1
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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2
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Hayamizu K, Koike K, Dodo K, Asanuma M, Egami H, Sodeoka M. Simple purification of small-molecule-labelled peptides via palladium enolate formation from β-ketoamide tags. Chem Sci 2023; 14:8249-8254. [PMID: 37564408 PMCID: PMC10411859 DOI: 10.1039/d2sc03112d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/04/2023] [Indexed: 08/12/2023] Open
Abstract
Palladium enolates derived from β-ketocarbonyl compounds serve as key intermediates in various catalytic asymmetric reactions. We found that the palladium enolate formed from β-ketoamide is stable in air and moisture and we applied this property to develop a peptide purification system using β-ketoamide as a small affinity tag in aqueous media. A solid-supported palladium complex successfully captured β-ketoamide-tagged molecules as palladium enolates and released them in high yield upon acid treatment. Optimum conditions for the catch and release of tagged peptides from a mixture of untagged peptides were established. To demonstrate the value of this methodology in identifying the binding site of a ligand to its target protein, we purified and identified a peptide containing the ligand-binding site from the tryptic digest of cathepsin B labelled with a covalent cathepsin B inhibitor containing a β-ketoamide tag.
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Affiliation(s)
- Kenji Hayamizu
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kota Koike
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Miwako Asanuma
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Hiromichi Egami
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
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3
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Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
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4
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Yashkin A, Rayo J, Grimm L, Welch M, Meijler MM. Short-chain reactive probes as tools to unravel the Pseudomonas aeruginosa quorum sensing regulon. Chem Sci 2021; 12:4570-4581. [PMID: 34163722 PMCID: PMC8179429 DOI: 10.1039/d0sc04444j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/28/2021] [Indexed: 11/21/2022] Open
Abstract
In recent years, the world has seen a troubling increase in antibiotic resistance among bacterial pathogens. In order to provide alternative strategies to combat bacterial infections, it is crucial deepen our understanding into the mechanisms that pathogens use to thrive in complex environments. Most bacteria use sophisticated chemical communication systems to sense their population density and coordinate gene expression in a collective manner, a process that is termed "quorum sensing" (QS). The human pathogen Pseudomonas aeruginosa uses several small molecules to regulate QS, and one of them is N-butyryl-l-homoserine lactone (C4-HSL). Using an activity-based protein profiling (ABPP) strategy, we designed biomimetic probes with a photoreactive group and a 'click' tag as an analytical handle. Using these probes, we have identified previously uncharacterized proteins that are part of the P. aeruginosa QS network, and we uncovered an additional role for this natural autoinducer in the virulence regulon of P. aeruginosa, through its interaction with PhzB1/2 that results in inhibition of pyocyanin production.
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Affiliation(s)
- Alex Yashkin
- Dept. of Chemistry, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev Be'er Sheva 8410501 Israel
| | - Josep Rayo
- Dept. of Chemistry, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev Be'er Sheva 8410501 Israel
| | - Larson Grimm
- Dept. of Biochemistry, University of Cambridge UK
| | - Martin Welch
- Dept. of Biochemistry, University of Cambridge UK
| | - Michael M Meijler
- Dept. of Chemistry, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev Be'er Sheva 8410501 Israel
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5
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Topa-Skwarczyńska M, Galek M, Jankowska M, Morlet-Savary F, Graff B, Lalevée J, Popielarz R, Ortyl J. Development of the first panchromatic BODIPY-based one-component iodonium salts for initiating the photopolymerization processes. Polym Chem 2021. [DOI: 10.1039/d1py01263k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein, new iodonium salts based on a 4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-indecene (B-1) chromophore have been introduced to 3D printing applications.
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Affiliation(s)
- Monika Topa-Skwarczyńska
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
| | - Mariusz Galek
- Photo HiTech Ltd., Bobrzyńskiego 14, 30-348 Cracow, Poland
| | - Magdalena Jankowska
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
| | - Fabrice Morlet-Savary
- Institut de Science des Matériaux de Mulhouse IS2 M, UMR CNRS 7361, UHA, 15, rue Jean Starcky, Cedex 68057 Mulhouse, France
| | - Bernadette Graff
- Institut de Science des Matériaux de Mulhouse IS2 M, UMR CNRS 7361, UHA, 15, rue Jean Starcky, Cedex 68057 Mulhouse, France
| | - Jacques Lalevée
- Institut de Science des Matériaux de Mulhouse IS2 M, UMR CNRS 7361, UHA, 15, rue Jean Starcky, Cedex 68057 Mulhouse, France
| | - Roman Popielarz
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
| | - Joanna Ortyl
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
- Photo HiTech Ltd., Bobrzyńskiego 14, 30-348 Cracow, Poland
- Photo4Chem Ltd., Lea 114, 30-133 Cracow, Poland
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6
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Technetium-99m-based simple and convenient radiolabeling of Escherichia coli for in vivo tracking of microorganisms. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-5941-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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Qin LH, Hu W, Long YQ. Bioorthogonal chemistry: Optimization and application updates during 2013–2017. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Lv J, Zhang Q, Cai M, Han Y, Luo S. Aromatic Aminocatalysis. Chem Asian J 2018; 13:740-753. [PMID: 29493891 DOI: 10.1002/asia.201701773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/01/2018] [Indexed: 11/08/2022]
Abstract
Aromatic aminocatalysis refers to transformations that employ aromatic amines, such as anilines or aminopyridines, as catalysts. Owing to the conjugation of the amine moiety with the aromatic ring, aromatic amines demonstrate distinctive features in aminocatalysis compared with their aliphatic counterparts. For example, aromatic aminocatalysis typically proceeds with slower turnover, but is more active and conformationally rigid as a result of the stabilized aromatic imine or iminium species. In fact, the advent of aromatic aminocatalysis can be traced back to before the renaissance of organocatalysis in the early 2000s. So far, aromatic aminocatalysis has been widely applied in bioconjugation reactions through transamination; in asymmetric organocatalysis through imine/enamine tautomerization; and in cooperative catalysis with transition metals through C-H/C-C activation and functionalization. This Focus Review summarizes the advent of and major advances in the use of aromatic aminocatalysis in bioconjugation reactions and organic synthesis.
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Affiliation(s)
- Jian Lv
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qi Zhang
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Mao Cai
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yanfang Han
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Sanzhong Luo
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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9
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Dandela R, Mantin D, Cravatt BF, Rayo J, Meijler MM. Proteome-wide mapping of PQS-interacting proteins in Pseudomonas aeruginosa. Chem Sci 2018; 9:2290-2294. [PMID: 29719702 PMCID: PMC5897874 DOI: 10.1039/c7sc04287f] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 01/31/2023] Open
Abstract
Development and application of chemical probes to globally map key virulence proteins of pathogenic bacteria.
The opportunistic human pathogen Pseudomonas aeruginosa secretes 2-heptyl-3-hydroxy-4-quinolone (PQS), a quorum sensing (QS) signal that regulates the expression of numerous virulence genes. Here we report the development and application of chemical probes to globally map quinolone binding proteins. The revealed quinolone interactome contains both known as well as newly identified virulence factors and presents new targets for the treatment of bacterial infections.
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Affiliation(s)
- Rambabu Dandela
- Dept. of Chemistry , The National Institute for Biotechnology in the Negev , Ben-Gurion University of the Negev , Be'er Sheva , Israel . ;
| | - Danielle Mantin
- Dept. of Chemistry , The National Institute for Biotechnology in the Negev , Ben-Gurion University of the Negev , Be'er Sheva , Israel . ;
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology , Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Josep Rayo
- Dept. of Chemistry , The National Institute for Biotechnology in the Negev , Ben-Gurion University of the Negev , Be'er Sheva , Israel . ;
| | - Michael M Meijler
- Dept. of Chemistry , The National Institute for Biotechnology in the Negev , Ben-Gurion University of the Negev , Be'er Sheva , Israel . ;
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10
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Convenient Preparation of 18F-Labeled Peptide Probes for Potential Claudin-4 PET Imaging. Pharmaceuticals (Basel) 2017; 10:ph10040099. [PMID: 29258264 PMCID: PMC5748654 DOI: 10.3390/ph10040099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 01/08/2023] Open
Abstract
Since pancreatic cancer is often diagnosed in a late state of cancer development, diagnostic opportunities allowing early disease detection are highly sought after. As such, cancer expression of claudin proteins is markedly dysregulated, making it an attractive target for molecular imaging like positron emission tomography (PET). Claudins are a family of transmembrane proteins that have a pivotal role as members of the tight junctions. In particular, claudin-3 and claudin-4 are frequently overexpressed in pancreatic cancer. 18F-Labeled claudin selective peptides would provide access to a novel kind of imaging tools for pancreatic cancer. In this work we describe the synthesis of the first 18F-labeled probes potentially suitable for PET imaging of claudin-4 expression. These probes were prepared using oxime ligation of 5-[18F]fluoro-5-deoxyribose (5-[18F]FDR) to claudin selective peptides. As a proof-of-principle, one of them, 5-[18F]FDR-Clone 27, was isolated in >98% radiochemical purity and in 15% radiochemical yield (EOB) within 98 min, and with a molar activity of 4.0 GBq/μmol (for 30 MBq of tracer). Moreover, we present first biological data for the prepared 5-FDR-conjugates. These tracers could pave the way for an early diagnosis of pancreatic tumor, and thus improve the outcome of anticancer therapy.
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11
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Abstract
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.
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Affiliation(s)
- Dominik K Kölmel
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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12
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Patil M. A revised mechanism for the α-ketoacid hydroxylamine amide forming ligations. Org Biomol Chem 2017; 15:416-425. [DOI: 10.1039/c6ob02057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The α-ketoacid-hydroxylamine amide-forming (KAHA) ligation reactions were investigated using computational methods to provide improved insights on the mechanism of these reactions.
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Affiliation(s)
- Mahendra Patil
- UM-DAE Centre for Excellence in Basic Sciences
- Health Centre
- University of Mumbai
- Mumbai 400098
- India
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13
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Dandela R, Mashiach R, Adepu R, Gregor R, Athamna M, Zecharia E, Ernst O, Zor T, Meijler MM. Synthesis and evaluation of a tag-free photoactive phospho-ceramide analogue-1 (PCERA-1) probe to study immunomodulation in macrophages. Chem Commun (Camb) 2017; 53:3842-3845. [DOI: 10.1039/c6cc09849e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospho-ceramide analogue-1 (PCERA-1), a synthetic analogue of ceramide-1-phosphate (C1P), has been previously shown to act as a potent modulator of macrophage activity and inflammation.
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Affiliation(s)
- Rambabu Dandela
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Roi Mashiach
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Raju Adepu
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Rachel Gregor
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
| | - Muhammad Athamna
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Efrat Zecharia
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Orna Ernst
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Tsaffrir Zor
- Department of Biochemistry & Molecular Biology
- Life Sciences Institute
- Tel-Aviv University
- Tel-Aviv 69978
- Israel
| | - Michael M. Meijler
- Dept. of Chemistry and the National Institute for Biotechnology in the Negev
- Ben-Gurion University of the Negev
- Be’er Sheva
- Israel
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14
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Herbst E, Shabat D. FRET-based cyanine probes for monitoring ligation reactions and their applications to mechanistic studies and catalyst screening. Org Biomol Chem 2016; 14:3715-28. [PMID: 26909686 DOI: 10.1039/c5ob02127h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an ever-increasing need to design better methods to selectively connect two molecules under mild aqueous conditions on a small scale. The process of finding such methods significantly relies on the employment of an appropriate assay. We report here a modular FRET-based assay to monitor such reactions and illustrate how the assay is used to monitor two particular reactions: native chemical ligation (NCL) and oxime ligation. For both reactions we show that by employing appropriately designed probes FRET measurements could be used to monitor the reaction's progress. We additionally demonstrate the usefulness of the developed probe system to study the mechanisms of the ligation reactions, for example, in monitoring the formation of a trimeric intermediate in the NCL reaction. Finally, we demonstrate that FRET measurements conducted in our system allow the quantification of the reaction yield and we show the application of our FRET-based assay to catalyst screening for the oxime ligation.
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Affiliation(s)
- E Herbst
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - D Shabat
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
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15
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Welsh MA, Blackwell HE. Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 2016; 40:774-94. [PMID: 27268906 DOI: 10.1093/femsre/fuw009] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.
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Affiliation(s)
- Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
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16
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Agten SM, Dawson PE, Hackeng TM. Oxime conjugation in protein chemistry: from carbonyl incorporation to nucleophilic catalysis. J Pept Sci 2016; 22:271-9. [PMID: 27006095 DOI: 10.1002/psc.2874] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
Abstract
Use of oxime forming reactions has become a widely applied strategy for peptide and protein bioconjugation. The efficiency of the reaction and robust stability of the oxime product has led to the development of a growing list of methods to introduce the required ketone or aldehyde functionality site specifically into proteins. Early methods focused on site-specific oxidation of an N-terminal serine or threonine and more recently transamination methods have been developed to convert a broader set of N-terminal amino acids into a ketone or aldehyde. More recently, site-specific modification of protein has been attained through engineering enzymes involved in posttranslational modifications in order to accommodate aldehyde-containing substrates. Similarly, a growing list of unnatural amino acids can be introduced through development of selective amino-acyl tRNA synthetase/tRNA pairs combined with codon reassignment. In the case of glycoproteins, glycans can be selectively modified chemically or enzymatically to introduce aldehyde functional groups. Finally, the total chemical synthesis of proteins complements these biological and chemoenzymatic approaches. Once introduced, the oxime ligation of these aldehyde and ketone groups can be catalyzed by aniline or a variety of aniline derivatives to tune the activity, pH preference, stability and solubility of the catalyst. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Stijn M Agten
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Tilman M Hackeng
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
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17
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Kowada T, Maeda H, Kikuchi K. BODIPY-based probes for the fluorescence imaging of biomolecules in living cells. Chem Soc Rev 2016; 44:4953-72. [PMID: 25801415 DOI: 10.1039/c5cs00030k] [Citation(s) in RCA: 852] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescence imaging techniques have been widely used to visualize biological molecules and phenomena. In particular, several studies on the development of small-molecule fluorescent probes have been carried out, because their fluorescence properties can be easily tuned by synthetic chemical modification. For this reason, various fluorescent probes have been developed for targeting biological components, such as proteins, peptides, amino acids, and ions, to the interior and exterior of cells. In this review, we cover advances in the development of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based fluorescent probes for biological studies over the past decade.
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Affiliation(s)
- Toshiyuki Kowada
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan.
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18
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O’Reilly MC, Blackwell HE. Structure-Based Design and Biological Evaluation of Triphenyl Scaffold-Based Hybrid Compounds as Hydrolytically Stable Modulators of a LuxR-Type Quorum Sensing Receptor. ACS Infect Dis 2016; 2:32-38. [PMID: 26807436 PMCID: PMC4709822 DOI: 10.1021/acsinfecdis.5b00112] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 12/28/2022]
Abstract
![]()
Many
common bacterial pathogens utilize quorum sensing to coordinate group
behaviors and initiate virulence at high cell densities. The use of
small molecules to block quorum sensing provides a means of abrogating
pathogenic phenotypes, but many known quorum sensing modulators have
limitations, including hydrolytic instability and displaying non-monotonic
dose curves (indicative of additional targets and/or modes of action).
To address these issues, we undertook a structure-based scaffold-hopping
approach to develop new chemical modulators of the LasR quorum sensing
receptor in Pseudomonas aeruginosa.
We combined components from a triphenyl derivative known to strongly
agonize LasR with chemical moieties known for LasR antagonism and
generated potent LasR antagonists that are hydrolytically stable across
a range of pH values. Additionally, many of these antagonists do not
exhibit non-monotonic dose effects, delivering probes that inhibit
LasR across a wider range of assay conditions relative to known lactone-based
ligands.
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Affiliation(s)
- Matthew C. O’Reilly
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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19
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Moore JD, Rossi FM, Welsh MA, Nyffeler KE, Blackwell HE. A Comparative Analysis of Synthetic Quorum Sensing Modulators in Pseudomonas aeruginosa: New Insights into Mechanism, Active Efflux Susceptibility, Phenotypic Response, and Next-Generation Ligand Design. J Am Chem Soc 2015; 137:14626-39. [PMID: 26491787 PMCID: PMC4665086 DOI: 10.1021/jacs.5b06728] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quorum sensing (QS) is a chemical signaling mechanism that allows bacterial populations to coordinate gene expression in response to social and environmental cues. Many bacterial pathogens use QS to initiate infection at high cell densities. Over the past two decades, chemical antagonists of QS in pathogenic bacteria have attracted substantial interest for use both as tools to further elucidate QS mechanisms and, with further development, potential anti-infective agents. Considerable recent research has been devoted to the design of small molecules capable of modulating the LasR QS receptor in the opportunistic pathogen Pseudomonas aeruginosa. These molecules hold significant promise in a range of contexts; however, as most compounds have been developed independently, comparative activity data for these compounds are scarce. Moreover, the mechanisms by which the bulk of these compounds act are largely unknown. This paucity of data has stalled the choice of an optimal chemical scaffold for further advancement. Herein, we submit the best-characterized LasR modulators to standardized cell-based reporter and QS phenotypic assays in P. aeruginosa, and we report the first comprehensive set of comparative LasR activity data for these compounds. Our experiments uncovered multiple interesting mechanistic phenomena (including a potential alternative QS-modulatory ligand binding site/partner) that provide new, and unexpected, insights into the modes by which many of these LasR ligands act. The lead compounds, data trends, and mechanistic insights reported here will significantly aid the design of new small molecule QS inhibitors and activators in P. aeruginosa, and in other bacteria, with enhanced potencies and defined modes of action.
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Affiliation(s)
- Joseph D Moore
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Francis M Rossi
- Department of Chemistry, SUNY Cortland , Cortland, New York 13045, United States
| | - Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kayleigh E Nyffeler
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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20
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Rhodium(III)-catalyzed coupling of aromatic ketazines or oximes with 2-vinyloxirane via C–H activation. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Gherbi K, Briddon SJ, Hill SJ. Detection of the secondary, low-affinity β1 -adrenoceptor site in living cells using the fluorescent CGP 12177 derivative BODIPY-TMR-CGP. Br J Pharmacol 2015; 171:5431-45. [PMID: 25052258 PMCID: PMC4261997 DOI: 10.1111/bph.12858] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/11/2014] [Accepted: 07/18/2014] [Indexed: 02/06/2023] Open
Abstract
Background and Purpose CGP 12177 not only inhibits agonist effects mediated through the catecholamine site of the β1-adrenoceptor with high affinity, but also exhibits agonist effects of its own at higher concentrations through a secondary, low-affinity β1-adrenoceptor site or conformation. β-blocker affinities for this ‘CGP 12177’ site of the human β1-adrenoceptor have thus far only been characterized in functional studies. Here, we used the fluorescent CGP 12177 analogue BODIPY-TMR-CGP to directly investigate receptor–ligand interactions at the secondary binding site of the β1-adrenoceptor. Experimental Approach The human β1-adrenoceptor was stably expressed in CHO cells containing a cAMP response element (CRE)-secreted placental alkaline phosphatase (SPAP) reporter gene construct. Functional responses of BODIPY-TMR-CGP were determined in the CRE-SPAP reporter gene assay, and manual and automated confocal microscopy platforms used to investigate the binding properties of BODIPY-TMR-CGP. Key Results BODIPY-TMR-CGP displayed a pharmacological profile similar to that of CGP 12177, retaining agonist activity at the secondary β1-adrenoceptor site. In confocal microscopy studies, specific BODIPY-TMR-CGP binding allowed clear visualization of β1-adrenoceptors in live cells. Using a wider concentration range of labelled ligand in a high-content fluorescence-based binding assay than is possible in radioligand binding assays, two-site inhibition binding curves of β-adrenoceptor antagonists were revealed in CHO cells expressing the human β1-adrenoceptor, but not the β2-adrenoceptor. Conclusions and Implications The fluorescent CGP 12177 analogue allowed the detection of the β1-adrenoceptor secondary site in both functional and binding studies. This suggests that BODIPY-TMR-CGP presents an important and novel fluorescent tool to investigate the nature of the secondary β1-adrenoceptor site.
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Affiliation(s)
- K Gherbi
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Nottingham, UK
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22
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Nandi S, Malishev R, Parambath Kootery K, Mirsky Y, Kolusheva S, Jelinek R. Membrane analysis with amphiphilic carbon dots. Chem Commun (Camb) 2015; 50:10299-302. [PMID: 25057851 DOI: 10.1039/c4cc03504f] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Newly-synthesized amphiphilic carbon dots were used for spectroscopic analysis and multicolour microscopic imaging of membranes and live cells. We show that Förster resonance energy transfer (FRET) occurred from the amphiphilic carbon dots to different membrane-associated fluorescence acceptors. The amphiphilic carbon dots enabled imaging of membrane disruption by the beta-amyloid peptide.
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Affiliation(s)
- Sukhendu Nandi
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
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23
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Recent advances in bioorthogonal reactions for site-specific protein labeling and engineering. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.065] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Lv J, Zha X, Pang S, Jia H, Zhang Y, Shang J. Synthesis and melanogenesis evaluation of 3′,4′,7-trihydroxyflavanone derivatives and characterization of flavanone–BODIPY. Bioorg Med Chem Lett 2015; 25:1607-10. [DOI: 10.1016/j.bmcl.2015.01.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/20/2015] [Accepted: 01/30/2015] [Indexed: 11/28/2022]
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25
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Xu Y, Xu L, Xia Y, Guan CJ, Guo QX, Fu Y, Wang C, Li YM. Fast and catalyst-free hydrazone ligation via ortho-halo-substituted benzaldehydes for protein C-terminal labeling at neutral pH. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc04382d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rapid and catalyst-free hydrazone ligation reaction between ortho-halobenzaldehyde derivatives and peptide/protein hydrazides was observed at neutral pH and room temperature.
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Affiliation(s)
- Yang Xu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
- School of Medical Engineering
| | - Ling Xu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Yuan Xia
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing 312000
- China
| | - Chao-Jian Guan
- School of Medical Engineering
- Hefei University of Technology
- Hefei
- China
| | - Qing-Xiang Guo
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Yao Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Chen Wang
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing 312000
- China
| | - Yi-Ming Li
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
- School of Medical Engineering
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26
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Hahn A, Reschke S, Leimkühler S, Risse T. Ketoxime Coupling of p-Acetylphenylalanine at Neutral pH for Site-Directed Spin Labeling of Human Sulfite Oxidase. J Phys Chem B 2014; 118:7077-84. [DOI: 10.1021/jp503471j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Aaron Hahn
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Stefan Reschke
- Institut
für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse
24-25, 14476 Golm, Germany
| | - Silke Leimkühler
- Institut
für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse
24-25, 14476 Golm, Germany
| | - Thomas Risse
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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27
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 781] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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28
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Volkova Y, Brizet B, Harvey PD, Denat F, Goze C. High Yield SNAr on 8-Halogenophenyl-BODIPY with Cyclic and Acyclic Polyamines. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Bertucci MA, Lee SJ, Gagné MR. Selective transamidation of 3-oxo-N-acyl homoserine lactones by hydrazine derivatives. Org Biomol Chem 2014; 12:7197-200. [DOI: 10.1039/c4ob01156b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrazine derivatives are employed for selective amide cleavage of 3-oxo-N-acyl homoserine lactones under physiologically relevant conditions.
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Affiliation(s)
- Michael A. Bertucci
- Department of Chemistry
- University of North Carolina at Chapel Hill
- Chapel Hill, USA
| | | | - Michel R. Gagné
- Department of Chemistry
- University of North Carolina at Chapel Hill
- Chapel Hill, USA
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30
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Using 5-deoxy-5-[18F]fluororibose to glycosylate peptides for positron emission tomography. Nat Protoc 2013; 9:138-45. [PMID: 24356772 DOI: 10.1038/nprot.2013.170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
So far seven peptide-based (18)F-radiopharmaceuticals for diagnostic applications with positron emission tomography (PET) have entered into clinical trials. Three candidates out of these seven are glycosylated peptides, which may be explained by the beneficial influence of glycosylation on in vivo pharmacokinetics of peptide tracers. This protocol describes the method for labeling peptides with 5-deoxy-5-[(18)F]fluororibose ([(18)F]FDR) as a prosthetic group. The synthesis of [(18)F]FDR is effected by a nucleophilic fluorination step by using dried Kryptofix 2.2.2-K2CO3-K(18)F complex and a subsequent HCl-catalyzed hydrolysis. The conjugation of [(18)F]FDR to the N-terminus aminooxy (-ONH2)-functionalized peptides is carried out in anilinium buffer at pH 4.6 and at room temperature (RT, 21-23 °C), with the concentration of peptide precursors being 0.3 mM. The procedure takes about 120 min and includes two cartridge isolation steps and two reversed-phase (RP) HPLC purification steps. The quaternary methyl amine (QMA) anion exchange cartridge and the hydrophilic-lipophilic balanced (HLB) cartridge are used for the isolation of (18)F-fluoride and [(18)F]FDR-conjugated peptides, respectively. The first HPLC purification provides the (18)F-fluorinated precursor of [(18)F]FDR and the second HPLC purification is to separate labeled peptides from their unlabeled precursors. The final product is formulated in PBS ready for injection, with a radiochemical purity of >98% and a radiochemical yield (RCY) of 27-37% starting from the end of bombardment (EOB). The carbohydrate nature of [(18)F]FDR and the operational convenience of this protocol should facilitate its general use.
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31
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Wendeler M, Grinberg L, Wang X, Dawson PE, Baca M. Enhanced catalysis of oxime-based bioconjugations by substituted anilines. Bioconjug Chem 2013; 25:93-101. [PMID: 24320725 DOI: 10.1021/bc400380f] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conjugation of biomolecules by chemoselective oxime ligation is of great interest for the site-specific modification of proteins, peptides, nucleic acids, and carbohydrates. These conjugations proceed optimally at a reaction pH of 4-5, but some biomolecules are not soluble or stable under these conditions. Aniline can be used as a nucleophilic catalyst to enhance the rate of oxime formation, but even in its presence, the reaction rate at neutral pH can be slower than desired, particularly at low reagent concentrations and/or temperature. Recently, alternative catalysts with improved properties were reported, including anthranilic acid derivatives for small molecule ligations, as well as m-phenylenediamine at high concentrations for protein conjugations. Here, we report that p-substituted anilines containing an electron-donating ring substituent are superior catalysts of oxime-based conjugations at pH 7. One such catalyst, p-phenylenediamine, was studied in greater detail. This catalyst was highly effective at neutral pH, even at the low concentration of 2 mM. In a model oxime ligation using aminooxy-functionalized PEG, catalysis at pH 7 resulted in a 120-fold faster rate of protein PEGylation as compared to an uncatalyzed reaction, and 19-fold faster than the equivalent aniline-catalyzed reaction. p-Phenylenediamine (10 mM) was also an effective catalyst under acidic conditions and was more efficient than aniline throughout the pH range 4-7. This catalyst allows efficient oxime bioconjugations to proceed under mild conditions and low micromolar concentrations, as demonstrated by the PEGylation of a small protein.
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Affiliation(s)
- Michaela Wendeler
- Department of Purification Process Sciences and ‡Department of Antibody Discovery and Protein Engineering, MedImmune, LLC , Gaithersburg, Maryland 20878, United States
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32
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McInnis CE, Blackwell HE. Non-native N-aroyl L-homoserine lactones are potent modulators of the quorum sensing receptor RpaR in Rhodopseudomonas palustris. Chembiochem 2013; 15:87-93. [PMID: 24281952 DOI: 10.1002/cbic.201300570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 12/14/2022]
Abstract
Quorum sensing (QS) is a process by which bacteria use low-molecular-weight signaling molecules (or autoinducers) to assess their local population densities and alter gene expression levels at high cell numbers. Many Gram-negative bacteria use N-acyl L-homoserine lactones (AHLs) with aliphatic acyl groups as signaling molecules for QS. However, bacteria that utilize AHLs with aroyl acyl groups have been recently discovered; they include the metabolically versatile soil bacterium Rhodopseudomonas palustris, which uses p-coumaroyl HL (p-cAHL) as its QS signal. This autoinducer is especially unusual because its acyl group is believed to originate from a monolignol (i.e., p-coumarate) produced exogenously by plants in the R. palustris environment, rather than through the endogenous fatty acid biosynthesis pathway like other native AHLs. As such, p-cAHL could signal not only bacterial density, but also the availability of an exogenous plant-derived substrate and might even constitute an interkingdom signal. Like other Gram-negative bacteria, QS in R. palustris is controlled by the p-cAHL signal binding its cognate LuxR-type receptor, RpaR. We sought to determine if non-native aroyl HLs (ArHLs) could potentially activate or inhibit RpaR in R. palustris, and thereby modulate QS in this bacterium. Herein, we report the testing of a set of synthetic ArHLs for RpaR agonism and antagonism by using a R. palustris reporter strain. Several potent non-native RpaR agonists and antagonists were identified. Additionally, the screening data revealed that lower concentrations of ArHL are required to strongly agonize RpaR than to antagonize it. Structure-activity relationship analyses of the active ArHLs indicated that potent RpaR agonists tend to have sterically small substituents on their aryl groups, most notably in the ortho position. In turn, the most potent RpaR antagonists were based on either the phenylpropionyl HL (PPHL) or the phenoxyacetyl HL (POHL) scaffold, and many contained an electron-withdrawing group at either the meta or para positions of the aryl ring. To our knowledge, the compounds reported herein represent the first abiotic chemical modulators of RpaR, and more generally, the first abiotic ligands capable of intercepting QS in bacteria that utilize native ArHL signals. In view of the origins of the p-cAHL signal in R. palustris, the largely unknown role of QS in this bacterium, and R. palustris' unique environmental lifestyles, we anticipate that these compounds could be valuable as chemical probes to study QS in R. palustris in a range of fundamental and applied contexts.
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Affiliation(s)
- Christine E McInnis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA); Current address: Dow Microbial Control, The Dow Chemical Company, 727 Norristown Rd., P. O. Box 904, Spring House, PA 19477 (USA)
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33
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Kool ET, Park DH, Crisalli P. Fast hydrazone reactants: electronic and acid/base effects strongly influence rate at biological pH. J Am Chem Soc 2013; 135:17663-6. [PMID: 24224646 DOI: 10.1021/ja407407h] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Kinetics studies with structurally varied aldehydes and ketones in aqueous buffer at pH 7.4 reveal that carbonyl compounds with neighboring acid/base groups form hydrazones at accelerated rates. Similarly, tests of a hydrazine with a neighboring carboxylic acid group show that it also reacts at an accelerated rate. Rate constants for the fastest carbonyl/hydrazine combinations are 2-20 M(-1) s(-1), which is faster than recent strain-promoted cycloaddition reactions.
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Affiliation(s)
- Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
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34
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Loskot SA, Zhang J, Langenhan JM. Nucleophilic catalysis of MeON-neoglycoside formation by aniline derivatives. J Org Chem 2013; 78:12189-93. [PMID: 24180591 DOI: 10.1021/jo401688p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Neoglycosylations are increasingly being employed in the synthesis of natural products, drug candidates, glycopeptide mimics, oligosaccharide analogues, and other applications, but the efficiency of these reactions is usually limited by slow reaction times. Here, we show that aniline derivatives such as 2-amino-5-methoxybenzoic acid enhance the rate of acid-catalyzed neoglycosylation for a range of sugar substrates up to a factor of 32 relative to the uncatalyzed reaction.
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Affiliation(s)
- Steven A Loskot
- Department of Chemistry, Seattle University , Seattle, Washington 98122, United States
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35
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Castelhano Santos N, Pereira MO, Lourenço A. Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties. Brief Bioinform 2013; 16:169-82. [PMID: 24106130 DOI: 10.1093/bib/bbt071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has been significant, with converging evidence from multiple high-throughput technologies. Notably, network reconstructions are already of considerable size and quality, tackling both intracellular regulation and signal mediation in microbial infection. Therefore, it stands to reason that in silico investigations would play a more active part in this research. Drug target identification and drug repurposing could take much advantage of the ability to simulate pathogen regulatory systems, host-pathogen interactions and pathogen cross-talking. Here, we review the bioinformatics resources and tools available for the study of the gram-negative bacterium Pseudomonas aeruginosa, the gram-positive bacterium Staphylococcus aureus and the fungal species Candida albicans. The choice of these three microorganisms fits the rationale of the review converging into pathogens of great clinical importance, which thrive in biofilm consortia and manifest growing antimicrobial resistance.
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36
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Shao Q, Zheng Y, Dong X, Tang K, Yan X, Xing B. A Covalent Reporter of β-Lactamase Activity for Fluorescent Imaging and Rapid Screening of Antibiotic-Resistant Bacteria. Chemistry 2013; 19:10903-10. [DOI: 10.1002/chem.201301654] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 01/16/2023]
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37
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Guo P, Yan S, Hu J, Xing X, Wang C, Xu X, Qiu X, Ma W, Lu C, Weng X, Zhou X. Selective detection of 5-formyl-2'-deoxycytidine in DNA using a fluorogenic hydroxylamine reagent. Org Lett 2013; 15:3266-9. [PMID: 23767758 DOI: 10.1021/ol401290d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorogenic hydroxylamine reagents were used for detecting 5-fC through a labeling pathway. Chemical synthesis, HPLC, denaturing PAGE, and DNA MS were applied to testify that the probe reacted with 5-fC with oligodeoxynucleotide selectivity to achieve 5-fC detection conveniently and quantificationally with the method of fluorescence. The feasibility of fluorescently detecting 5-fC in a genome was also investigated.
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Affiliation(s)
- Pu Guo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Hubei, Wuhan, 430072, P. R. of China
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38
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Gomes J, Huber N, Grunau A, Eberl L, Gademann K. Fluorescent Labeling Agents for Quorum-Sensing Receptors (FLAQS) in Live Cells. Chemistry 2013; 19:9766-70. [DOI: 10.1002/chem.201301387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Indexed: 11/06/2022]
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39
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Takaoka Y, Ojida A, Hamachi I. Organische Proteinchemie und ihre Anwendung für Markierungen und Engineering in Lebendzellsystemen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207089] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Takaoka Y, Ojida A, Hamachi I. Protein organic chemistry and applications for labeling and engineering in live-cell systems. Angew Chem Int Ed Engl 2013; 52:4088-106. [PMID: 23426903 DOI: 10.1002/anie.201207089] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Indexed: 12/11/2022]
Abstract
The modification of proteins with synthetic probes is a powerful means of elucidating and engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we review recent progress in chemistry-based protein modification methods and their application in protein engineering, with particular emphasis on the following four strategies: 1) the bioconjugation reactions of amino acids on the surfaces of natural proteins, mainly applied in test-tube settings; 2) the bioorthogonal reactions of proteins with non-natural functional groups; 3) the coupling of recognition and reactive sites using an enzyme or short peptide tag-probe pair for labeling natural amino acids; and 4) ligand-directed labeling chemistries for the selective labeling of endogenous proteins in living systems. Overall, these techniques represent a useful set of tools for application in chemical biology, with the methods 2-4 in particular being applicable to crude (living) habitats. Although still in its infancy, the use of organic chemistry for the manipulation of endogenous proteins, with subsequent applications in living systems, represents a worthy challenge for many chemists.
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Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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41
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Crisalli P, Kool ET. Water-soluble organocatalysts for hydrazone and oxime formation. J Org Chem 2013; 78:1184-9. [PMID: 23289546 DOI: 10.1021/jo302746p] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The formation of oximes and hydrazones is widely used in chemistry and biology as a molecular conjugation strategy for achieving ligation, attachment, and bioconjugation. However, the relatively slow rate of reaction has hindered its utility. Here, we report that simple, commercially available anthranilic acids and aminobenzoic acids act as superior catalysts for hydrazone and oxime formation, speeding the reaction considerably over the traditional aniline-catalyzed reaction at neutral pH. This efficient nucleophilic catalysis, involving catalyst-imine intermediates, allows rapid hydrazone/oxime formation even with relatively low concentrations of the two reactants. The most efficient catalysts are found to be 5-methoxyanthranilic acid and 3,5-diaminobenzoic acid; we find that they can enhance rates by factors of as much as 1-2 orders of magnitude over the aniline-catalyzed reaction. Evidence based on a range of differently substituted arylamines suggests that the ortho-carboxylate group in the anthranilate catalysts serves to aid in intramolecular proton transfer during imine and hydrazone formation.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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42
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Ye JH, Hu Z, Wang Y, Zhang W, Zhang Y. A new practical and highly efficient iodination of BODIPY derivatives with hypervalent iodine reagent. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Florian A, Mayoral MJ, Stepanenko V, Fernández G. Alternated Stacks of Nonpolar Oligo(p-phenyleneethynylene)-BODIPY Systems. Chemistry 2012; 18:14957-61. [DOI: 10.1002/chem.201203279] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Indexed: 12/21/2022]
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44
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Praneenararat T, Palmer AG, Blackwell HE. Chemical methods to interrogate bacterial quorum sensing pathways. Org Biomol Chem 2012; 10:8189-99. [PMID: 22948815 PMCID: PMC3480174 DOI: 10.1039/c2ob26353j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria frequently manifest distinct phenotypes as a function of cell density in a phenomenon known as quorum sensing (QS). This intercellular signalling process is mediated by "chemical languages" comprised of low-molecular weight signals, known as autoinducers, and their cognate receptor proteins. As many of the phenotypes regulated by QS can have a significant impact on the success of pathogenic or mutualistic prokaryotic-eukaryotic interactions, there is considerable interest in methods to probe and modulate QS pathways with temporal and spatial control. Such methods would be valuable for both basic research in bacterial ecology and in practical medicinal, agricultural, and industrial applications. Toward this goal, considerable recent research has been focused on the development of chemical approaches to study bacterial QS pathways. In this Perspective, we provide an overview of the use of chemical probes and techniques in QS research. Specifically, we focus on: (1) combinatorial approaches for the discovery of small molecule QS modulators, (2) affinity chromatography for the isolation of QS receptors, (3) reactive and fluorescent probes for QS receptors, (4) antibodies as quorum "quenchers," (5) abiotic polymeric "sinks" and "pools" for QS signals, and (6) the electrochemical sensing of QS signals. The application of such chemical methods can offer unique advantages for both elucidating and manipulating QS pathways in culture and under native conditions.
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Affiliation(s)
| | | | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA. Fax: +1 (608) 265-4534; Tel: +1 (608) 262-1503
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45
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Rashidian M, Song JM, Pricer RE, Distefano MD. Chemoenzymatic reversible immobilization and labeling of proteins without prior purification. J Am Chem Soc 2012; 134:8455-67. [PMID: 22435540 DOI: 10.1021/ja211308s] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Site-specific chemical modification of proteins is important for many applications in biology and biotechnology. Recently, our laboratory and others have exploited the high specificity of the enzyme protein farnesyltransferase (PFTase) to site-specifically modify proteins through the use of alternative substrates that incorporate bioorthogonal functionality including azides and alkynes. In this study, we evaluate two aldehyde-containing molecules as substrates for PFTase and as reactants in both oxime and hydrazone formation. Using green fluorescent protein (GFP) as a model system, we demonstrate that the purified protein can be enzymatically modified with either analogue to yield aldehyde-functionalized proteins. Oxime or hydrazone formation was then employed to immobilize, fluorescently label, or PEGylate the resulting aldehyde-containing proteins. Immobilization via hydrazone formation was also shown to be reversible via transoximization with a fluorescent alkoxyamine. After characterizing this labeling strategy using pure protein, the specificity of the enzymatic process was used to selectively label GFP present in crude E. coli extract followed by capture of the aldehyde-modified protein using hydrazide-agarose. Subsequent incubation of the immobilized protein using a fluorescently labeled or PEGylated alkoxyamine resulted in the release of pure GFP containing the desired site-specific covalent modifications. This procedure was also employed to produce PEGylated glucose-dependent insulinotropic polypeptide (GIP), a protein with potential therapeutic activity for diabetes. Given the specificity of the PFTase-catalyzed reaction coupled with the ability to introduce a CAAX-box recognition sequence onto almost any protein, this method shows great potential as a general approach for selective immobilization and labeling of recombinant proteins present in crude cellular extract without prior purification. Beyond generating site-specifically modified proteins, this approach for polypeptide modification could be particularly useful for large-scale production of protein conjugates for therapeutic or industrial applications.
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Affiliation(s)
- Mohammad Rashidian
- Department of Chemistry, University of Minnesota, Minneapolis, 55454, United States
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46
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Cavalli S, Carbajo D, Acosta M, Lope-Piedrafita S, Candiota AP, Arús C, Royo M, Albericio F. Efficient γ-amino-proline-derived cell penetrating peptide-superparamagnetic iron oxide nanoparticle conjugates via aniline-catalyzed oxime chemistry as bimodal imaging nanoagents. Chem Commun (Camb) 2012; 48:5322-4. [PMID: 22516929 DOI: 10.1039/c2cc17937g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aniline-catalyzed oxime chemistry was employed to conjugate a γ-amino-proline-derived cell penetrating peptide to superparamagnetic iron oxide nanoparticles (SPIONs). Internalization of the novel nanoconjugate into HeLa cells was found to be remarkably higher compared to the analogous TAT-SPION conjugate.
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Affiliation(s)
- Silvia Cavalli
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials, and Nanomedicine, 08028 Barcelona, Spain.
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47
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Abstract
The 4th ASM Conference on Cell-Cell Communication in Bacteria was held in Miami, FL, from 6 to 9 November 2011. This review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication.
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48
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Fujishima SH, Yasui R, Miki T, Ojida A, Hamachi I. Ligand-Directed Acyl Imidazole Chemistry for Labeling of Membrane-Bound Proteins on Live Cells. J Am Chem Soc 2012; 134:3961-4. [DOI: 10.1021/ja2108855] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sho-hei Fujishima
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Ryosuke Yasui
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Takayuki Miki
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Akio Ojida
- Graduate School of
Pharmaceutical
Sciences, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
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49
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Key JA, Li C, Cairo CW. Detection of Cellular Sialic Acid Content Using Nitrobenzoxadiazole Carbonyl-Reactive Chromophores. Bioconjug Chem 2012; 23:363-71. [DOI: 10.1021/bc200276k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jessie A. Key
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Caishun Li
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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50
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Li GL, Kung KKY, Zou L, Chong HC, Leung YC, Wong KH, Wong MK. Multifunctional bioconjugation by Morita–Baylis–Hillman reaction in aqueous medium. Chem Commun (Camb) 2012; 48:3527-9. [DOI: 10.1039/c2cc17116c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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