1
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Oppenheimer KG, Hager NA, McAtee CK, Filiztekin E, Shang C, Warnick JA, Bruchez MP, Brodsky JL, Prosser DC, Kwiatkowski AV, O’Donnell AF. Optimization of the fluorogen-activating protein tag for quantitative protein trafficking and colocalization studies in S. cerevisiae. Mol Biol Cell 2024; 35:mr5. [PMID: 38809589 PMCID: PMC11244157 DOI: 10.1091/mbc.e24-04-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Spatial and temporal tracking of fluorescent proteins (FPs) in live cells permits visualization of proteome remodeling in response to extracellular cues. Historically, protein dynamics during trafficking have been visualized using constitutively active FPs fused to proteins of interest. While powerful, such FPs label all cellular pools of a protein, potentially masking the dynamics of select subpopulations. To help study protein subpopulations, bioconjugate tags, including the fluorogen activation proteins (FAPs), were developed. FAPs are comprised of two components: a single-chain antibody (SCA) fused to the protein of interest and a malachite-green (MG) derivative, which fluoresces only when bound to the SCA. Importantly, the MG derivatives can be either cell-permeant or -impermeant, thus permitting isolated detection of SCA-tagged proteins at the cell surface and facilitating quantitative endocytic measures. To expand FAP use in yeast, we optimized the SCA for yeast expression, created FAP-tagging plasmids, and generated FAP-tagged organelle markers. To demonstrate FAP efficacy, we coupled the SCA to the yeast G-protein coupled receptor Ste3. We measured Ste3 endocytic dynamics in response to pheromone and characterized cis- and trans-acting regulators of Ste3. Our work significantly expands FAP technology for varied applications in S. cerevisiae.
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Affiliation(s)
| | - Natalie A. Hager
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Ceara K. McAtee
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Elif Filiztekin
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Chaowei Shang
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | | | - Marcel P. Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213
| | | | - Derek C. Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284
| | - Adam V. Kwiatkowski
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
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2
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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3
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Auvray M, Naud-Martin D, Fontaine G, Bolze F, Clavier G, Mahuteau-Betzer F. Ultrabright two-photon excitable red-emissive fluorogenic probes for fast and wash-free bioorthogonal labelling in live cells. Chem Sci 2023; 14:8119-8128. [PMID: 37538830 PMCID: PMC10395273 DOI: 10.1039/d3sc01754k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
Fluorogenic bioorthogonal reactions are promising tools for tracking small molecules or biomolecules in living organisms. Two-photon excitation, by shifting absorption towards the red, significantly increases the signal-to-noise ratio and decreases photodamage, while allowing imaging about 10 times deeper than with a confocal microscope. However, efficient two-photon excitable fluorogenic probes are currently lacking. We report here the design and synthesis of fluorogenic probes based on a two-photon excitable fluorophore and a tetrazine quenching moiety. These probes react with bicyclo[6.1.0]no-4-yn-9ylmethanol (BCN) with a good to impressive kinetic rate constant (up to 1.1 × 103 M-1 s-1) and emit in the red window with moderate to high turn-on ratios. TDDFT allowed the rationalization of both the kinetic and fluorogenic performance of the different probes. The best candidate displays a 13.8-fold turn-on measured by quantifying fluorescence intensities in live cells under one-photon excitation, whereas a value of 3 is sufficient for high contrast live-cell imaging. In addition, live-cell imaging under two-photon excitation confirmed that there was no need for washing to monitor the reaction between BCN and this probe since an 8.0-fold turn-on was measured under two-photon excitation. Finally, the high two-photon brightness of the clicked adduct (>300 GM) allows the use of a weak laser power compatible with in vivo imaging.
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Affiliation(s)
- Marie Auvray
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Delphine Naud-Martin
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Gaëlle Fontaine
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Frédéric Bolze
- UMR7199, Faculté de Pharmacie 67401 Illkirch-Graffenstaden France
| | | | - Florence Mahuteau-Betzer
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
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4
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Ruan Q, Zhao C. A method for parallel microscale protein labeling and precise control over the average degree of labeling (aDoL). Sci Rep 2023; 13:8961. [PMID: 37268718 DOI: 10.1038/s41598-023-36163-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
A widely used approach for protein conjugation is through the lysine residues reacting with NHS- or other active esters. However, it is a challenge to precisely control the degree of labeling (DoL) due to the instability of active ester and variability of reaction efficiencies. Here, we provide a protocol for better control of aDoL using existing Copper-free Click Chemistry reagents. It is a two-step reaction with one purification in between. Briefly, proteins of interest were first activated with azide-NHS. After removing unreacted azide-NHS, the protein-N3 is then reacted with a limited amount of complementary click tag. Our studies have shown the click tag will fully react with the protein-N3 after 24 h' incubation, and therefore does not require additional purification steps. As such, the aDoL is equal to the input molar ratio of the click tag and the protein. Furthermore, this approach offers a much simpler and more economical way to perform parallel microscale labeling. Once a protein is pre-activated with N3-NHS, any fluorophore or molecule with the complementary click tag can be attached to the protein by mixing the two ingredients. Quantities of the protein used in the click reaction can be at any desired amount. In one example, we labeled an antibody in parallel with 9 different fluorophores using a total of 0.5 mg of antibody. In another example, we labeled Ab with targeted aDoL value from 2 to 8. In a stability comparison study, we have found the conjugated fluorophore using the suggested click protocol stayed attached to the protein longer than with standard NHS-fluorophore labeling.
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Affiliation(s)
- Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, AP-20, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL, 60064-6016, USA.
| | - Cheng Zhao
- Applied Research and Technology, Abbott Diagnostics Division, AP-20, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL, 60064-6016, USA
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5
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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6
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Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
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Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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7
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Mandler MD, Degnan AP, Zhang S, Aulakh D, Georges K, Sandhu B, Sarjeant A, Zhu Y, Traeger SC, Cheng PT, Ellsworth BA, Regueiro-Ren A. Structural and Thermal Characterization of Halogenated Azidopyridines: Under-Reported Synthons for Medicinal Chemistry. Org Lett 2022; 24:799-803. [PMID: 34714083 DOI: 10.1021/acs.orglett.1c03201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Owing to their participation in Click reactions, bifunctional azides are valuable intermediates in the preparation of medicines and biochemical tool compounds. Despite the privileged nature of pyridines among pharmaceutical scaffolds, reports of the synthesis and characterization of azidopyridines bearing a halogen substituent for further elaboration are almost completely unknown in the literature. As azidopyridines carry nearly equal numbers of nitrogen and carbon atoms, we hypothesized that safety concerns limited the application of these useful bifunctional building blocks in medicinal and biological chemistry. To address this concern, we prepared and characterized nine azidopyridines bearing a single fluorine, chlorine, or bromine atom. All were examined by differential scanning calorimetry (DSC), in which they demonstrated exotherms of 228-326 kJ/mol and onset temperatures between 119 and 135 °C. Selected azidopyridines were advanced to mechanical stress testing, in which impact sensitivity was noted for one regioisomer of C5H3FN4. The utility of these versatile intermediates was demonstrated through their use in a variety of Click reactions and the diversification of the halogen handles.
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Affiliation(s)
- Michael D Mandler
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew P Degnan
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Shasha Zhang
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Darpandeep Aulakh
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Ketleine Georges
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Bhupinder Sandhu
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Yeheng Zhu
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Sarah C Traeger
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Peter T Cheng
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Bruce A Ellsworth
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Alicia Regueiro-Ren
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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8
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Kim HR, Sarkar S, Ahn KH. A Two-Photon, Ratiometric Sensing Platform Based on a Solid State Luminescent Benzocoumarin: Application to Prolonged Bioimaging of Hydrogen Peroxide. Chem Asian J 2021; 17:e202101317. [PMID: 34962711 DOI: 10.1002/asia.202101317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Indexed: 11/06/2022]
Abstract
Fluorescent probes provide essential tools for studying biological systems. For the prolonged imaging of cellular analytes, the fast clearance of small-molecular probes and products is a matter of concern in the quantitative analysis. The activatable probes that produce insoluble products inside cell can be used for the prolonged imaging, but those with ratiometric imaging capability are rare. We disclose the novel sensing platform that is capable of the prolonged imaging, in addition to ratiometric signaling for the reliable quantitative analysis. Specifically, 3-(pyridin-4-yl)-8-(pyrrolidin-1-yl)-2 H benzo[ g ]chromen-2-one and its pyridinium salt as a dye couple constitute the ratiometric sensing platform. As the former dye produces highly emissive insoluble nanoaggregates inside cells, a fluorescent probe in the latter form, enables prolonged imaging of the target analyte in cells as well as in tissue by two-photon microscopy.
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Affiliation(s)
- Hye Rim Kim
- Pohang University of Science and Technology, chemistry, KOREA, REPUBLIC OF
| | - Sourav Sarkar
- Pohang University of Science and Technology, chemistry, KOREA, REPUBLIC OF
| | - Kyo Han Ahn
- POSTECH, Department of Chemistry, 77 Cheongam-Ro, 790-784, Pohang, KOREA, REPUBLIC OF
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9
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Schirer A, Rouch A, Marcheteau E, Stojko J, Sophie Landron, Jeantet E, Fould B, Ferry G, Boutin JA. Further assessments of ligase LplA-mediated modifications of proteins in vitro and in cellulo. Mol Biol Rep 2021; 49:149-161. [PMID: 34718939 DOI: 10.1007/s11033-021-06853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/23/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Posttranslational modifications of proteins are catalyzed by a large family of enzymes catalyzing many chemical modifications. One can hijack the natural use of those enzymes to modify targeted proteins with synthetic chemical moieties. The lipoic acid ligase LplA mutants can be used to introduce onto the lysine sidechain lipoic acid moiety synthetic analogues. Substrate protein candidates of the ligase must obey a few a priori rules. METHODS AND RESULTS In the present report, we technically detailed the use of a cell line stably expressing both the ligase and a model protein (thioredoxin). Although the goal can be reach, and the protein visualized in situ, many experimental difficulties must be fixed. The sequence of events comprises (i) in cellulo labeling of the target protein with a N3-lipoic acid derivative catalyzed by the mutant ligase, (ii) the further introduction by click chemistry onto this lysine sidechain of a fluorophore and (iii) the following of the labeled protein in living cells. One of the main difficulties was to assess the click chemistry step onto the living cells, because images from both control and experimental cells were similar. Alternatively, we describe at that stage, the preferred use of another technique: the Halo-Tag one that led to the obtention of clear images of the targeted protein in its cellular context. Although the ligase-mediated labeling of protein in situ is a rich domain for which many cellular tools must be developed, many difficulties must be considered before entering a systematic use of this approach. CONCLUSIONS In the present contribution, we added several steps of analytical characterization, both in vitro and in cellulo that were previously lacking. Furthermore, we show that the use of the click chemistry should be manipulated with care, as the claimed specificity might be not complete whenever living cells are used. Finally, we added another approach-the Halo Tag-to complete the previously suggested approaches for labelling proteins in cells, as we found difficult to strictly apply the previously reported methodology.
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Affiliation(s)
- Alicia Schirer
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France.,, Techno Parc de Thudinie 2, 6536, Thuin, Belgium
| | - Anne Rouch
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Estelle Marcheteau
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Johann Stojko
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Sophie Landron
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Elodie Jeantet
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Benjamin Fould
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Gilles Ferry
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Jean A Boutin
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France. .,Institut de Recherches Internationales Servier, 50 rue Carnot, 92284, Suresnes, France. .,Faculté de Pharmacie, PHARMADEV (Pharmacochimie et Biologie Pour le Développement), Université Toulouse 3 Paul Sabatier, 35 chemin des maraîchers, 31062, Toulouse Cedex 9, France.
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10
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Liu S, Lin C, Xu Y, Luo H, Peng L, Zeng X, Zheng H, Chen PR, Zou P. A far-red hybrid voltage indicator enabled by bioorthogonal engineering of rhodopsin on live neurons. Nat Chem 2021; 13:472-479. [PMID: 33859392 DOI: 10.1038/s41557-021-00641-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 01/15/2021] [Indexed: 01/24/2023]
Abstract
Membrane potential is a key aspect of cellular signalling and is dynamically regulated by an array of ion-selective pumps and channels. Fluorescent voltage indicators enable non-invasive optical recording of the cellular membrane potential with high spatial resolution. Here, we report a palette of bright and sensitive hybrid voltage indicators (HVIs) with fluorescence intensities sensitive to changes in membrane potential via electrochromic Förster resonance energy transfer. Enzyme-mediated site-specific incorporation of a probe, followed by an inverse-electron-demand Diels-Alder cycloaddition, was used to create enhanced voltage-sensing rhodopsins with hybrid dye-protein architectures. The most sensitive indicator, HVI-Cy3, displays high voltage sensitivity (-39% ΔF/F0 per 100 mV) and millisecond response kinetics, enabling optical recording of action potentials at a sampling rate of 400 Hz over 10 min across a large neuronal population. The far-red indicator HVI-Cy5 could be paired with optogenetic actuators and green/red-emitting fluorescent indicators, allowing an all-optical investigation of neuronal electrophysiology.
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Affiliation(s)
- Shuzhang Liu
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Chang Lin
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Yongxian Xu
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Huixin Luo
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Luxin Peng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Peng R Chen
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China.
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China. .,PKU-IDG/McGovern Institute for Brain Research, Beijing, China. .,Chinese Institute for Brain Research (CIBR), Beijing, China.
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11
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Shao C, Hedberg C, Qian Y. In Vivo Imaging of the Macrophage Migration Inhibitory Factor in Liver Cancer with an Activity-Based Probe. Anal Chem 2021; 93:2152-2159. [PMID: 33406831 DOI: 10.1021/acs.analchem.0c03964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The macrophage migration inhibitory factor (MIF), a vital cytokine and biomarker, has been suggested to closely associate with the pathogenesis of liver cancer. However, a simple and effective approach for monitoring the change and distribution of cellular MIF is currently lacking and urgently needed, which could be helpful for a better understanding of its role in the progression of cancer. Herein, we report a novel activity-based probe, TPP2, which allows for direct labeling and imaging of endogenous MIF activity within live cells, clinical tissues, and in vivo in a mouse model of liver cancer. With this probe, we have intuitively observed the dynamic change of intracellular MIF activity by both flow cytometry and confocal imaging. We further found that TPP2 permits the identification and distinguishing of liver cancer in vitro and in vivo with high sensitivity and selectivity toward MIF. Our observations indicate that TPP2 could provide a promising new imaging approach for elucidating the MIF-related biological functions in liver cancer.
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Affiliation(s)
- Chenwen Shao
- School of Chemistry and Materials Science, Nanjing Normal University, Wenyuan Road 1, Nanjing 210046, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Christian Hedberg
- Department of Chemistry, Chemical Biology Centre (KBC), Umeå University, Umeå 90187, Sweden
| | - Yong Qian
- School of Chemistry and Materials Science, Nanjing Normal University, Wenyuan Road 1, Nanjing 210046, China
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12
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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13
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Sueda S. Enzyme-based protein-tagging systems for site-specific labeling of proteins in living cells. ACTA ACUST UNITED AC 2020; 69:156-166. [PMID: 32166307 DOI: 10.1093/jmicro/dfaa011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 11/13/2022]
Abstract
Various protein-labeling methods based on the specific interactions between genetically encoded tags and synthetic probes have been proposed to complement fluorescent protein-based labeling. In particular, labeling methods based on enzyme reactions have been intensively developed by taking advantage of the highly specific interactions between enzymes and their substrates. In this approach, the peptides or proteins are genetically attached to the target proteins as a tag, and the various labels are then incorporated into the tags by enzyme reactions with the substrates carrying those labels. On the other hand, we have been developing an enzyme-based protein-labeling system distinct from the existing ones. In our system, the substrate protein is attached to the target proteins as a tag, and the labels are incorporated into the tag by post-translational modification with an enzyme carrying those labels followed by tight complexation between the enzyme and the substrate protein. In this review, I summarize the enzyme-based protein-labeling systems with a focus on several typical methods and then describe our labeling system based on tight complexation between the enzyme and the substrate protein.
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Affiliation(s)
- Shinji Sueda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu 804-8550, Japan
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14
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Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry 2020; 59:3993-4002. [PMID: 32970423 DOI: 10.1021/acs.biochem.0c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for β-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Jeff A Brewer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Nicole K Jacobsen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Michael McKenna
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Joshua R Uzarski
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Shaun F Filocamo
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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15
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Dai M, Sarkar S, Song CW, Reo YJ, Yang YJ, Ahn KH. Bent Benzocoumarin Dyes that Fluoresce in Solution and in Solid State and Their Application to Bioimaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mingchong Dai
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
| | - Sourav Sarkar
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
| | - Chang Wook Song
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
| | - Ye Jin Reo
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
| | - Yun Jae Yang
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
| | - Kyo Han Ahn
- Department of ChemistryPohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang, Gyungbuk 37673 Republic of Korea
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16
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Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV. Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access. Org Lett 2020; 22:381-385. [PMID: 31825225 DOI: 10.1021/acs.orglett.9b03981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A synthesis of the carbopyronine dye Carboxy ATTO 647N from simple materials is reported. This route proceeds in 11 forward steps from 3-bromoaniline with the key xanthone intermediate formed using a new oxidation methodology. The step utilizes an oxidation cycle with base, water, iodine, and more than doubles the yield of the standard permanganate oxidation methodology, accessing gram-scale quantities of this late-stage product. From this, Carboxy ATTO 647N was prepared in only four additional steps. This facile route to a complex fluorophore is expected to enable further studies in fluorescence imaging.
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Affiliation(s)
- James L Bachman
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Cyprian I Pavlich
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Alexander J Boley
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Edward M Marcotte
- Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Eric V Anslyn
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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17
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Stüber JC, Plückthun A. Labeling surface proteins with high specificity: Intrinsic limitations of phosphopantetheinyl transferase systems. PLoS One 2019; 14:e0226579. [PMID: 31856184 PMCID: PMC6922365 DOI: 10.1371/journal.pone.0226579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/28/2019] [Indexed: 12/04/2022] Open
Abstract
Objective Fluorescent labeling of specific cell-surface proteins enables a manifold of techniques to study their function in health and disease. A frequently cited family of methods employs phosphopantetheinyl transferases (PPTases) to attach probes, provided as conjugates of Coenzyme A. This method appears attractive, as only short peptide tags genetically fused to the protein of interest are needed as conjugation sites. Here, we describe observations we made when evaluating such protocols for delicate single-molecule applications where we require a particular combination of dyes, low background binding or low labeling of other proteins, and a high degree of labeling. Results When we tested a PPTase-acceptor peptide couple with several experimental protocols and various CoA conjugates for labeling of a protein on the cell surface, we noticed substantial non-specific labeling. For the first time, we provide here a quantification of the non-specific fraction of the signals obtained using appropriate controls. We further present evidence that this background is due to CoA-dye conjugates entering the cell, where they may be covalently attached to endogenous proteins. However, when studying cell-surface proteins, most fluorescent readouts require that labeling is strictly limited to the protein of interest located at the cell surface. While such data have so far been missing in the literature, they suggest that for applications where labeling of unwanted molecules would affect the conclusions, researchers need to be aware of this potential non-specificity of PPTase methods when selecting a labeling strategy. We show, again by quantitative comparison, that the HaloTag is a viable alternative.
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Affiliation(s)
- Jakob C. Stüber
- Department of Biochemistry, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- * E-mail:
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18
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Gallo E. Fluorogen-Activating Proteins: Next-Generation Fluorescence Probes for Biological Research. Bioconjug Chem 2019; 31:16-27. [DOI: 10.1021/acs.bioconjchem.9b00710] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, University of Toronto, Charles Best Institute, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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19
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McNelles SA, Pantaleo JL, Meichsner E, Adronov A. Strain-Promoted Azide-Alkyne Cycloaddition-Mediated Step-Growth Polymerization. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Stuart A. McNelles
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Julia L. Pantaleo
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Eric Meichsner
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Alex Adronov
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
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20
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Putti M, de Jong SMJ, Stassen OMJA, Sahlgren CM, Dankers PYW. A Supramolecular Platform for the Introduction of Fc-Fusion Bioactive Proteins on Biomaterial Surfaces. ACS APPLIED POLYMER MATERIALS 2019; 1:2044-2054. [PMID: 31423488 PMCID: PMC6691680 DOI: 10.1021/acsapm.9b00334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Bioorthogonal chemistry is an excellent method for functionalization of biomaterials with bioactive molecules, as it allows for decoupling of material processing and bioactivation. Here, we report on a modular system created by means of tetrazine/trans-cyclooctene (Tz/TCO) click chemistry undergoing an inverse electron demand Diels-Alder cycloaddition. A reactive supramolecular surface based on ureido-pyrimidinones (UPy) is generated via a UPy-Tz additive, in order to introduce a versatile TCO-protein G conjugate for immobilization of Fc-fusion proteins. As a model bioactive protein, we introduced Fc-Jagged1, a Notch ligand, to induce Notch signaling activity on the material. Interestingly, HEK293 FLN1 cells expressing the Notch1 receptor were repelled by films modified with TCO-protein G but adhered and spread on functionalized electrospun meshes. This indicates that the material processing method influences the biocompatibility of the postmodification. Notch signaling activity was upregulated 5.6-fold with respect to inactive controls on electrospun materials modified with TCO-protein G/Fc-Jagged1. Furthermore, downstream effects of Notch signaling were detected on the gene level in vascular smooth muscle cells expressing the Notch3 receptor. Taken together, our results demonstrate the successful use of a modular supramolecular system for the postprocessing modification of solid materials with functional proteins.
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Affiliation(s)
- Matilde Putti
- Department
of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven, The Netherlands
- Department
of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Simone M. J. de Jong
- Department
of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven, The Netherlands
- Department
of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Oscar M. J. A. Stassen
- Department
of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Cecilia M. Sahlgren
- Institute
for Complex Molecular Systems, Eindhoven, The Netherlands
- Department
of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Faculty
for Science and Engineering, Biosciences, Åbo Akademi University, Turku, Finland
- Turku
Centre for Biotechnology, University of
Turku and Åbo Akademi University, Turku, Finland
| | - Patricia Y. W. Dankers
- Department
of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven, The Netherlands
- Department
of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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21
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Prasher P, Sharma M. Tailored therapeutics based on 1,2,3-1 H-triazoles: a mini review. MEDCHEMCOMM 2019; 10:1302-1328. [PMID: 31534652 PMCID: PMC6748286 DOI: 10.1039/c9md00218a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Contemporary drug discovery approaches rely on library synthesis coupled with combinatorial methods and high-throughput screening to identify leads. However, due to the multitude of components involved, a majority of optimization techniques face persistent challenges related to the efficiency of synthetic processes and the purity of compound libraries. These methods have recently found an upgradation as fragment-based approaches for target-guided synthesis of lead molecules with active involvement of their biological target. The click chemistry approach serves as a promising tool for tailoring the therapeutically relevant biomolecules of interest, improving their bioavailability and bioactivity and redirecting them as efficacious drugs. 1,2,3-1H-Triazole nucleus, being a planar and biologically acceptable scaffold, plays a crucial role in the design of biomolecular mimetics and tailor-made molecules with therapeutic relevance. This versatile scaffold also forms an integral part of the current fragment-based approaches for drug design, kinetic target guided synthesis and bioorthogonal methodologies.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
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22
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Hyaluronan-Based Grafting Strategies for Liver Stem Cell Therapy and Tracking Methods. Stem Cells Int 2019; 2019:3620546. [PMID: 31354838 PMCID: PMC6636496 DOI: 10.1155/2019/3620546] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/29/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
Cell adhesion is essential for survival, it plays important roles in physiological cell functions, and it is an innovative target in regenerative medicine. Among the molecular interactions and the pathways triggered during cell adhesion, the binding of cluster of differentiation 44 (CD44), a cell-surface glycoprotein involved in cell-cell interactions, to hyaluronic acid (HA), a major component of the extracellular matrix, is a crucial step. Cell therapy has emerged as a promising treatment for advanced liver diseases; however, so far, it has led to low cell engraftment and limited cell repopulation of the target tissue. Currently, different strategies are under investigation to improve cell grafting in the liver, including the use of organic and inorganic biomatrices that mimic the microenvironment of the extracellular matrix. Hyaluronans, major components of stem cell niches, are attractive candidates for coating stem cells since they improve viability, proliferation, and engraftment in damaged livers. In this review, we will discuss the new strategies that have been adopted to improve cell grafting and track cells after transplantation.
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23
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Baalmann M, Ziegler MJ, Werther P, Wilhelm J, Wombacher R. Enzymatic and Site-Specific Ligation of Minimal-Size Tetrazines and Triazines to Proteins for Bioconjugation and Live-Cell Imaging. Bioconjug Chem 2019; 30:1405-1414. [PMID: 30883100 DOI: 10.1021/acs.bioconjchem.9b00157] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Diels-Alder reactions with inverse electron demand (DAinv) have emerged as an indispensable tool for bioorthogonal labeling and the manipulation of biomolecules. In this context, reactions between tetrazines and strained dienophiles have received attention because of high reaction rates. Current methods for the DAinv-mediated functionalization of proteins suffer from slow reactivity, impaired stability, isomerization, or elimination of the incorporated strained dienophiles. We report here a versatile platform for the posttranslational, highly selective, and quantitative modification of proteins with stable dienes. New synthetic access to minimal size tetrazine and triazine derivatives enabled us to synthesize tailored diene substrates for the lipoic acid protein ligase A (LplA) from Escherichia coli, which we employ for the rapid, mild, and quantitative bioconjugation of proteins by DAinv. The presented method benefits from the minimal tag size for LplA recognition and can be applied to proteins from any source organism. We demonstrate its broad suitability by site-specific in vitro protein labeling and live cell labeling for fluorescence microscopy. With this work we expand the scope of DAinv bioorthogonal chemistry for site-specific protein labeling, providing additional experimental flexibility for preparing well-defined bioconjugates and addressing biological questions in complex biological environments.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Jonas Wilhelm
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
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24
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Ayele TM, Knutson SD, Ellipilli S, Hwang H, Heemstra JM. Fluorogenic Photoaffinity Labeling of Proteins in Living Cells. Bioconjug Chem 2019; 30:1309-1313. [PMID: 30978287 DOI: 10.1021/acs.bioconjchem.9b00203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genetically encoded fluorescent proteins or small-molecule probes that recognize specific protein binding partners can be used to label proteins to study their localization and function with fluorescence microscopy. However, these approaches are limited in signal-to-background resolution and the ability to temporally control labeling. Herein, we describe a covalent protein labeling technique using a fluorogenic malachite green probe functionalized with a photoreactive cross-linker. This enables a controlled covalent attachment to a genetically encodable fluorogen activating protein (FAP) with low background signal. We demonstrate covalent labeling of a protein in vitro as well as in live mammalian cells. This method is straightforward, displays high labeling specificity, and results in improved signal-to-background ratios in photoaffinity labeling of target proteins. Additionally, this probe provides temporal control over reactivity, enabling future applications in real-time monitoring of cellular events.
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Affiliation(s)
- Tewoderos M Ayele
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Steve D Knutson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Satheesh Ellipilli
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Hyun Hwang
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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25
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Shchegravina ES, Tretiakova DS, Alekseeva AS, Galimzyanov TR, Utkin YN, Ermakov YA, Svirshchevskaya EV, Negrebetsky VV, Karpechenko NY, Chernikov VP, Onishchenko NR, Vodovozova EL, Fedorov AY, Boldyrev IA. Phospholipidic Colchicinoids as Promising Prodrugs Incorporated into Enzyme-Responsive Liposomes: Chemical, Biophysical, and Enzymological Aspects. Bioconjug Chem 2019; 30:1098-1113. [PMID: 30817133 DOI: 10.1021/acs.bioconjchem.9b00051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Enzyme-responsive liposomes release their cargo in response to pathologically increased levels of enzymes at the target site. We report herein an assembly of phospholipase A2-responsive liposomes based on colchicinoid lipid prodrugs incorporated into lipid bilayer of the nanosized vesicles. The liposomes were constructed to addresses two important issues: (i) the lipid prodrugs were designed to fit the structure of the enzyme binding site; and (ii) the concept of lateral pressure profile was used to design lipid prodrugs that introduce almost no distortions into the lipid bilayer packing, thus ensuring that corresponding liposomes are stable. The colchicinoid agents exhibit antiproliferative activity in subnanomolar range of concentrations.
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Affiliation(s)
- Ekaterina S Shchegravina
- Lobachevsky State University of Niznhy Novgorod , 23 Gagarin Prospest , Nizhny Novgorod , 603950 Russian Federation.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Daria S Tretiakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Timur R Galimzyanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences , 31/4 Leninskii Prospekt , Moscow , 119071 Russian Federation.,National University of Science and Technology MISiS , 4 Leninskiy Prospekt , Moscow , 119049 Russian Federation
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Yuri A Ermakov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences , 31/4 Leninskii Prospekt , Moscow , 119071 Russian Federation
| | - Elena V Svirshchevskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Vadim V Negrebetsky
- Pirogov Russian National Research Medical University , 1 Ostrovityanov Street , Moscow , 117997 Russian Federation
| | - Natalia Yu Karpechenko
- N. N. Blokhin National Medical Research Center of Oncology , 24 Kashirskoye Shosse , Moscow , 115478 Russian Federation
| | - Valery P Chernikov
- Scientific Research Institute of Human Morphology , 3 Tsurupa Street , Moscow , 117418 Russian Federation
| | - Natalia R Onishchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Elena L Vodovozova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
| | - Alexey Yu Fedorov
- Lobachevsky State University of Niznhy Novgorod , 23 Gagarin Prospest , Nizhny Novgorod , 603950 Russian Federation
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 16/10 Miklukho-Maklaya Street , Moscow , 117997 Russian Federation
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26
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Fischer-Durand N, Lizinska D, Guérineau V, Rudolf B, Salmain M. ‘Clickable’ cyclopentadienyl iron carbonyl complexes for bioorthogonal conjugation of mid-infrared labels to a model protein and PAMAM dendrimer. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nathalie Fischer-Durand
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM); Sorbonne Université; 4 place Jussieu 75005 Paris France
| | - Daria Lizinska
- Department of Organic Chemistry; University of Lodz; Tamka 12 91-403 Lodz Poland
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301; Université Paris-Sud, Université Paris-Saclay; Avenue de la Terrasse 91198 Gif-sur-Yvette Cedex France
| | - Bogna Rudolf
- Department of Organic Chemistry; University of Lodz; Tamka 12 91-403 Lodz Poland
| | - Michèle Salmain
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM); Sorbonne Université; 4 place Jussieu 75005 Paris France
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27
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Plaks JG, Kaar JL. Lipoic Acid Ligase-Promoted Bioorthogonal Protein Modification and Immobilization. Methods Mol Biol 2019; 2012:279-297. [PMID: 31161513 DOI: 10.1007/978-1-4939-9546-2_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein bioconjugation benefits from precise regional and temporal control. One notable way of achieving this control is through the enzymatic attachment of bioorthogonal reactive handles to peptide recognition sequences that are genetically fused to target proteins of interest. The lipoic acid ligase variant, LplAW37V, functionalizes proteins by covalently attaching an azide-bearing lipoic acid derivative to a 13-amino acid recognition sequence known as the lipoic acid ligase acceptor peptide (LAP). Once attached, the azide group can be modified with diverse chemical entities through azide-alkyne click chemistry, enabling conjugation of chemical probes such as fluorophores and facilitating polymer attachment, glycosylation, and protein immobilization in addition to many other possible chemical modifications. The versatility of the attached azide group is complemented by the modular nature of the LAP sequence, which can be introduced within a protein at internal and/or terminal sites as well as at multiple sites simultaneously. In this chapter we describe the in vitro LplAW37V-mediated ligation of 10-azidodecanoic acid to a LAP-containing target protein (i.e., green fluorescent protein (GFP)) and the characterization of the ligation reaction products. Additionally, methods for the modification and immobilization of azide-functionalized LAP-GFP are discussed.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA.
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28
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Yoshida S. Controlled Reactive Intermediates Enabling Facile Molecular Conjugation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180104] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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29
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Zhou Z, Chitneni SK, Devoogdt N, Zalutsky MR, Vaidyanathan G. Fluorine-18 labeling of an anti-HER2 VHH using a residualizing prosthetic group via a strain-promoted click reaction: Chemistry and preliminary evaluation. Bioorg Med Chem 2018. [PMID: 29534937 DOI: 10.1016/j.bmc.2018.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a previous study, we evaluated a HER2-specific single domain antibody fragment (sdAb) 2Rs15d labeled with 18F via conjugation of a residualizing prosthetic agent that was synthesized by copper-catalyzed azide-alkyne cycloaddition (CuAAC). In order to potentially increase overall efficiency and decrease the time required for labeling, we now investigate the use of a strain-promoted azide-alkyne cycloaddition (SPAAC) between the 2Rs15d sdAb, which had been pre-derivatized with an azide-containing residualizing moiety, and an 18F-labeled aza-dibenzocyclooctyne derivative. The HER2-targeted sdAb 2Rs15d and a nonspecific sdAb R3B23 were pre-conjugated with a moiety containing both azide- and guanidine functionalities. The thus derivatized sdAbs were radiolabeled with 18F using an 18F-labeled aza-dibenzocyclooctyne derivative ([18F]F-ADIBO) via SPAAC, generating the desired conjugate ([18F]RL-II-sdAb). For comparison, unmodified 2Rs15d was labeled with N-succinimidyl 4-guanidinomethyl-3-[125I]iodobenzoate ([125I]SGMIB), the prototypical residualizing agent for radioiodination. Radiochemical purity (RCP), immunoreactive fraction (IRF), HER2-binding affinity and cellular uptake of [18F]RL-II-2Rs15d were assessed in vitro. Paired label biodistribution of [18F]RL-II-2Rs15d and [125I]SGMIB-2Rs15d, and microPET/CT imaging of [18F]RL-II-2Rs15d and the [18F]RL-II-R3B23 control sdAb were performed in nude mice bearing HER2-expressing SKOV-3 xenografts. A radiochemical yield of 23.9 ± 6.9% (n = 8) was achieved for the SPAAC reaction between [18F]F-ADIBO and azide-modified 2Rs15d and the RCP of the labeled sdAb was >95%. The affinity (Kd) and IRF for the binding of [18F]RL-II-2Rs15d to HER2 were 5.6 ± 1.3 nM and 73.1 ± 22.5% (n = 3), respectively. The specific uptake of [18F]RL-II-2Rs15d by HER2-expressing BT474M1 breast carcinoma cells in vitro was 14-17% of the input dose at 1, 2, and 4 h, slightly higher than seen for co-incubated [125I]SGMIB-2Rs15d. The uptake of [18F]RL-II-2Rs15d in SKOV-3 xenografts at 1 h and 2 h p.i. were 5.54 ± 0.77% ID/g and 6.42 ± 1.70% ID/g, respectively, slightly higher than those for co-administered [125I]SGMIB-2Rs15d (4.80 ± 0.78% ID/g and 4.78 ± 1.39% ID/g). MicroPET/CT imaging with [18F]RL-II-2Rs15d at 1-3 h p.i. clearly delineated SKOV-3 tumors while no significant accumulation of activity in tumor was seen for [18F]RL-II-R3B23. With the exception of kidneys, normal tissue levels for [18F]RL-II-2Rs15d were low and cleared rapidly. To our knowledge, this is the first time SPAAC method has been used to label an sdAb with 18F, especially with residualizing functionality.
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Affiliation(s)
- Zhengyuan Zhou
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Satish K Chitneni
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nick Devoogdt
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, (VUB), 1090 Brussels, Belgium
| | - Michael R Zalutsky
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA
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30
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Baalmann M, Best M, Wombacher R. Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction. Methods Mol Biol 2018; 1728:365-387. [PMID: 29405010 DOI: 10.1007/978-1-4939-7574-7_23] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplAW37V) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest. In a second step, a molecular probe can be attached to the chemical handle in a bioorthogonal Diels-Alder reaction with inverse electron demand (DAinv). This method is a complementary approach to protein labeling using genetic code expansion and circumvents larger protein tags while maintaining label specificity, providing experimental flexibility and straightforwardness.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Marcel Best
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany.
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31
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Di Paolo D, Afanzar O, Armitage JP, Berry RM. Single-molecule imaging of electroporated dye-labelled CheY in live Escherichia coli. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0492. [PMID: 27672145 PMCID: PMC5052738 DOI: 10.1098/rstb.2015.0492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2016] [Indexed: 11/12/2022] Open
Abstract
For the past two decades, the use of genetically fused fluorescent proteins (FPs) has greatly contributed to the study of chemotactic signalling in Escherichia coli including the activation of the response regulator protein CheY and its interaction with the flagellar motor. However, this approach suffers from a number of limitations, both biological and biophysical: for example, not all fusions are fully functional when fused to a bulky FP, which can have a similar molecular weight to its fused counterpart; they may interfere with the native interactions of the protein and the chromophores of FPs have low brightness and photostability and fast photobleaching rates. A recently developed technique for the electroporation of fluorescently labelled proteins in live bacteria has enabled us to bypass these limitations and study the in vivo behaviour of CheY at the single-molecule level. Here we show that purified CheY proteins labelled with organic dyes can be internalized into E. coli cells in controllable concentrations and imaged with video fluorescence microscopy. The use of this approach is illustrated by showing single CheY molecules diffusing within cells and interacting with the sensory clusters and the flagellar motors in real time. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Diana Di Paolo
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Oshri Afanzar
- Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Richard M Berry
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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32
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Witten AJ, Ejendal KFK, Gengelbach LM, Traore MA, Wang X, Umulis DM, Calve S, Kinzer-Ursem TL. Fluorescent imaging of protein myristoylation during cellular differentiation and development. J Lipid Res 2017; 58:2061-2070. [PMID: 28754825 PMCID: PMC5625117 DOI: 10.1194/jlr.d074070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/26/2017] [Indexed: 11/20/2022] Open
Abstract
Protein post-translational modifications (PTMs) serve to give proteins new cellular functions and can influence spatial distribution and enzymatic activity, greatly enriching the complexity of the proteome. Lipidation is a PTM that regulates protein stability, function, and subcellular localization. To complement advances in proteomic identification of lipidated proteins, we have developed a method to image the spatial distribution of proteins that have been co- and post-translationally modified via the addition of myristic acid (Myr) to the N terminus. In this work, we use a Myr analog, 12-azidododecanoic acid (12-ADA), to facilitate fluorescent detection of myristoylated proteins in vitro and in vivo. The azide moiety of 12-ADA does not react to natural biological chemistries, but is selectively reactive with alkyne functionalized fluorescent dyes. We find that the spatial distribution of myristoylated proteins varies dramatically between undifferentiated and differentiated muscle cells in vitro. Further, we demonstrate that our methodology can visualize the distribution of myristoylated proteins in zebrafish muscle in vivo. Selective protein labeling with noncanonical fatty acids, such as 12-ADA, can be used to determine the biological function of myristoylation and other lipid-based PTMs and can be extended to study deregulated protein lipidation in disease states.
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Affiliation(s)
- Andrew J Witten
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | - Karin F K Ejendal
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | | | - Meghan A Traore
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | - Xu Wang
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN
| | - David M Umulis
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN
| | - Sarah Calve
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
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33
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Pan S, Jang SY, Wang D, Liew SS, Li Z, Lee JS, Yao SQ. A Suite of “Minimalist” Photo-Crosslinkers for Live-Cell Imaging and Chemical Proteomics: Case Study with BRD4 Inhibitors. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sijun Pan
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5, Seongbuk-gu Seoul 136-791 Korea
| | - Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Si Si Liew
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Zhengqiu Li
- College of Pharmacy; Jinan University; Guangzhou 510632 China
| | - 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 136-791 Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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34
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Pan S, Jang SY, Wang D, Liew SS, Li Z, Lee JS, Yao SQ. A Suite of "Minimalist" Photo-Crosslinkers for Live-Cell Imaging and Chemical Proteomics: Case Study with BRD4 Inhibitors. Angew Chem Int Ed Engl 2017; 56:11816-11821. [PMID: 28783236 DOI: 10.1002/anie.201706076] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Indexed: 11/08/2022]
Abstract
Affinity-based probes (AfBPs) provide a powerful tool for large-scale chemoproteomic studies of drug-target interactions. The development of high-quality probes capable of recapitulating genuine drug-target engagement, however, could be challenging. "Minimalist" photo-crosslinkers, which contain an alkyl diazirine group and a chemically tractable tag, could alleviate such challenges, but few are currently available. Herein, we have developed new alkyl diazirine-containing photo-crosslinkers with different bioorthogonal tags. They were subsequently used to create a suite of AfBPs based on GW841819X (a small molecule inhibitor of BRD4). Through in vitro and in situ studies under conditions that emulated native drug-target interactions, we have obtained better insights into how a tag might affect the probe's performance. Finally, SILAC-based chemoproteomic studies have led to the discovery of a novel off-target, APEX1. Further studies showed GW841819X binds to APEX1 and caused up-regulation of endogenous DNMT1 expression under normoxia conditions.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Korea
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Si Si Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Zhengqiu Li
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - 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, 136-791, Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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35
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Gallo E, Jarvik JW. Breaking the color barrier - a multi-selective antibody reporter offers innovative strategies of fluorescence detection. J Cell Sci 2017; 130:2644-2653. [PMID: 28615413 DOI: 10.1242/jcs.202952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/08/2017] [Indexed: 01/14/2023] Open
Abstract
A novel bi-partite fluorescence platform exploits the high affinity and selectivity of antibody scaffolds to capture and activate small-molecule fluorogens. In this report, we investigated the property of multi-selectivity activation by a single antibody against diverse cyanine family fluorogens. Our fluorescence screen identified three cell-impermeant fluorogens, each with unique emission spectra (blue, green and red) and nanomolar affinities. Most importantly, as a protein fusion tag to G-protein-coupled receptors, the antibody biosensor retained full activity - displaying bright fluorogen signals with minimal background on live cells. Because fluorogen-activating antibodies interact with their target ligands via non-covalent interactions, we were able to perform advanced multi-color detection strategies on live cells, previously difficult or impossible with conventional reporters. We found that by fine-tuning the concentrations of the different color fluorogen molecules in solution, a user may interchange the fluorescence signal (onset versus offset), execute real-time signal exchange via fluorogen competition, measure multi-channel fluorescence via co-labeling, and assess real-time cell surface receptor traffic via pulse-chase experiments. Thus, here we inform of an innovative reporter technology based on tri-color signal that allows user-defined fluorescence tuning in live-cell applications.
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Affiliation(s)
- Eugenio Gallo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jonathan W Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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36
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Nainar S, Kubota M, McNitt C, Tran C, Popik VV, Spitale RC. Temporal Labeling of Nascent RNA Using Photoclick Chemistry in Live Cells. J Am Chem Soc 2017; 139:8090-8093. [DOI: 10.1021/jacs.7b03121] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Christopher McNitt
- Department
of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | | | - Vladimir V. Popik
- Department
of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
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37
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Kulkarni C, Finley JE, Bessire AJ, Zhong X, Musto S, Graziani EI. Development of Fluorophore-Labeled Thailanstatin Antibody-Drug Conjugates for Cellular Trafficking Studies. Bioconjug Chem 2017; 28:1041-1047. [PMID: 28191936 DOI: 10.1021/acs.bioconjchem.6b00718] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the antibody-drug conjugate (ADC) field grows increasingly important for cancer treatment, it is vital for researchers to establish a firm understanding of how ADCs function at the molecular level. To gain insight into ADC uptake, trafficking, and catabolism-processes that are critical to ADC efficacy and toxicity-imaging studies have been performed with fluorophore-labeled conjugates. However, such labels may alter the properties and behavior of the ADC under investigation. As an alternative approach, we present here the development of a "clickable" ADC bearing an azide-functionalized linker-payload (LP) poised for "click" reaction with alkyne fluorophores; the azide group represents a significantly smaller structural perturbation to the LP than most fluorophores. Notably, the clickable ADC shows excellent potency in target-expressing cells, whereas the fluorophore-labeled product ADC suffers from a significant loss of activity, underscoring the impact of the label itself on the payload. Live-cell confocal microscopy reveals robust uptake of the clickable ADC, which reacts selectively in situ with a derivatized fluorescent label. Time-course trafficking studies show greater and more rapid net internalization of the ADCs than the parent antibody. More generally, the application of chemical biology tools to the study of ADCs should improve our understanding of how ADCs are processed in biological systems.
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Affiliation(s)
| | | | | | - Xiaotian Zhong
- Global Biotherapeutics Technologies, Pfizer Worldwide R&D , Cambridge, Massachusetts 02139, United States
| | - Sylvia Musto
- Oncology Research Unit, Pfizer Worldwide R&D , Pearl River, New York 10965, United States
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38
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Kim S, Ko W, Park H, Lee HS. Efficient and Site-specific Antibody Labeling by Strain-promoted Azide-alkyne Cycloaddition. J Vis Exp 2016:54922. [PMID: 28060353 PMCID: PMC5226445 DOI: 10.3791/54922] [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: 10/31/2022] Open
Abstract
There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is protein conjugation by genetically introducing an unnatural amino acid containing a bioorthogonal functional group. This report describes a detailed protocol for site-specific antibody conjugation. The protocol includes experimental details for the genetic incorporation of an azide-containing amino acid, and the conjugation reaction by strain-promoted azide-alkyne cycloaddition (SPAAC). This strain-promoted reaction proceeds by simple mixing of the reacting molecules at physiological pH and temperature, and does not require additional reagents such as copper(I) ions and copper-chelating ligands. Therefore, this method would be useful for general protein conjugation and development of antibody drug conjugates (ADCs).
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Affiliation(s)
| | - Wooseok Ko
- Department of Chemistry, Sogang University
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39
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Peng T, Hang HC. Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. J Am Chem Soc 2016; 138:14423-14433. [PMID: 27768298 DOI: 10.1021/jacs.6b08733] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells. While this approach has been used to label extracellular proteins for live cell imaging studies, site-specific bioorthogonal labeling and fluorescence imaging of intracellular proteins in live cells is still challenging. Herein, we systematically evaluate site-specific incorporation of diastereomerically pure bioorthogonal UAAs bearing stained alkynes or alkenes into intracellular proteins for inverse-electron-demand Diels-Alder cycloaddition reactions with tetrazine-functionalized fluorophores for live cell labeling and imaging in mammalian cells. Our studies show that site-specific incorporation of axial diastereomer of trans-cyclooct-2-ene-lysine robustly affords highly efficient and specific bioorthogonal labeling with monosubstituted tetrazine fluorophores in live mammalian cells, which enabled us to image the intracellular localization and real-time dynamic trafficking of IFITM3, a small membrane-associated protein with only 137 amino acids, for the first time. Our optimized UAA incorporation and bioorthogonal labeling conditions also enabled efficient site-specific fluorescence labeling of other intracellular proteins for live cell imaging studies in mammalian cells.
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Affiliation(s)
- Tao Peng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen 518055, China.,Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
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40
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Hoogenboom J, Berghuis N, Cramer D, Geurts R, Zuilhof H, Wennekes T. Direct imaging of glycans in Arabidopsis roots via click labeling of metabolically incorporated azido-monosaccharides. BMC PLANT BIOLOGY 2016; 16:220. [PMID: 27724898 PMCID: PMC5056477 DOI: 10.1186/s12870-016-0907-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/26/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Carbohydrates, also called glycans, play a crucial but not fully understood role in plant health and development. The non-template driven formation of glycans makes it impossible to image them in vivo with genetically encoded fluorescent tags and related molecular biology approaches. A solution to this problem is the use of tailor-made glycan analogs that are metabolically incorporated by the plant into its glycans. These metabolically incorporated probes can be visualized, but techniques documented so far use toxic copper-catalyzed labeling. To further expand our knowledge of plant glycobiology by direct imaging of its glycans via this method, there is need for novel click-compatible glycan analogs for plants that can be bioorthogonally labelled via copper-free techniques. RESULTS Arabidopsis seedlings were incubated with azido-containing monosaccharide analogs of N-acetylglucosamine, N-acetylgalactosamine, L-fucose, and L-arabinofuranose. These azido-monosaccharides were metabolically incorporated in plant cell wall glycans of Arabidopsis seedlings. Control experiments indicated active metabolic incorporation of the azido-monosaccharide analogs into glycans rather than through non-specific absorption of the glycan analogs onto the plant cell wall. Successful copper-free labeling reactions were performed, namely an inverse-electron demand Diels-Alder cycloaddition reaction using an incorporated N-acetylglucosamine analog, and a strain-promoted azide-alkyne click reaction. All evaluated azido-monosaccharide analogs were observed to be non-toxic at the used concentrations under normal growth conditions. CONCLUSIONS Our results for the metabolic incorporation and fluorescent labeling of these azido-monosaccharide analogs expand the possibilities for studying plant glycans by direct imaging. Overall we successfully evaluated five azido-monosaccharide analogs for their ability to be metabolically incorporated in Arabidopsis roots and their imaging after fluorescent labeling. This expands the molecular toolbox for direct glycan imaging in plants, from three to eight glycan analogs, which enables more extensive future studies of spatiotemporal glycan dynamics in a wide variety of plant tissues and species. We also show, for the first time in metabolic labeling and imaging of plant glycans, the potential of two copper-free click chemistry methods that are bio-orthogonal and lead to more uniform labeling. These improved labeling methods can be generalized and extended to already existing and future click chemistry-enabled monosaccharide analogs in Arabidopsis.
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Affiliation(s)
- Jorin Hoogenboom
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nathalja Berghuis
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dario Cramer
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Rene Geurts
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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41
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Rutkowska A, Thomson DW, Vappiani J, Werner T, Mueller KM, Dittus L, Krause J, Muelbaier M, Bergamini G, Bantscheff M. A Modular Probe Strategy for Drug Localization, Target Identification and Target Occupancy Measurement on Single Cell Level. ACS Chem Biol 2016; 11:2541-50. [PMID: 27384741 DOI: 10.1021/acschembio.6b00346] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Late stage failures of candidate drug molecules are frequently caused by off-target effects or inefficient target engagement in vivo. In order to address these fundamental challenges in drug discovery, we developed a modular probe strategy based on bioorthogonal chemistry that enables the attachment of multiple reporters to the same probe in cell extracts and live cells. In a systematic evaluation, we identified the inverse electron demand Diels-Alder reaction between trans-cyclooctene labeled probe molecules and tetrazine-tagged reporters to be the most efficient bioorthogonal reaction for this strategy. Bioorthogonal biotinylation of the probe allows the identification of drug targets in a chemoproteomics competition binding assay using quantitative mass spectrometry. Attachment of a fluorescent reporter enables monitoring of spatial localization of probes as well as drug-target colocalization studies. Finally, direct target occupancy of unlabeled drugs can be determined at single cell resolution by competitive binding with fluorescently labeled probe molecules. The feasibility of the modular probe strategy is demonstrated with noncovalent PARP inhibitors.
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Affiliation(s)
- Anna Rutkowska
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Douglas W. Thomson
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Katrin M. Mueller
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Lars Dittus
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Jana Krause
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
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42
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One-Step Selective Exoenzymatic Labeling (SEEL) Strategy for the Biotinylation and Identification of Glycoproteins of Living Cells. J Am Chem Soc 2016; 138:11575-11582. [PMID: 27541995 DOI: 10.1021/jacs.6b04049] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Technologies that can visualize, capture, and identify subsets of biomolecules that are not encoded by the genome in the context of healthy and diseased cells will offer unique opportunities to uncover the molecular mechanism of a multitude of physiological and disease processes. We describe here a chemical reporter strategy for labeling of cell surface glycoconjugates that takes advantage of recombinant glycosyltransferases and a corresponding sugar nucleotide functionalized by biotin. The exceptional efficiency of this method, termed one-step selective exoenzymatic labeling, or SEEL, greatly improved the ability to enrich and identify large numbers of tagged glycoproteins by LC-MS/MS. We further demonstrated that this labeling method resulted in far superior enrichment and detection of glycoproteins at the plasma membrane compared to a sulfo-NHS-activated biotinylation or two-step SEEL. This new methodology will make it possible to profile cell surface glycoproteomes with unprecedented sensitivity in the context of physiological and disease states.
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43
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Gao F, Gao T, Zhou K, Zeng W. Small Molecule-Photoactive Yellow Protein Labeling Technology in Live Cell Imaging. Molecules 2016; 21:molecules21091163. [PMID: 27589715 PMCID: PMC6273459 DOI: 10.3390/molecules21091163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
Characterization of the chemical environment, movement, trafficking and interactions of proteins in live cells is essential to understanding their functions. Labeling protein with functional molecules is a widely used approach in protein research to elucidate the protein location and functions both in vitro and in live cells or in vivo. A peptide or a protein tag fused to the protein of interest and provides the opportunities for an attachment of small molecule probes or other fluorophore to image the dynamics of protein localization. Here we reviewed the recent development of no-wash small molecular probes for photoactive yellow protein (PYP-tag), by the means of utilizing a quenching mechanism based on the intramolecular interactions, or an environmental-sensitive fluorophore. Several fluorogenic probes have been developed, with fast labeling kinetics and cell permeability. This technology allows quick live-cell imaging of cell-surface and intracellular proteins without a wash-out procedure.
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Affiliation(s)
- Feng Gao
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
- The Third Xiangya Hospital, Central South University, Changsha 410013, China.
| | - Tang Gao
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
| | - Kechao Zhou
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
| | - Wenbin Zeng
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
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44
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Baranczak A, Connelly S, Liu Y, Choi S, Grimster NP, Powers ET, Wilson IA, Kelly JW. Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn. Biopolymers 2016; 101:484-95. [PMID: 24105107 DOI: 10.1002/bip.22407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/03/2013] [Indexed: 01/03/2023]
Abstract
We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037
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45
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Affiliation(s)
- Suguru Yoshida
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University
| | - Isao Kii
- RIKEN Center for Life Science Technologies
| | - Takamitsu Hosoya
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University
- RIKEN Center for Life Science Technologies
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46
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Lotze J, Reinhardt U, Seitz O, Beck-Sickinger AG. Peptide-tags for site-specific protein labelling in vitro and in vivo. MOLECULAR BIOSYSTEMS 2016; 12:1731-45. [DOI: 10.1039/c6mb00023a] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide-tag based labelling can be achieved by (i) enzymes (ii) recognition of metal ions or small molecules and (iii) peptide–peptide interactions and enables site-specific protein visualization to investigate protein localization and trafficking.
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Affiliation(s)
- Jonathan Lotze
- Institut für Biochemie
- Universität Leipzig
- D-04103 Leipzig
- Germany
| | - Ulrike Reinhardt
- Institut für Chemie
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
| | - Oliver Seitz
- Institut für Chemie
- Humboldt-Universität zu Berlin
- D-12489 Berlin
- Germany
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47
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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48
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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49
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Fu H, Li Y, Sun L, He P, Duan X. Ratiometric Fluorescence Azide–Alkyne Cycloaddition for Live Mammalian Cell Imaging. Anal Chem 2015; 87:11332-6. [DOI: 10.1021/acs.analchem.5b02612] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hongxia Fu
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi
Province and ‡Experimental Chemistry Teaching Center, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, 620 Xi Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
| | - Yanru Li
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi
Province and ‡Experimental Chemistry Teaching Center, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, 620 Xi Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
| | - Lingbo Sun
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi
Province and ‡Experimental Chemistry Teaching Center, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, 620 Xi Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
| | - Pan He
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi
Province and ‡Experimental Chemistry Teaching Center, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, 620 Xi Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
| | - Xinrui Duan
- Key
Laboratory of Analytical Chemistry for Life Science of Shaanxi
Province and ‡Experimental Chemistry Teaching Center, School of Chemistry and Chemical
Engineering, Shaanxi Normal University, 620 Xi Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
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50
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Murrey HE, Judkins JC, Am Ende CW, Ballard TE, Fang Y, Riccardi K, Di L, Guilmette ER, Schwartz JW, Fox JM, Johnson DS. Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging. J Am Chem Soc 2015; 137:11461-75. [PMID: 26270632 PMCID: PMC4572613 DOI: 10.1021/jacs.5b06847] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Bioorthogonal
reactions, including the strain-promoted azide–alkyne
cycloaddition (SPAAC) and inverse electron demand Diels–Alder
(iEDDA) reactions, have become increasingly popular for live-cell
imaging applications. However, the stability and reactivity of reagents
has never been systematically explored in the context of a living
cell. Here we report a universal, organelle-targetable system based
on HaloTag protein technology for directly comparing bioorthogonal
reagent reactivity, specificity, and stability using clickable HaloTag
ligands in various subcellular compartments. This system enabled a
detailed comparison of the bioorthogonal reactions in live cells and
informed the selection of optimal reagents and conditions for live-cell
imaging studies. We found that the reaction of sTCO with monosubstituted
tetrazines is the fastest reaction in cells; however, both reagents
have stability issues. To address this, we introduced a new variant
of sTCO, Ag-sTCO, which has much improved stability and can be used
directly in cells for rapid bioorthogonal reactions with tetrazines.
Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when
paired with less reactive, more stable tetrazines.
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Affiliation(s)
- Heather E Murrey
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joshua C Judkins
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Christopher W Am Ende
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - T Eric Ballard
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States.,Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Yinzhi Fang
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Keith Riccardi
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Edward R Guilmette
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joel W Schwartz
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joseph M Fox
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Douglas S Johnson
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
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