-PG interactions. Here methyl N,O-hydroxylamine linkers are incorporated onto a synthetic PG derivative, muramyl dipeptide (MDP). The modification of MDP maintained the ability to stimulate a nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) immune response dependent on the expression of nucleotide-binding oligomerization domain-containing protein 2 (Nod2). Intrigued by this modification's maintenance of biological activity, several applications were explored. Methyl N,O-hydroxylamine MDP was amendable to N-hydroxylsuccinimide (NHS) chemistry for bioconjugation to fluorophores as well as a self-assembled monolayer for Nod2 surface plasmon resonance analysis. Finally, linker incorporation was applicable to larger PG fragments, both enzymatically generated from Escherichia coli or chemically synthesized. This methodology provides rapid access to PG probes in one step and allows for the installation of a variety of chemical handles to advance the molecular understanding of PG and the innate immune system.
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Affiliation(s)
- Klare M Lazor
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Junhui Zhou
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Elizabeth A D'Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA.,Department of Biological Sciences, University of Delaware, 140 Brown Lab, Newark, DE, 19716, USA
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66
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Long S, Qiao Q, Miao L, Xu Z. A self-assembly/disassembly two-photo ratiometric fluorogenic probe for bacteria imaging. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.11.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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67
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Qian L, Pan S, Lee JS, Ge J, Li L, Yao SQ. Live-cell imaging and profiling of c-Jun N-terminal kinases using covalent inhibitor-derived probes. Chem Commun (Camb) 2019; 55:1092-1095. [PMID: 30620026 DOI: 10.1039/c8cc09558b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
c-Jun N-terminal kinases (JNKs) are involved in critical cellular functions. Herein, small-molecule JNK-targeting probes are reported based on a covalent inhibitor. Together with newly developed two-photon fluorescence Turn-ON reporters and chemoproteomic studies, we showed that some probes may be suitable for live-cell imaging and profiling of JNKs.
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Affiliation(s)
- Linghui Qian
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore. and Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, South Korea
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211800, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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68
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Abstract
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
| | - Péter Kele
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
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69
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Spangler B, Dovala D, Sawyer WS, Thompson KV, Six DA, Reck F, Feng BY. Molecular Probes for the Determination of Subcellular Compound Exposure Profiles in Gram-Negative Bacteria. ACS Infect Dis 2018; 4:1355-1367. [PMID: 29846057 DOI: 10.1021/acsinfecdis.8b00093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Gram-negative cell envelope presents a formidable barrier to xenobiotics, and achieving sufficient compound exposure inside the cell is a key challenge for the discovery of new antibiotics. To provide insight on the molecular determinants governing compound exposure in Gram-negative bacteria, we developed a methodology leveraging a cyclooctyne-based bioorthogonal probe to assess compartment-specific compound exposure. This probe can be selectively localized to the periplasmic or cytoplasmic compartments of Gram-negative bacteria. Once localized, the probe is used to test azide-containing compounds for exposure within each compartment by quantifying the formation of click-reaction products by mass spectrometry. We demonstrate this approach is an accurate and sensitive method of determining compartment-specific compound exposure profiles. We then apply this technology to study the compartment-specific exposure profiles of a small panel of azide-bearing compounds with known permeability characteristics in Gram-negative bacteria, demonstrating the utility of the system and the insight it is able to provide regarding compound exposure within intact bacteria.
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Affiliation(s)
- Benjamin Spangler
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - William S. Sawyer
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Katherine V. Thompson
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - David A. Six
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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70
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Liu G, Hu J, Liu S. Emerging Applications of Fluorogenic and Non-fluorogenic Bifunctional Linkers. Chemistry 2018; 24:16484-16505. [PMID: 29893499 DOI: 10.1002/chem.201801290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Indexed: 01/06/2023]
Abstract
Homo- and hetero-bifunctional linkers play vital roles in constructing a variety of functional systems, ranging from protein bioconjugates with drugs and functional agents, to surface modification of nanoparticles and living cells, and to the cyclization/dimerization of synthetic polymers and biomolecules. Conventional approaches for assaying conjugation extents typically rely on ex situ techniques, such as mass spectrometry, gel electrophoresis, and size-exclusion chromatography. If the conjugation process involving bifunctional linkers was rendered fluorogenic, then in situ monitoring, quantification, and optical tracking/visualization of relevant processes would be achieved. In this review, conventional non-fluorogenic linkers are first discussed. Then the focus is on the evolution and emerging applications of fluorogenic bifunctional linkers, which are categorized into hetero-bifunctional single-caging fluorogenic linkers, homo-bifunctional double-caging fluorogenic linkers, and hetero-bifunctional double-caging fluorogenic linkers. In addition, stimuli-cleavable bifunctional linkers designed for both conjugation and subsequent site-specific triggered release are also summarized.
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Affiliation(s)
- Guhuan Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Jinming Hu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Shiyong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
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71
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DeMeester KE, Liang H, Jensen MR, Jones ZS, D'Ambrosio EA, Scinto SL, Zhou J, Grimes CL. Synthesis of Functionalized N-Acetyl Muramic Acids To Probe Bacterial Cell Wall Recycling and Biosynthesis. J Am Chem Soc 2018; 140:9458-9465. [PMID: 29986130 DOI: 10.1021/jacs.8b03304] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Uridine diphosphate N-acetyl muramic acid (UDP NAM) is a critical intermediate in bacterial peptidoglycan (PG) biosynthesis. As the primary source of muramic acid that shapes the PG backbone, modifications installed at the UDP NAM intermediate can be used to selectively tag and manipulate this polymer via metabolic incorporation. However, synthetic and purification strategies to access large quantities of these PG building blocks, as well as their derivatives, are challenging. A robust chemoenzymatic synthesis was developed using an expanded NAM library to produce a variety of 2 -N-functionalized UDP NAMs. In addition, a synthetic strategy to access bio-orthogonal 3-lactic acid NAM derivatives was developed. The chemoenzymatic UDP synthesis revealed that the bacterial cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1 phosphate uridylyl transferase (MurU) were permissive to permutations at the two and three positions of the sugar donor. We further explored the utility of these derivatives in the fluorescent labeling of both Gram (-) and Gram (+) PG in whole cells using a variety of bio-orthogonal chemistries including the tetrazine ligation. This report allows for rapid and scalable access to a variety of functionalized NAMs and UDP NAMs, which now can be used in tandem with other complementary bio-orthogonal labeling strategies to address fundamental questions surrounding PG's role in immunology and microbiology.
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72
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Favre C, Friscourt F. Fluorogenic Sydnone-Modified Coumarins Switched-On by Copper-Free Click Chemistry. Org Lett 2018; 20:4213-4217. [PMID: 29995429 DOI: 10.1021/acs.orglett.8b01587] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis, photophysical characterization, and biochemical application of sydnone-modified coumarins, a novel class of fluorogenic clickable reagents, are reported. The sydnone moiety, a stable aromatic 1,3-dipole, efficiently quenched the fluorescence of coumarin, which could be restored, with a 132-fold enhancement, upon cycloadditions with cyclooctynes, thereby expanding the fluorogenic click toolbox. TD-DFT calculations suggest that the fluorescence quenching of the sydnone-modified coumarins is likely due to the presence of an energetically low-lying nonemissive charge-separated state.
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Affiliation(s)
- Camille Favre
- Institut Européen de Chimie et Biologie , Université de Bordeaux , 2 rue Robert Escarpit , 33607 Pessac , France.,Institut de Neurosciences Cognitives et Intégratives d'Aquitaine , CNRS UMR5287 , Bordeaux , France
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie , Université de Bordeaux , 2 rue Robert Escarpit , 33607 Pessac , France.,Institut de Neurosciences Cognitives et Intégratives d'Aquitaine , CNRS UMR5287 , Bordeaux , France
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73
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van Elsland DM, Pujals S, Bakkum T, Bos E, Oikonomeas‐Koppasis N, Berlin I, Neefjes J, Meijer AH, Koster AJ, Albertazzi L, van Kasteren SI. Ultrastructural Imaging of Salmonella-Host Interactions Using Super-resolution Correlative Light-Electron Microscopy of Bioorthogonal Pathogens. Chembiochem 2018; 19:1766-1770. [PMID: 29869826 PMCID: PMC6120560 DOI: 10.1002/cbic.201800230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 01/06/2023]
Abstract
The imaging of intracellular pathogens inside host cells is complicated by the low resolution and sensitivity of fluorescence microscopy and by the lack of ultrastructural information to visualize the pathogens. Herein, we present a new method to visualize these pathogens during infection that circumvents these problems: by using a metabolic hijacking approach to bioorthogonally label the intracellular pathogen Salmonella Typhimurium and by using these bioorthogonal groups to introduce fluorophores compatible with stochastic optical reconstruction microscopy (STORM) and placing this in a correlative light electron microscopy (CLEM) workflow, the pathogen can be imaged within its host cell context Typhimurium with a resolution of 20 nm. This STORM-CLEM approach thus presents a new approach to understand these pathogens during infection.
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Affiliation(s)
- Daphne M. van Elsland
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Sílvia Pujals
- Department of Nanoscopy for NanomedicineInstitute of Bioengineering of Catalonia (IBEC)Barcelona Institute of Science and Technology08028BarcelonaSpain
| | - Thomas Bakkum
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
| | - Erik Bos
- Department of Electron MicroscopyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Nikolaos Oikonomeas‐Koppasis
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Annemarie H. Meijer
- Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Abraham J. Koster
- Department of Electron MicroscopyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Lorenzo Albertazzi
- Department of Nanoscopy for NanomedicineInstitute of Bioengineering of Catalonia (IBEC)Barcelona Institute of Science and Technology08028BarcelonaSpain
- Department of Biomedical Engineering and Institute of Complex Molecular SystemsEindhoven University of Technology5600 MBEindhovenThe Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
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74
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Wan SJ, Sullivan AB, Shieh P, Metruccio MME, Evans DJ, Bertozzi CR, Fleiszig SMJ. IL-1R and MyD88 Contribute to the Absence of a Bacterial Microbiome on the Healthy Murine Cornea. Front Microbiol 2018; 9:1117. [PMID: 29896179 PMCID: PMC5986933 DOI: 10.3389/fmicb.2018.01117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/11/2018] [Indexed: 01/09/2023] Open
Abstract
Microbial communities are important for the health of mucosal tissues. Traditional culture and gene sequencing have demonstrated bacterial populations on the conjunctiva. However, it remains unclear if the cornea, a transparent tissue critical for vision, also hosts a microbiome. Corneas of wild-type, IL-1R (-/-) and MyD88 (-/-) C57BL/6 mice were imaged after labeling with alkyne-functionalized D-alanine (alkDala), a probe that only incorporates into the peptidoglycan of metabolically active bacteria. Fluorescence in situ hybridization (FISH) was also used to detect viable bacteria. AlkDala labeling was rarely observed on healthy corneas. In contrast, adjacent conjunctivae harbored filamentous alkDala-positive forms, that also labeled with DMN-Tre, a Corynebacterineae-specific probe. FISH confirmed the absence of viable bacteria on healthy corneas, which also cleared deliberately inoculated bacteria within 24 h. Differing from wild-type, both IL-1R (-/-) and MyD88 (-/-) corneas harbored numerous alkDala-labeled bacteria, a result abrogated by topical antibiotics. IL-1R (-/-) corneas were impermeable to fluorescein suggesting that bacterial colonization did not reflect decreased epithelial integrity. Thus, in contrast to the conjunctiva and other mucosal surfaces, healthy murine corneas host very few viable bacteria, and this constitutive state requires the IL-1R and MyD88. While this study cannot exclude the presence of fungi, viruses, or non-viable or dormant bacteria, the data suggest that healthy murine corneas do not host a resident viable bacterial community, or microbiome, the absence of which could have important implications for understanding the homeostasis of this tissue.
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Affiliation(s)
- Stephanie J Wan
- Vision Science Program, University of California, Berkeley, Berkeley, CA, United States
| | - Aaron B Sullivan
- School of Optometry, University of California, Berkeley, Berkeley, CA, United States
| | - Peyton Shieh
- College of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Matteo M E Metruccio
- School of Optometry, University of California, Berkeley, Berkeley, CA, United States
| | - David J Evans
- School of Optometry, University of California, Berkeley, Berkeley, CA, United States
- College of Pharmacy, Touro University California, Vallejo, CA, United States
| | - Carolyn R Bertozzi
- School of Optometry, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Suzanne M J Fleiszig
- School of Optometry, University of California, Berkeley, Berkeley, CA, United States
- Graduate Groups in Vision Sciences, Microbiology, and Infectious Diseases & Immunity, University of California, Berkeley, Berkeley, CA, United States
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75
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Bakkum T, van Leeuwen T, Sarris AJC, van Elsland DM, Poulcharidis D, Overkleeft HS, van Kasteren SI. Quantification of Bioorthogonal Stability in Immune Phagocytes Using Flow Cytometry Reveals Rapid Degradation of Strained Alkynes. ACS Chem Biol 2018; 13:1173-1179. [PMID: 29693370 PMCID: PMC5962927 DOI: 10.1021/acschembio.8b00355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
One of the areas
in which bioorthogonal chemistry—chemistry
performed inside a cell or organism—has become of pivotal importance
is in the study of host–pathogen interactions. The incorporation
of bioorthogonal groups into the cell wall or proteome of intracellular
pathogens has allowed study within the endolysosomal system. However,
for the approach to be successful, the incorporated bioorthogonal
groups must be stable to chemical conditions found within these organelles,
which are some of the harshest found in metazoans: the groups are
exposed to oxidizing species, acidic conditions, and reactive thiols.
Here we present an assay that allows the assessment of the stability
of bioorthogonal groups within host cell phagosomes. Using a flow
cytometry-based assay, we have quantified the relative label stability
inside dendritic cell phagosomes of strained and unstrained alkynes.
We show that groups that were shown to be stable in other systems
were degraded by as much as 79% after maturation of the phagosome.
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Affiliation(s)
- Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daphne M. van Elsland
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dimitrios Poulcharidis
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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76
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Feigman MJS, Pires MM. Synthetic Immunobiotics: A Future Success Story in Small Molecule-Based Immunotherapy? ACS Infect Dis 2018; 4:664-672. [PMID: 29431421 DOI: 10.1021/acsinfecdis.7b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Drug resistance to our current stock of antibiotics is projected to increase to levels that threaten our ability to reduce and eliminate bacterial infections, which is now considered one of the primary health care crises of the 21st century. Traditional antibiotic agents (e.g., penicillin) paved the way for massive advances in human health, but we need novel strategies to maintain the upper hand in the battle against pathogenic bacteria. Nontraditional strategies, such as targeted immunotherapies, could prove fruitful in complementing our antibiotic arsenal.
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Affiliation(s)
- Mary J. Sabulski Feigman
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, Pennsylvania 18015, United States
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77
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Mao D, Hu F, Ji S, Wu W, Ding D, Kong D, Liu B. Metal-Organic-Framework-Assisted In Vivo Bacterial Metabolic Labeling and Precise Antibacterial Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706831. [PMID: 29504163 DOI: 10.1002/adma.201706831] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/22/2017] [Indexed: 05/19/2023]
Abstract
Bacterial infection is one of the most serious physiological conditions threatening human health. There is an increasing demand for more effective bacterial diagnosis and treatment through noninvasive theranostic approaches. Herein, a new strategy is reported to achieve in vivo metabolic labeling of bacteria through the use of MIL-100 (Fe) nanoparticles (NPs) as the nanocarrier for precise delivery of 3-azido-d-alanine (d-AzAla). After intravenous injection, MIL-100 (Fe) NPs can accumulate preferentially and degrade rapidly within the high H2 O2 inflammatory environment, releasing d-AzAla in the process. d-AzAla is selectively integrated into the cell walls of bacteria, which is confirmed by fluorescence signals from clickable DBCO-Cy5. Ultrasmall photosensitizer NPs with aggregation-induced emission characteristics are subsequently designed to react with the modified bacteria through in vivo click chemistry. Through photodynamic therapy, the amount of bacteria on the infected tissue can be significantly reduced. Overall, this study demonstrates the advantages of metal-organic-framework-assisted bacteria metabolic labeling strategy for precise bacterial detection and therapy guided by fluorescence imaging.
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Affiliation(s)
- Duo Mao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Fang Hu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Shenglu Ji
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Wenbo Wu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deling Kong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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78
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Abstract
Control and manipulation of bacterial populations requires an understanding of the factors that govern growth, division, and antibiotic action. Fluorescent and chemically reactive small molecule probes of cell envelope components can visualize these processes and advance our knowledge of cell envelope biosynthesis (e.g., peptidoglycan production). Still, fundamental gaps remain in our understanding of the spatial and temporal dynamics of cell envelope assembly. Previously described reporters require steps that limit their use to static imaging. Probes that can be used for real-time imaging would advance our understanding of cell envelope construction. To this end, we synthesized a fluorogenic probe that enables continuous live cell imaging in mycobacteria and related genera. This probe reports on the mycolyltransferases that assemble the mycolic acid membrane. This peptidoglycan-anchored bilayer-like assembly functions to protect these cells from antibiotics and host defenses. Our probe, quencher-trehalose-fluorophore (QTF), is an analog of the natural mycolyltransferase substrate. Mycolyltransferases process QTF by diverting their normal transesterification activity to hydrolysis, a process that unleashes fluorescence. QTF enables high contrast continuous imaging and the visualization of mycolyltransferase activity in cells. QTF revealed that mycolyltransferase activity is augmented before cell division and localized to the septa and cell poles, especially at the old pole. This observed localization suggests that mycolyltransferases are components of extracellular cell envelope assemblies, in analogy to the intracellular divisomes and polar elongation complexes. We anticipate QTF can be exploited to detect and monitor mycobacteria in physiologically relevant environments.
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79
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Rodriguez-Rivera FP, Zhou X, Theriot JA, Bertozzi CR. Acute Modulation of Mycobacterial Cell Envelope Biogenesis by Front-Line Tuberculosis Drugs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Frances P. Rodriguez-Rivera
- Department of Chemistry; University of California; Berkeley CA 94720 USA
- Department of Chemistry; Stanford University; Stanford CA 94305 USA
| | - Xiaoxue Zhou
- Department of Biochemistry; Stanford University School of Medicine; Stanford CA 94305 USA
| | - Julie A. Theriot
- Department of Biochemistry; Stanford University School of Medicine; Stanford CA 94305 USA
- Department of Microbiology and Immunology; Stanford University School of Medicine; Stanford CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford CA 94305 USA
| | - Carolyn R. Bertozzi
- Department of Chemistry; Stanford University; Stanford CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford CA 94305 USA
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80
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Rodriguez-Rivera FP, Zhou X, Theriot JA, Bertozzi CR. Acute Modulation of Mycobacterial Cell Envelope Biogenesis by Front-Line Tuberculosis Drugs. Angew Chem Int Ed Engl 2018; 57:5267-5272. [PMID: 29392891 DOI: 10.1002/anie.201712020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/28/2018] [Indexed: 02/06/2023]
Abstract
Front-line tuberculosis (TB) drugs have been characterized extensively in vitro and in vivo with respect to gene expression and cell viability. However, little work has been devoted to understanding their effects on the physiology of the cell envelope, one of the main targets of this clinical regimen. Herein, we use metabolic labeling methods to visualize the effects of TB drugs on cell envelope dynamics in mycobacterial species. We developed a new fluorophore-trehalose conjugate to visualize trehalose monomycolates of the mycomembrane using super-resolution microscopy. We also probed the relationship between mycomembrane and peptidoglycan dynamics using a dual metabolic labeling strategy. Finally, we found that metabolic labeling of both cell envelope structures reports on drug effects on cell physiology in two hours, far faster than a genetic sensor of cell envelope stress. Our work provides insight into acute drug effects on cell envelope biogenesis in live mycobacteria.
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Affiliation(s)
- Frances P Rodriguez-Rivera
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Xiaoxue Zhou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
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81
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Yip AMH, Lo KKW. Luminescent rhenium(I), ruthenium(II), and iridium(III) polypyridine complexes containing a poly(ethylene glycol) pendant or bioorthogonal reaction group as biological probes and photocytotoxic agents. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.01.021] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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82
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Abstract
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis. In this chapter, we will overview recent advances in understanding the biosynthetic machinery for terminal alkyne synthesis. We will first describe how to elucidate terminal alkyne biosynthetic mechanism through heterologous expression, purification, and in vitro biochemical assays of individual pathway proteins. This will be followed by the description of an in vivo reporting system for the characterization of a membrane-bound bifunctional desaturase/acetylenase involved in terminal alkyne formation. The chapter will also cover the strategies for discovering additional protein homologs for terminal alkyne synthesis from microbes as well as the applications of click chemistry to identify and quantify terminal alkyne-bearing metabolites from microbial cultures. We will conclude this chapter with current challenges and future directions in this field.
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Affiliation(s)
- Xuejun Zhu
- University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- University of California, Berkeley, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States.
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83
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Kozma E, Estrada Girona G, Paci G, Lemke EA, Kele P. Bioorthogonal double-fluorogenic siliconrhodamine probes for intracellular super-resolution microscopy. Chem Commun (Camb) 2018; 53:6696-6699. [PMID: 28530747 DOI: 10.1039/c7cc02212c] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of double-fluorogenic siliconrhodamine probes were synthesized. These tetrazine-functionalized, membrane-permeable labels allowed site-specific bioorthogonal tagging of genetically manipulated intracellular proteins and subsequent imaging using super-resolution microscopy.
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Affiliation(s)
- E Kozma
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary.
| | - G Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - G Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - E A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - P Kele
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary.
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84
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Favre C, de Cremoux L, Badaut J, Friscourt F. Sydnone Reporters for Highly Fluorogenic Copper-Free Click Ligations. J Org Chem 2018; 83:2058-2066. [DOI: 10.1021/acs.joc.7b03004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Camille Favre
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Lucie de Cremoux
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Jerome Badaut
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
- Basic
Science Department, Loma Linda University, Loma Linda, California 92350, United States
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
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85
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Fischer C, Sparr C. Direct Transformation of Esters into Heterocyclic Fluorophores. Angew Chem Int Ed Engl 2018; 57:2436-2440. [DOI: 10.1002/anie.201711296] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Christian Fischer
- Department of Chemistry; University of Basel; St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry; University of Basel; St. Johanns-Ring 19 4056 Basel Switzerland
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86
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Fischer C, Sparr C. Direkte Umwandlung von Estern in heterocyclische Fluorophore. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christian Fischer
- Departement Chemie; Universität Basel; St. Johanns-Ring 19 4056 Basel Schweiz
| | - Christof Sparr
- Departement Chemie; Universität Basel; St. Johanns-Ring 19 4056 Basel Schweiz
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87
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Siegl SJ, Vázquez A, Dzijak R, Dračínský M, Galeta J, Rampmaier R, Klepetářová B, Vrabel M. Design and Synthesis of Aza-Bicyclononene Dienophiles for Rapid Fluorogenic Ligations. Chemistry 2018; 24:2426-2432. [PMID: 29243853 DOI: 10.1002/chem.201705188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Indexed: 12/15/2022]
Abstract
Fluorogenic bioorthogonal reactions enable visualization of biomolecules under native conditions with excellent signal-to-noise ratio. Here, we present the design and synthesis of conformationally-strained aziridine-fused trans-cyclooctene (aza-TCO) dienophiles, which lead to the formation of fluorescent products in tetrazine ligations without the need for attachment of an extra fluorophore moiety. The presented aza-TCOs adopt the highly strained "half-chair" conformation, which was predicted computationally and confirmed by NMR measurements and X-ray crystallography. Kinetic studies revealed that the aza-TCOs belong to the most reactive dienophiles known to date. The potential of the newly developed aza-TCO probes for bioimaging applications is demonstrated by protein labeling experiments, imaging of cellular glycoconjugates and peptidoglycan imaging of live bacteria.
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Affiliation(s)
- Sebastian J Siegl
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Arcadio Vázquez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Juraj Galeta
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Robert Rampmaier
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
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88
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Wang Q, Huang K, Cai S, Liu C, Jiao X, He S, Zhao L, Zeng X. Synthesis of near-infrared fluorescent rhodamines via an SNArH reaction and their biological applications. Org Biomol Chem 2018; 16:7163-7169. [DOI: 10.1039/c8ob01701h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Seven rectilinearly π-extended NIR fluorescent rhodamines were synthesized via an intramolecular SNArH reaction under mild conditions without any transition metal catalyst or extra oxidant.
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Affiliation(s)
- Qing Wang
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
| | - Kun Huang
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
| | - Songtao Cai
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Chang Liu
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
| | - Xiaojie Jiao
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
| | - Song He
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
| | - Liancheng Zhao
- School of Materials Science and Engineering
- Harbin Institute of Technology
- Harbin 150001
- China
| | - Xianshun Zeng
- Tianjin Key Laboratory for Photoelectric Materials and Devices
- Department of Function Materials
- School of Materials Science and Engineering
- Tianjin University of Technology
- Tianjin 300384
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89
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Kozma E, Paci G, Estrada Girona G, Lemke EA, Kele P. Fluorogenic Tetrazine-Siliconrhodamine Probe for the Labeling of Noncanonical Amino Acid Tagged Proteins. Methods Mol Biol 2018; 1728:337-363. [PMID: 29405009 DOI: 10.1007/978-1-4939-7574-7_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Tetrazine-bearing fluorescent labels enable site-specific tagging of proteins that are genetically manipulated with dienophile modified noncanonical amino acids. The inverse electron demand Diels-Alder reaction between the tetrazine and the dienophile fulfills the criteria of bioorthogonality allowing fluorescent labeling schemes of live cells. Here, we describe the detailed synthetic and labeling protocols of a near infrared emitting siliconrhodamine-tetrazine probe suitable for super-resolution imaging of residue-specifically engineered proteins in mammalian cells.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Research Centre for Natural Sciences, Institute of Organic Chemistry, Hungarian Academy of Sciences, Magyar tudósok krt 2, Budapest, 1117, Hungary
| | - Giulia Paci
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University, Johannes-von-Mullerweg 6, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Péter Kele
- Chemical Biology Research Group, Research Centre for Natural Sciences, Institute of Organic Chemistry, Hungarian Academy of Sciences, Magyar tudósok krt 2, Budapest, 1117, Hungary.
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90
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Wang Y, Lazor KM, DeMeester KE, Liang H, Heiss TK, Grimes CL. Postsynthetic Modification of Bacterial Peptidoglycan Using Bioorthogonal N-Acetylcysteamine Analogs and Peptidoglycan O-Acetyltransferase B. J Am Chem Soc 2017; 139:13596-13599. [PMID: 28898061 PMCID: PMC5837961 DOI: 10.1021/jacs.7b06820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bacteria have the natural ability to install protective postsynthetic modifications onto its bacterial peptidoglycan (PG), the coat woven into bacterial cell wall. Peptidoglycan O-acetyltransferase B (PatB) catalyzes the O-acetylation of PG in Gram (-) bacteria, which aids in bacterial survival, as it prevents autolysins such as lysozyme from cleaving the PG. We explored the mechanistic details of PatB's acetylation function and determined that PatB has substrate specificity for bioorthgonal short N-acetyl cysteamine (SNAc) donors. A variety of functionality including azides and alkynes were installed on tri-N-acetylglucosamine (NAG)3, a PG mimic, as well as PG isolated from various Gram (+) and Gram (-) bacterial species. The bioorthogonal modifications protect the isolated PG against lysozyme degradation in vitro. We further demonstrate that this postsynthetic modification of PG can be extended to use click chemistry to fluorescently label the mature PG in whole bacterial cells of Bacillus subtilis. Modifying PG postsynthetically can aid in the development of antibiotics and immune modulators by expanding the understanding of how PG is processed by lytic enzymes.
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Affiliation(s)
- Yiben Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Klare M. Lazor
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kristen E. DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Tyler K. Heiss
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Biological Chemistry, University of Delaware, Newark, DE 19716, USA
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91
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Mao Z, Jiang H, Song X, Hu W, Liu Z. Development of a Silicon-Rhodamine Based Near-Infrared Emissive Two-Photon Fluorescent Probe for Nitric Oxide. Anal Chem 2017; 89:9620-9624. [PMID: 28845669 DOI: 10.1021/acs.analchem.7b02697] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two-photon (TP) fluorescent probes are potential candidates for near-infrared (NIR) imaging which holds great promise in biological research. However, currently, most TP probes emit at wavelength <600 nm, which impedes their practical applications. In this work, we explored the TP properties of a silicon-rhodamine (SiR) derivative and hence developed the first SiR scaffold based "NIR-to-NIR" TP probe (SiRNO) for nitric oxide (NO). SiRNO exhibited high sensitivity and specificity, as well as fast response for NO detection. It was able to track the subtle variation of intracellular NO content in live cells. Owing to the NIR excitation and emission, SiRNO enabled the detection of NO in situ in the xenograft tumor mouse model, revealing the NO generation during the tumor progression. This work indicates that SiR can be an ideal platform for the development of NIR emissive TP probe and may thus promote the advancement of NIR imaging.
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Affiliation(s)
- Zhiqiang Mao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, Hubei 430072, China
| | - Hong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, Hubei 430072, China
| | - Xinjian Song
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, Hubei 430072, China
| | - Wei Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, Hubei 430072, China
| | - Zhihong Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, Hubei 430072, China
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92
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Pidgeon SE, Pires MM. Cell Wall Remodeling of Staphylococcus aureus in Live Caenorhabditis elegans. Bioconjug Chem 2017; 28:2310-2315. [DOI: 10.1021/acs.bioconjchem.7b00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sean E. Pidgeon
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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93
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Atwal S, Giengkam S, Chaemchuen S, Dorling J, Kosaisawe N, VanNieuwenhze M, Sampattavanich S, Schumann P, Salje J. Evidence for a peptidoglycan-like structure in Orientia tsutsugamushi. Mol Microbiol 2017; 105:440-452. [PMID: 28513097 PMCID: PMC5523937 DOI: 10.1111/mmi.13709] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2017] [Indexed: 01/04/2023]
Abstract
Bacterial cell walls are composed of the large cross-linked macromolecule peptidoglycan, which maintains cell shape and is responsible for resisting osmotic stresses. This is a highly conserved structure and the target of numerous antibiotics. Obligate intracellular bacteria are an unusual group of organisms that have evolved to replicate exclusively within the cytoplasm or vacuole of a eukaryotic cell. They tend to have reduced amounts of peptidoglycan, likely due to the fact that their growth and division takes place within an osmotically protected environment, and also due to a drive to reduce activation of the host immune response. Of the two major groups of obligate intracellular bacteria, the cell wall has been much more extensively studied in the Chlamydiales than the Rickettsiales. Here, we present the first detailed analysis of the cell envelope of an important but neglected member of the Rickettsiales, Orientia tsutsugamushi. This bacterium was previously reported to completely lack peptidoglycan, but here we present evidence supporting the existence of a peptidoglycan-like structure in Orientia, as well as an outer membrane containing a network of cross-linked proteins, which together confer cell envelope stability. We find striking similarities to the unrelated Chlamydiales, suggesting convergent adaptation to an obligate intracellular lifestyle.
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Affiliation(s)
- Sharanjeet Atwal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok Thailand
| | - Suparat Giengkam
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok Thailand
| | - Suwittra Chaemchuen
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok Thailand
| | - Jack Dorling
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Nont Kosaisawe
- Siriraj Laboratory for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Bangkok, Thailand
| | | | - Somponnat Sampattavanich
- Siriraj Laboratory for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Bangkok, Thailand
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok Thailand
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94
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Evidence of Multi-Domain Morphological Structures in Living Escherichia coli. Sci Rep 2017; 7:5660. [PMID: 28720785 PMCID: PMC5516040 DOI: 10.1038/s41598-017-05897-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/23/2017] [Indexed: 01/08/2023] Open
Abstract
A combination of light-microscopy and image processing was used to elaborate on the fluctuation in the width of the cylindrical part of Escherichia coli at sub-pixel-resolution, and under in vivo conditions. The mean-squared-width-difference along the axial direction of the cylindrical part of a number of bacteria was measured. The results reveal that the cylindrical part of Escherichia coli is composed of multi-domain morphological structures. The length of the domains starts at 150 nm in newborn cells, and linearly increases in length up to 300 nm in aged cells. The fluctuation in the local-cell-widths in each domain is less than the fluctuation of local-cell-widths between different domains. Local cell width correlations along the cell body occur on a length scale of less than 50 nm. This finding could be associated with the flexibility of the cell envelope in the radial versus longitudinal directions.
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95
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Stuhr‐Hansen N, Vagianou C, Blixt O. Synthesis of BODIPY‐Labeled Cholesterylated Glycopeptides by Tandem Click Chemistry for Glycocalyxification of Giant Unilamellar Vesicles (GUVs). Chemistry 2017; 23:9472-9476. [DOI: 10.1002/chem.201702104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Nicolai Stuhr‐Hansen
- Department of Chemistry, Chemical BiologyUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Charikleia‐Despoina Vagianou
- Department of Chemistry, Chemical BiologyUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Ola Blixt
- Department of Chemistry, Chemical BiologyUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg C Denmark
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96
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Ikeno T, Nagano T, Hanaoka K. Silicon-substituted Xanthene Dyes and Their Unique Photophysical Properties for Fluorescent Probes. Chem Asian J 2017; 12:1435-1446. [DOI: 10.1002/asia.201700385] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/26/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Takayuki Ikeno
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Drug Discovery Initiative; The University of Tokyo; 7-3-1, Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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97
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Progress and prospects for small-molecule probes of bacterial imaging. Nat Chem Biol 2017; 12:472-8. [PMID: 27315537 DOI: 10.1038/nchembio.2109] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/13/2016] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy is an essential tool for the exploration of cell growth, division, transcription and translation in eukaryotes and prokaryotes alike. Despite the rapid development of techniques to study bacteria, the size of these organisms (1-10 μm) and their robust and largely impenetrable cell envelope present major challenges in imaging experiments. Fusion-based strategies, such as attachment of the protein of interest to a fluorescent protein or epitope tag, are by far the most common means for examining protein localization and expression in prokaryotes. While valuable, the use of genetically encoded tags can result in mislocalization or altered activity of the desired protein, does not provide a readout of the catalytic state of enzymes and cannot enable visualization of many other important cellular components, such as peptidoglycan, lipids, nucleic acids or glycans. Here, we highlight the use of biomolecule-specific small-molecule probes for imaging in bacteria.
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98
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Liang H, DeMeester KE, Hou CW, Parent MA, Caplan JL, Grimes CL. Metabolic labelling of the carbohydrate core in bacterial peptidoglycan and its applications. Nat Commun 2017; 8:15015. [PMID: 28425464 PMCID: PMC5411481 DOI: 10.1038/ncomms15015] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cells are surrounded by a polymer known as peptidoglycan (PG), which protects the cell from changes in osmotic pressure and small molecule insults. A component of this material, N-acetyl-muramic acid (NAM), serves as a core structural element for innate immune recognition of PG fragments. We report the synthesis of modifiable NAM carbohydrate derivatives and the installation of these building blocks into the backbone of Gram-positive and Gram-negative bacterial PG utilizing metabolic cell wall recycling and biosynthetic machineries. Whole cells are labelled via click chemistry and visualized using super-resolution microscopy, revealing higher resolution PG structural details and allowing the cell wall biosynthesis, as well as its destruction in immune cells, to be tracked. This study will assist in the future identification of mechanisms that the immune system uses to recognize bacteria, glean information about fundamental cell wall architecture and aid in the design of novel antibiotics. N-acetyl-muramic acid (NAM) is a core component of the bacterial peptidoglycan (PG) cell wall, and is recognised by the innate immune system. Here the authors engineer Gram-negative and Gram-positive bacteria to incorporate a modified NAM into the backbone of PG, which can be labelled with click chemistry for imaging and tracking.
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Affiliation(s)
- Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Ching-Wen Hou
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Michelle A Parent
- Department of Medical Laboratory Sciences, University of Delaware, Newark, Delaware 19716, USA.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L Caplan
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA.,Bioimaging Center, Delaware Biotechnology Institute, Newark, Delaware 19716, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA
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99
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Xu AM, Wang DS, Shieh P, Cao Y, Melosh NA. Direct Intracellular Delivery of Cell-Impermeable Probes of Protein Glycosylation by Using Nanostraws. Chembiochem 2017; 18:623-628. [PMID: 28130882 DOI: 10.1002/cbic.201600689] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Bioorthogonal chemistry is an effective tool for elucidating metabolic pathways and measuring cellular activity, yet its use is currently limited by the difficulty of getting probes past the cell membrane and into the cytoplasm, especially if more complex probes are desired. Here we present a simple and minimally perturbative technique to deliver functional probes of glycosylation into cells by using a nanostructured "nanostraw" delivery system. Nanostraws provide direct intracellular access to cells through fluid conduits that remain small enough to minimize cell perturbation. First, we demonstrate that our platform can deliver an unmodified azidosugar, N-azidoacetylmannosamine, into cells with similar effectiveness to a chemical modification strategy (peracetylation). We then show that the nanostraw platform enables direct delivery of an azidosugar modified with a charged uridine diphosphate group (UDP) that prevents intracellular penetration, thereby bypassing multiple enzymatic processing steps. By effectively removing the requirement for cell permeability from the probe, the nanostraws expand the toolbox of bioorthogonal probes that can be used to study biological processes on a single, easy-to-use platform.
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Affiliation(s)
- Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA.,Present address: Chemistry and Chemical Engineering Division, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91106, USA
| | - Derek S Wang
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Peyton Shieh
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
| | - Yuhong Cao
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
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O’Connor LJ, Mistry IN, Collins SL, Folkes LK, Brown G, Conway SJ, Hammond EM. CYP450 Enzymes Effect Oxygen-Dependent Reduction of Azide-Based Fluorogenic Dyes. ACS CENTRAL SCIENCE 2017; 3:20-30. [PMID: 28149949 PMCID: PMC5269656 DOI: 10.1021/acscentsci.6b00276] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Indexed: 05/06/2023]
Abstract
Azide-containing compounds have broad utility in organic synthesis and chemical biology. Their use as powerful tools for the labeling of biological systems in vitro has enabled insights into complex cellular functions. To date, fluorogenic azide-containing compounds have primarily been employed in the context of click chemistry and as sensitive functionalities for hydrogen sulfide detection. Here, we report an alternative use of this functionality: as fluorogenic probes for the detection of depleted oxygen levels (hypoxia). Oxygen is imperative to all life forms, and probes that enable quantification of oxygen tension are of high utility in many areas of biology. Here we demonstrate the ability of an azide-based dye to image hypoxia in a range of human cancer cell lines. We have found that cytochrome P450 enzymes are able to reduce these probes in an oxygen-dependent manner, while hydrogen sulfide does not play an important role in their reduction. These data indicate that the azide group is a new bioreductive functionality that can be employed in prodrugs and dyes. We have uncovered a novel mechanism for the cellular reduction of azides, which has implications for the use of click chemistry in hypoxia.
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Affiliation(s)
- Liam J. O’Connor
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Mansfield
Road, Oxford, OX1 3TA, U.K.
- CRUK/MRC Oxford Institute for Radiation
Oncology, Department of Oncology, University
of Oxford, Old Road Campus
Research Building, Oxford, OX3 7DQ, U.K.
| | - Ishna N. Mistry
- CRUK/MRC Oxford Institute for Radiation
Oncology, Department of Oncology, University
of Oxford, Old Road Campus
Research Building, Oxford, OX3 7DQ, U.K.
| | - Sarah L. Collins
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Mansfield
Road, Oxford, OX1 3TA, U.K.
| | - Lisa K. Folkes
- CRUK/MRC Oxford Institute for Radiation
Oncology, Department of Oncology, University
of Oxford, Old Road Campus
Research Building, Oxford, OX3 7DQ, U.K.
| | - Graham Brown
- CRUK/MRC Oxford Institute for Radiation
Oncology, Department of Oncology, University
of Oxford, Old Road Campus
Research Building, Oxford, OX3 7DQ, U.K.
| | - Stuart J. Conway
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Mansfield
Road, Oxford, OX1 3TA, U.K.
| | - Ester M. Hammond
- CRUK/MRC Oxford Institute for Radiation
Oncology, Department of Oncology, University
of Oxford, Old Road Campus
Research Building, Oxford, OX3 7DQ, U.K.
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