1
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Townsend CA, Petropavlovskiy AA, Kogut JA, Church AM, Sanders SS. Protocol to identify S-acylated proteins in hippocampal neurons using ω-alkynyl fatty acid analogs and click chemistry. STAR Protoc 2024; 5:103068. [PMID: 38762884 DOI: 10.1016/j.xpro.2024.103068] [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: 01/30/2024] [Revised: 03/15/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024] Open
Abstract
S-acylation, commonly palmitoylation, is the addition of fatty acids to cysteines to regulate protein localization and function. S-acylation detection has been hampered by limited sensitivity and selectivity in low-protein, costly samples like cultured neurons. Here, we present a protocol for sensitive and selective bioorthogonal labeling and click-chemistry-based detection of S-acylated proteins in primary hippocampal neurons. We describe steps for metabolically labeling neurons with alkynyl fatty acid, click chemistry, NeutrAvidin-based capture, and elution with hydroxylamine.
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Affiliation(s)
- Charlotte A Townsend
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
| | - Andrey A Petropavlovskiy
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | - Jordan A Kogut
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | - Alysha M Church
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | - Shaun S Sanders
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada.
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2
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Chen J, Bhat V, Hawker CJ. High-Throughput Synthesis, Purification, and Application of Alkyne-Functionalized Discrete Oligomers. J Am Chem Soc 2024; 146:8650-8658. [PMID: 38489842 PMCID: PMC10979451 DOI: 10.1021/jacs.4c00751] [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: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024]
Abstract
The development of synthetic oligomers as discrete single molecular entities with accurate control over the number and nature of functional groups along the backbone has enabled a variety of new research opportunities. From fundamental studies of self-assembly in materials science to understanding efficacy and safety profiles in biology and pharmaceuticals, future directions are significantly impacted by the availability of discrete, multifunctional oligomers. However, the preparation of diverse libraries of discrete and stereospecific oligomers remains a significant challenge. We report a novel strategy for accelerating the synthesis and isolation of discrete oligomers in a high-throughput manner based on click chemistry and simplified bead-based purification. The resulting synthetic platform allows libraries of discrete polyether oligomers to be prepared and the impact of variables such as chain length, number, and nature of side chain functionalities and molecular dispersity on antibacterial behavior examined. Significantly, discrete oligomers were shown to exhibit enhanced activity with lower toxicity compared with traditional disperse samples. This work provides a practical and scalable methodology for nonexperts to prepare libraries of multifunctional discrete oligomers and demonstrates the advantages of discrete materials in biological applications.
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Affiliation(s)
- Junfeng Chen
- Materials
Department, Materials Research Laboratory, and Department of Chemistry
and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Vittal Bhat
- Materials
Department, Materials Research Laboratory, and Department of Chemistry
and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department
of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Craig J. Hawker
- Materials
Department, Materials Research Laboratory, and Department of Chemistry
and Biochemistry, University of California, Santa Barbara, California 93106, United States
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3
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Petrovskii SK, Grachova EV, Monakhov KY. Bioorthogonal chemistry of polyoxometalates - challenges and prospects. Chem Sci 2024; 15:4202-4221. [PMID: 38516091 PMCID: PMC10952089 DOI: 10.1039/d3sc06284h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Bioorthogonal chemistry has enabled scientists to carry out controlled chemical processes in high yields in vivo while minimizing hazardous effects. Its extension to the field of polyoxometalates (POMs) could open up new possibilities and new applications in molecular electronics, sensing and catalysis, including inside living cells. However, this comes with many challenges that need to be addressed to effectively implement and exploit bioorthogonal reactions in the chemistry of POMs. In particular, how to protect POMs from the biological environment but make their reactivity selective towards specific bioorthogonal tags (and thereby reduce their toxicity), as well as which bioorthogonal chemistry protocols are suitable for POMs and how reactions can be carried out are questions that we are exploring herein. This perspective conceptualizes and discusses advances in the supramolecular chemistry of POMs, their click chemistry, and POM-based surface engineering to develop innovative bioorthogonal approaches tailored to POMs and to improve POM biological tolerance.
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Affiliation(s)
| | - Elena V Grachova
- Institute of Chemistry, St Petersburg University Universitetskii pr. 26 St. Petersburg 198504 Russia
| | - Kirill Yu Monakhov
- Leibniz Institute of Surface Engineering (IOM) Permoserstr. 15 Leipzig 04318 Germany
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4
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [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: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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5
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Mehak, Singh G, Singh R, Singh G, Stanzin J, Singh H, Kaur G, Singh J. Clicking in harmony: exploring the bio-orthogonal overlap in click chemistry. RSC Adv 2024; 14:7383-7413. [PMID: 38433942 PMCID: PMC10906366 DOI: 10.1039/d4ra00494a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
In the quest to scrutinize and modify biological systems, the global research community has continued to explore bio-orthogonal click reactions, a set of reactions exclusively targeting non-native molecules within biological systems. These methodologies have brought about a paradigm shift, demonstrating the feasibility of artificial chemical reactions occurring on cellular surfaces, in the cell cytosol, or within the body - an accomplishment challenging to achieve with the majority of conventional chemical reactions. This review delves into the principles of bio-orthogonal click chemistry, contrasting metal-catalyzed and metal-free reactions of bio-orthogonal nature. It comprehensively explores mechanistic details and applications, highlighting the versatility and potential of this methodology in diverse scientific contexts, from cell labelling to biosensing and polymer synthesis. Researchers globally continue to advance this powerful tool for precise and selective manipulation of biomolecules in complex biological systems.
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Affiliation(s)
- Mehak
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurleen Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Riddima Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University Chandigarh-160014 India
| | - Jigmat Stanzin
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University Chandigarh-160014 India
| | - Harminder Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
| | - Gurpreet Kaur
- Department of Chemistry, Gujranwala Guru Nanak Khalsa College Civil Lines Ludhiana-141001 Punjab India
| | - Jandeep Singh
- School of Chemical Engineering and Physical Sciences, Lovely Professional University Phagwara-144411 Punjab India
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6
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Tan Y, Pierrard F, Frédérick R, Riant O. Enhancing Tsuji-Trost deallylation in living cells with an internal-nucleophile coumarin-based probe. RSC Adv 2024; 14:5492-5498. [PMID: 38352674 PMCID: PMC10862660 DOI: 10.1039/d3ra08938j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
In recent years, bioorthogonal uncaging reactions have been developed to proceed efficiently under physiological conditions. However, limited progress has been made in the development of protecting groups combining stability under physiological settings with the ability to be quickly removed via bioorthogonal catalysis. Herein, we present a new water-soluble coumarin-derived probe bearing an internal nucleophilic group capable of promoting Tsuji-Trost deallylation under palladium catalysis. This probe can be cleaved by a bioorthogonal palladium complex at a faster rate than the traditional probe, namely N-Alloc-7-amino-4-methylcoumarin. As the deallylation process proved to be efficient in mammalian cells, we envision that this probe may find applications in chemical biology, bioengineering, and medicine.
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Affiliation(s)
- Yonghua Tan
- Institute of Condensed Matter and Nanosciences (IMCN), Université catholique de Louvain Louvain-la-Neuve 1348 Belgium
- Louvain Drug Research Institute (LDRI), Université catholique de Louvain Brussels B-1200 Belgium
| | - François Pierrard
- Institute of Condensed Matter and Nanosciences (IMCN), Université catholique de Louvain Louvain-la-Neuve 1348 Belgium
- Louvain Drug Research Institute (LDRI), Université catholique de Louvain Brussels B-1200 Belgium
| | - Raphaël Frédérick
- Louvain Drug Research Institute (LDRI), Université catholique de Louvain Brussels B-1200 Belgium
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences (IMCN), Université catholique de Louvain Louvain-la-Neuve 1348 Belgium
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7
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Dudchak R, Podolak M, Holota S, Szewczyk-Roszczenko O, Roszczenko P, Bielawska A, Lesyk R, Bielawski K. Click chemistry in the synthesis of antibody-drug conjugates. Bioorg Chem 2024; 143:106982. [PMID: 37995642 DOI: 10.1016/j.bioorg.2023.106982] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Antibody-Drug Conjugates (ADC) are a new class of anticancer therapeutics with immense potential. They have been rapidly advancing in the last two decades. This fast speed of development has become possible due to several new technologies and methods. One of them is Click Chemistry, an approach that was created only two decades ago, but already is actively utilized for bioconjugation, material science and drug discovery. In this review, we researched the impact of Click Chemistry reactions on the synthesis and development of ADCs. The information about the most frequently utilized reactions, such as Michael's addition, Copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC), Strain-promoted azide-alkyne [3+2] cycloaddition (SPAAC), oxime bond formation, hydrazine-iso-Pictet-Spengler Ligation (HIPS), Diels-Alder reactions have been summarized. The implementation of thiol-maleimide Click Chemistry reaction in the synthesis of numerous FDA-approved Antibody-Drug Conjugates has been reported. The data amassed in the present review provides better understanding of the importance of Click Chemistry in the synthesis, development and improvement of the Antibody-Drug Conjugates and it will be helpful for further researches related to ADCs.
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Affiliation(s)
- Rostyslav Dudchak
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Magdalena Podolak
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
| | - Olga Szewczyk-Roszczenko
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Piotr Roszczenko
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Anna Bielawska
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine.
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
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8
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Sun Y, Jiang L, Zhang Z, Xu N, Jiang Y, Tan C. Conjugated Polyelectrolyte/Single Strand DNA Hybrid Polyplexes for Efficient Nucleic Acid Delivery and Targeted Protein Degradation. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 38108633 DOI: 10.1021/acsami.3c14640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Nucleic acid-based therapeutics have gained increasing attention due to their ability to regulate various genetic disorders. However, the safe and effective delivery of nucleic acids to their intended cellular sites remains a challenge, primarily due to poor cell membrane permeation and low in vivo stability. Limitations associated with the commonly used nucleic acid delivering agent viral vectors such as carcinogenesis and immunogenicity have driven scientists to develop various nonviral vectors. In this study, we present a highly efficient nucleic acid delivery system based on cationic conjugated polyelectrolytes and single-strand DNA polyplexes with further application in efficient ubiquitin-regulated targeting protein degradation. These polyplexes, formed by 9TC, an aptamer sequence for estrogen receptor (ERα), and cationic PPET3N2 through electrostatic and hydrophobic interactions, demonstrate improved cellular uptake efficiency as well as enhanced stability against nuclease degradation. Furthermore, by incorporation of 9TC into a proteolysis targeting chimera (PROTAC) molecule (P9TC), PPET3N2/P9TC polyplexes significantly enhance the target protein ERα degradation efficiency. Collectively, our findings suggest that PPET3N2 provides a versatile, low cytotoxicity platform for safe, efficient, and simplified delivery of nucleic acids.
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Affiliation(s)
- Yuanjie Sun
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
| | - Li Jiang
- State Assets Management Office, Shenzhen Polytechnic University, Shenzhen 518055, People's Republic of China
| | - Zhilin Zhang
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
| | - Naihan Xu
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen 518055, People's Republic of China
| | - Yuyang Jiang
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
| | - Chunyan Tan
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
- Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
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9
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Hanaee-Ahvaz H, Cserjan-Puschmann M, Mayer F, Tauer C, Albrecht B, Furtmüller PG, Wiltschi B, Hahn R, Striedner G. Antibody fragments functionalized with non-canonical amino acids preserving structure and functionality - A door opener for new biological and therapeutic applications. Heliyon 2023; 9:e22463. [PMID: 38046162 PMCID: PMC10686840 DOI: 10.1016/j.heliyon.2023.e22463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Functionalization of proteins by incorporating reactive non-canonical amino acids (ncAAs) has been widely applied for numerous biological and therapeutic applications. The requirement not to lose the intrinsic properties of these proteins is often underestimated and not considered. Main purpose of this study was to answer the question whether functionalization via residue-specific incorporation of the ncAA N6-[(2-Azidoethoxy) carbonyl]-l-lysine (Azk) influences the properties of the anti-tumor-necrosis-factor-α-Fab (FTN2). Therefore, FTN2Azk variants with different Azk incorporation sites were designed and amber codon suppression was used for production. The functionalized FTN2Azk variants were efficiently produced in fed-batch like μ-bioreactor cultivations in the periplasm of E. coli displaying correct structure and antigen binding affinities comparable to those of wild-type FTN2. Our FTN2Azk variants with reactive handles for diverse conjugates enable tracking of recombinant protein in the production cell, pharmacological studies and translation into new pharmaceutical applications.
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Affiliation(s)
- Hana Hanaee-Ahvaz
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Biopharma Austria, Process Science, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1121, Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Birgit Wiltschi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
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10
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Mironova D, Bogdanov I, Akhatova A, Sultanova E, Garipova R, Khannanov A, Burilov V, Solovieva S, Antipin I. New Carboxytriazolyl Amphiphilic Derivatives of Calix[4]arenes: Aggregation and Use in CuAAC Catalysis. Int J Mol Sci 2023; 24:16663. [PMID: 38068985 PMCID: PMC10706699 DOI: 10.3390/ijms242316663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
This work focuses on the synthesis of a new series of amphiphilic derivatives of calix[4]arenes for the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The aggregation properties of synthesized calix[4]arenes were studied using various techniques (fluorescence spectroscopy, nanoparticle tracking analysis, and dynamic light scattering). Increasing the length of the alkyl substituent led to stronger hydrophobic interactions, which increased polydispersity in solution. The zwitterionic nature of the synthesized calix[4]arenes was established using different types of dyes (Eosin Y for anionic structures and Rhodamine 6G for cationic structures). The synthesized calix[4]arenes were used as organic stabilizers for CuI. The catalytic efficiency of CuI-calix[4]arene was compared with that of the phase transfer catalyst tetrabutylammonium bromide (TBAB) and the surfactant sodium dodecyl sulfate (SDS). For all calixarenes, the selectivity in the CuAAC reaction was higher than that observed when TBAB and SDS were estimated.
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Affiliation(s)
- Diana Mironova
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Ilshat Bogdanov
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Aliya Akhatova
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Elza Sultanova
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Ramilya Garipova
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Artur Khannanov
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Vladimir Burilov
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
| | - Svetlana Solovieva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Igor Antipin
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlevskaya Str., 420008 Kazan, Russia
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11
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Zheng X, Li Y, Cui T, Yang J, Meng X, Wang H, Chen L, He J, Chen N, Meng L, Ding L, Xie R. Traceless Protein-Selective Glycan Labeling and Chemical Modification. J Am Chem Soc 2023; 145:23670-23680. [PMID: 37857274 DOI: 10.1021/jacs.3c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Executing glycan editing at a molecular level not only is pivotal for the elucidation of complicated mechanisms involved in glycan-relevant biological processes but also provides a promising solution to potentiate disease therapy. However, the precision control of glycan modification or glyco-editing on a selected glycoprotein is by far a grand challenge. Of note is to preserve the intact cellular glycan landscape, which is preserved after editing events are completed. We report herein a versatile, traceless glycan modification methodology for customizing the glycoforms of targeted proteins (subtypes), by orchestrating chemical- and photoregulation in a protein-selective glycoenzymatic system. This method relies on a three-module, ligand-photocleavable linker-glycoenzyme (L-P-G) conjugate. We demonstrated that RGD- or synthetic carbohydrate ligand-containing conjugates (RPG and SPG) would not activate until after the ligand-receptor interaction is accomplished (chemical regulation). RPG and SPG can both release the glycoenzyme upon photoillumination (photoregulation). The adjustable glycoenzyme activity, combined with ligand recognition selectivity, minimizes unnecessary glycan editing perturbation, and photolytic cleavage enables precise temporal control of editing events. An altered target protein turnover and dimerization were observed in our system, emphasizing the significance of preserving the native physiological niche of a particular protein when precise modification on the carbohydrate epitope occurs.
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Affiliation(s)
- Xiaocui Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yiran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haiqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian He
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Nan Chen
- ChinaChomiX Biotech (Nanjing) Co., Ltd., Nanjing 210061, China
| | - Liying Meng
- Department of Medical Experimental Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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12
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Ziylan ZS, de Putter GJ, Roelofs M, van Dijl JM, Scheffers DJ, Walvoort MTC. Evaluation of Kdo-8-N 3 incorporation into lipopolysaccharides of various Escherichia coli strains. RSC Chem Biol 2023; 4:884-893. [PMID: 37920390 PMCID: PMC10619137 DOI: 10.1039/d3cb00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023] Open
Abstract
8-Azido-3,8-dideoxy-α/β-d-manno-oct-2-ulosonic acid (Kdo-8-N3) is a Kdo derivative used in metabolic labeling of lipopolysaccharide (LPS) structures found on the cell membrane of Gram-negative bacteria. Several studies have reported successful labeling of LPS using Kdo-8-N3 and visualization of LPS by a fluorescent reagent through click chemistry on a selection of Gram-negative bacteria such as Escherichia coli strains, Salmonella typhimurium, and Myxococcus xanthus. Motivated by the promise of Kdo-8-N3 to be useful in the investigation of LPS biosynthesis and cell surface labeling across different strains, we set out to explore the variability in nature and efficiency of LPS labeling using Kdo-8-N3 in a variety of E. coli strains and serotypes. We optimized the chemical synthesis of Kdo-8-N3 and subsequently used Kdo-8-N3 to metabolically label pathogenic E. coli strains from commercial and clinical origin. Interestingly, different extents of labeling were observed in different E. coli strains, which seemed to be dependent also on growth media, and the majority of labeled LPS appears to be of the 'rough' LPS variant, as visualized using SDS-PAGE and fluorescence microscopy. This knowledge is important for future application of Kdo-8-N3 in the study of LPS biosynthesis and dynamics, especially when working with clinical isolates.
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Affiliation(s)
- Zeynep Su Ziylan
- Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Geert-Jan de Putter
- Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Meike Roelofs
- Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Dirk-Jan Scheffers
- Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Marthe T C Walvoort
- Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7 9747 AG Groningen The Netherlands
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13
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Tavakoli S, Evans A, Oommen OP, Creemers L, Nandi JB, Hilborn J, Varghese OP. Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry. Mater Today Bio 2023; 22:100768. [PMID: 37600348 PMCID: PMC10432810 DOI: 10.1016/j.mtbio.2023.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.
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Affiliation(s)
- Shima Tavakoli
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Austin Evans
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Laura Creemers
- Department of Orthopedics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jharna Barman Nandi
- Department of Chemistry, Sarojini Naidu College for Women, 30 Jessore Road, Kolkata, 700028, India
| | - Jöns Hilborn
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Oommen P. Varghese
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
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14
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Mishra PK, Sharma N, Kim H, Lee C, Rhee HW. GEN-Click: Genetically Encodable Click Reactions for Spatially Restricted Metabolite Labeling. ACS CENTRAL SCIENCE 2023; 9:1650-1657. [PMID: 37637744 PMCID: PMC10450880 DOI: 10.1021/acscentsci.3c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/29/2023]
Abstract
Chemical reactions for the in situ modification of biomolecules within living cells are under development. Among these reactions, bio-orthogonal reactions such as click chemistry using copper(I) and Staudinger ligation are widely used for specific biomolecule tracking in live systems. However, currently available live cell copper(I)-catalyzed azide/alkyne cycloaddition reactions are not designed in a spatially resolved manner. Therefore, we developed the "GEN-Click" system, which can target the copper(I)-catalyzed azide/alkyne cycloaddition reaction catalysts proximal to the protein of interest and can be genetically expressed in a live cell. The genetically controlled, spatially restricted, metal-catalyzed biorthogonal reaction can be used for proximity biotin labeling of various azido-bearing biomolecules (e.g., protein, phospholipid, oligosaccharides) in living cell systems. Using GEN-Click, we successfully detected local metabolite-transferring events at cell-cell contact sites.
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Affiliation(s)
| | - Nirmali Sharma
- Department
of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunwoo Kim
- Department
of Biological Sciences, Ulsan National Institute
of Science and Technology, Ulsan 44919, Republic
of Korea
| | - Changwook Lee
- Department
of Biological Sciences, Ulsan National Institute
of Science and Technology, Ulsan 44919, Republic
of Korea
| | - Hyun-Woo Rhee
- Department
of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- School
of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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15
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Oerlemans RAJF, Shao J, Huisman SGAM, Li Y, Abdelmohsen LKEA, van Hest JCM. Compartmentalized Intracellular Click Chemistry with Biodegradable Polymersomes. Macromol Rapid Commun 2023; 44:e2200904. [PMID: 36607841 DOI: 10.1002/marc.202200904] [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: 11/18/2022] [Revised: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Polymersome nanoreactors that can be employed as artificial organelles have gained much interest over the past decades. Such systems often include biological catalysts (i.e., enzymes) so that they can undertake chemical reactions in cellulo. Examples of nanoreactor artificial organelles that acquire metal catalysts in their structure are limited, and their application in living cells remains fairly restricted. In part, this shortfall is due to difficulties associated with constructing systems that maintain their stability in vitro, let alone the toxicity they impose on cells. This study demonstrates a biodegradable and biocompatible polymersome nanoreactor platform, which can be applied as an artificial organelle in living cells. The ability of the artificial organelles to covalently and non-covalently incorporate tris(triazolylmethyl)amine-Cu(I) complexes in their membrane is shown. Such artificial organelles are capable of effectively catalyzing a copper-catalyzed azide-alkyne cycloaddition intracellularly, without compromising the cells' integrity. The platform represents a step forward in the application of polymersome-based nanoreactors as artificial organelles.
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Affiliation(s)
- Roy A J F Oerlemans
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jingxin Shao
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sander G A M Huisman
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yudong Li
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Loai K E A Abdelmohsen
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C M van Hest
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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16
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Ling B, Gungoren B, Yao Y, Dutka P, Smith CAB, Lee J, Swift MB, Shapiro MG. Truly tiny acoustic biomolecules for ultrasound imaging and therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546773. [PMID: 37425749 PMCID: PMC10327013 DOI: 10.1101/2023.06.27.546773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
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Affiliation(s)
- Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Bilge Gungoren
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Cameron A. B. Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Justin Lee
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Margaret B. Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, CA 91125, USA
- Division of Engineering and Applied Science, California Institute of Technology; Pasadena, CA 91125, USA
- Howard Hughes Medical Institute; Pasadena, CA 91125, USA
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17
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Higo S, Ishii H, Ozawa H. Recent Advances in High-sensitivity In Situ Hybridization and Costs and Benefits to Consider When Employing These Methods. Acta Histochem Cytochem 2023; 56:49-54. [PMID: 37425096 PMCID: PMC10323200 DOI: 10.1267/ahc.23-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/29/2023] [Indexed: 07/11/2023] Open
Abstract
In situ hybridization (ISH), which visualizes nucleic acids in tissues and cells, is a powerful tool in histology and pathology. Over 50 years since its invention, multiple attempts have been made to increase the sensitivity and simplicity of these methods. Therefore, several highly sensitive in situ hybridization methods have been developed that offer researchers a wide range of options. When selecting these in situ hybridization variants, their signal-amplification principles and characteristics must be understood. In addition, from a practical point of view, a method with good monetary and time-cost performance must be chosen. This review introduces recent high-sensitivity in situ hybridization variants and presents their principles, characteristics, and costs.
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Affiliation(s)
- Shimpei Higo
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Hirotaka Ishii
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Hitoshi Ozawa
- Faculty of Health Sciences, Bukkyo University, Kyoto, Japan
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18
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Lecat-Guillet N, Quast RB, Liu H, Bourrier E, Møller TC, Rovira X, Soldevila S, Lamarque L, Trinquet E, Liu J, Pin JP, Rondard P, Margeat E. Concerted conformational changes control metabotropic glutamate receptor activity. SCIENCE ADVANCES 2023; 9:eadf1378. [PMID: 37267369 PMCID: PMC10413646 DOI: 10.1126/sciadv.adf1378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 04/27/2023] [Indexed: 06/04/2023]
Abstract
Allosteric modulators bear great potential to fine-tune neurotransmitter action. Promising targets are metabotropic glutamate (mGlu) receptors, which are associated with numerous brain diseases. Orthosteric and allosteric ligands act in synergy to control the activity of these multidomain dimeric GPCRs. Here, we analyzed the effect of such molecules on the concerted conformational changes of full-length mGlu2 at the single-molecule level. We first established FRET sensors through genetic code expansion combined with click chemistry to monitor conformational changes on live cells. We then used single-molecule FRET and show that orthosteric agonist binding leads to the stabilization of most of the glutamate binding domains in their closed state, while the reorientation of the dimer into the active state remains partial. Allosteric modulators, interacting with the transmembrane domain, are required to stabilize the fully reoriented active dimer. These results illustrate how concerted conformational changes within multidomain proteins control their activity, and how these are modulated by allosteric ligands.
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Affiliation(s)
- Nathalie Lecat-Guillet
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Robert B. Quast
- Centre de Biologie Structurale (CBS), Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Hongkang Liu
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
- Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | | | - Thor C. Møller
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | | | | | - Eric Trinquet
- PerkinElmer Cisbio, Parc Marcel Boiteux, 30200 Codolet, France
| | - Jianfeng Liu
- Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Univ. Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), Univ. Montpellier, CNRS, INSERM, Montpellier, France
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19
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Swietlik JJ, Bärthel S, Falcomatà C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun 2023; 14:2642. [PMID: 37156840 PMCID: PMC10167354 DOI: 10.1038/s41467-023-38171-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Diana Fink
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Henrik Daub
- NEOsphere Biotechnologies GmbH, Martinsried, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany.
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20
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Chen X, Varki A. User-friendly bioorthogonal reactions click to explore glycan functions in complex biological systems. J Clin Invest 2023; 133:e169408. [PMID: 36919701 PMCID: PMC10014101 DOI: 10.1172/jci169408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Affiliation(s)
- Xi Chen
- Department of Chemistry, UCD, Davis, California, USA
| | - Ajit Varki
- Departments of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, UCSD, San Diego, California, USA
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21
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Jin GQ, Wang JX, Lu J, Zhang H, Yao Y, Ning Y, Lu H, Gao S, Zhang JL. Two birds one stone: β-fluoropyrrolyl-cysteine S NAr chemistry enabling functional porphyrin bioconjugation. Chem Sci 2023; 14:2070-2081. [PMID: 36845938 PMCID: PMC9944650 DOI: 10.1039/d2sc06209g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Bioconjugation, a synthetic tool that endows small molecules with biocompatibility and target specificity through covalent attachment of a biomolecule, holds promise for next-generation diagnosis or therapy. Besides the establishment of chemical bonding, such chemical modification concurrently allows alteration of the physicochemical properties of small molecules, but this has been paid less attention in designing novel bioconjugates. Here, we report a "two birds one stone" methodology for irreversible porphyrin bioconjugation based on β-fluoropyrrolyl-cysteine SNAr chemistry, in which the β-fluorine of porphyrin is selectively replaced by a cysteine in either peptides or proteins to generate novel β-peptidyl/proteic porphyrins. Notably, due to the distinct electronic nature between fluorine and sulfur, such replacement makes the Q band red-shift to the near-infrared region (NIR, >700 nm). This facilitates intersystem crossing (ISC) to enhance the triplet population and thus singlet oxygen production. This new methodology features water tolerance, a fast reaction time (15 min), good chemo-selectivity, and broad substrate scope, including various peptides and proteins under mild conditions. To demonstrate its potential, we applied porphyrin β-bioconjugates in several scenarios, including (1) cytosolic delivery of functional proteins, (2) metabolic glycan labeling, (3) caspase-3 detection, and (4) tumor-targeting phototheranostics.
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Affiliation(s)
- Guo-Qing Jin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jing-Xiang Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianhua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hang Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yuhang Yao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yingying Ning
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China.,Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology Guangzhou 510641 China
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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22
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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23
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Thomsen RP, Sørensen RS, Kjems J. Parallel Functionalization of DNA Origami. Methods Mol Biol 2023; 2639:175-194. [PMID: 37166718 DOI: 10.1007/978-1-0716-3028-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA origami enables the creation of large supramolecular structures, with precisely defined features at the nanoscale. The concept thus naturally lends itself to the concept of molecular patterning, i.e., the positioning of molecular moieties and functional features. Creation of nanoscale patterns was already disseminated by Rothemund in 2006, in which DNA hairpins were used to produce nanoscale patterns on the flat origami canvases (Rothemund PWK, Nature 440(7082):297-302, 2006). For this type of application, it is often desired to produce multiple different patterns using the same origami canvas by reusing existing origami staple strands, rather than ordering new, custom oligonucleotides for each unique pattern. This chapter presents a method where the enzyme terminal deoxynucleotidyl transferase (TdT) is used in a parallelized reaction to add functional moieties to the end of a selected pool of unmodified staple strand oligonucleotides, which are then incorporated at precisely defined positions in the DNA origami canvas. Introducing arrays of functional features using this enzymatic functionalization of origami staple strands offers a very high degree of flexibility, versatility, and ease of use and can often be obtained faster than custom synthesis. For small synthesis scales, typically employed during initial functional screening of many different molecular patterns, the method also offers a significant advantage in terms of cost. During the past years, we have utilized this to incorporate a large variety of molecules including bulky proteins (Sørensen RS, Okholm AH, Schaffert D, Kodal ALB, Gothelf KV, Kjems J, ACS Nano 7:8098-8104, 2013) in designed patterns from modified nucleotide triphosphate (NTP) building blocks (Jahn K, Tørring T, Voigt NV, Sørensen RS, Kodal ALB, Andersen ES, Bioconjug Chem 22:819-823, 2011). The near-quantitative yields obtained by enzymatic functionalization allow synthesis of a large set of oligonucleotides in a one-pot reaction from commercial starting materials without the need for individual post-purification. Based on the chosen subset of staple strand, it is possible to create any designed functionality, array, or pattern. Here we describe the process going from an idea/design of a DNA origami-specific molecular pattern to nucleotide synthesis and subsequent parallel functionalization of the DNA origami, assembly, and the final characterization.
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Affiliation(s)
- Rasmus P Thomsen
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Rasmus S Sørensen
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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Hu W, Zhang G, Zhou Y, Xia J, Zhang P, Xiao W, Xue M, Lu Z, Yang S. Recent development of analytical methods for disease-specific protein O-GlcNAcylation. RSC Adv 2022; 13:264-280. [PMID: 36605671 PMCID: PMC9768672 DOI: 10.1039/d2ra07184c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The enzymatic modification of protein serine or threonine residues by N-acetylglucosamine, namely O-GlcNAcylation, is a ubiquitous post-translational modification that frequently occurs in the nucleus and cytoplasm. O-GlcNAcylation is dynamically regulated by two enzymes, O-GlcNAc transferase and O-GlcNAcase, and regulates nearly all cellular processes in epigenetics, transcription, translation, cell division, metabolism, signal transduction and stress. Aberrant O-GlcNAcylation has been shown in a variety of diseases, including diabetes, neurodegenerative diseases and cancers. Deciphering O-GlcNAcylation remains a challenge due to its low abundance, low stoichiometry and extreme lability in most tandem mass spectrometry. Separation or enrichment of O-GlcNAc proteins or peptides from complex mixtures has been of great interest because quantitative analysis of protein O-GlcNAcylation can elucidate their functions and regulatory mechanisms in disease. However, valid and specific analytical methods are still lacking, and efforts are needed to further advance this direction. Here, we provide an overview of recent advances in various analytical methods, focusing on chemical oxidation, affinity of antibodies and lectins, hydrophilic interaction, and enzymatic addition of monosaccharides in conjugation with these methods. O-GlcNAcylation quantification has been described in detail using mass-spectrometric or non-mass-spectrometric techniques. We briefly summarized dysregulated changes in O-GlcNAcylation in disease.
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Affiliation(s)
- Wenhua Hu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow UniversitySuzhouJiangsu215123China
| | - Guolin Zhang
- Suzhou Institute for Drug ControlSuzhouJiangsu215104China
| | - Yu Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiang310014China
| | - Jun Xia
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiang310014China
| | - Peng Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Soochow UniversitySuzhouJiangsu215004China
| | - Wenjin Xiao
- Department of Endocrinology, The Second Affiliated Hospital of Soochow UniversitySuzhouJiangsu215004China
| | - Man Xue
- Suzhou Institute for Drug ControlSuzhouJiangsu215104China
| | - Zhaohui Lu
- Health Examination Center, The Second Affiliated Hospital of Soochow UniversitySuzhouJiangsu215004China
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow UniversitySuzhouJiangsu215123China
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25
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Zhang X, Zhang Z, Xue X, Fan T, Tan C, Liu F, Tan Y, Jiang Y. PROTAC Degrader of Estrogen Receptor α Targeting DNA-Binding Domain in Breast Cancer. ACS Pharmacol Transl Sci 2022; 5:1109-1118. [PMID: 36407946 PMCID: PMC9667539 DOI: 10.1021/acsptsci.2c00109] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 12/24/2022]
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) are a powerful class of drugs that selectively degrade the proteins of interest (POIs) through cellular ubiquitination mechanisms. Estrogen receptor α (ERα) plays a vital role in the pathogenesis and treatment of breast cancer. In this work, the DNA-binding domain (DBD) of ERα was selected as the target to avoid drug resistance caused by the ligand-binding domain (LBD) of ERα. The estrogen response element (ERE), a natural DNA sequence binding with DBD of ERα, was chosen as a recognized unit of PROTAC. Therefore, we designed a nucleic acid-conjugated PROTAC, ERE-PROTAC, via a click reaction, in which the ERE sequence recruits ERα and the typical small molecule VH032 recruits the von Hippel-Lindau (VHL) E3 ligase. The proposed ERE-PROTAC showed to efficiently and reversibly degrade ERα in different breast cancer cells by targeting the DBD, indicating its potential to overcome the current resistance caused by LBD mutations.
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Affiliation(s)
| | | | - Xiaoqi Xue
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Tingting Fan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Feng Liu
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Ying Tan
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical
Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School Tsinghua University, Shenzhen 518055, China
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26
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Cioce A, Calle B, Rizou T, Lowery SC, Bridgeman VL, Mahoney KE, Marchesi A, Bineva-Todd G, Flynn H, Li Z, Tastan OY, Roustan C, Soro-Barrio P, Rafiee MR, Garza-Garcia A, Antonopoulos A, Wood TM, Keenan T, Both P, Huang K, Parmeggian F, Snijders AP, Skehel M, Kjær S, Fascione MA, Bertozzi CR, Haslam SM, Flitsch SL, Malaker SA, Malanchi I, Schumann B. Cell-specific bioorthogonal tagging of glycoproteins. Nat Commun 2022; 13:6237. [PMID: 36284108 PMCID: PMC9596482 DOI: 10.1038/s41467-022-33854-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Altered glycoprotein expression is an undisputed corollary of cancer development. Understanding these alterations is paramount but hampered by limitations underlying cellular model systems. For instance, the intricate interactions between tumour and host cannot be adequately recapitulated in monoculture of tumour-derived cell lines. More complex co-culture models usually rely on sorting procedures for proteome analyses and rarely capture the details of protein glycosylation. Here, we report a strategy termed Bio-Orthogonal Cell line-specific Tagging of Glycoproteins (BOCTAG). Cells are equipped by transfection with an artificial biosynthetic pathway that transforms bioorthogonally tagged sugars into the corresponding nucleotide-sugars. Only transfected cells incorporate bioorthogonal tags into glycoproteins in the presence of non-transfected cells. We employ BOCTAG as an imaging technique and to annotate cell-specific glycosylation sites in mass spectrometry-glycoproteomics. We demonstrate application in co-culture and mouse models, allowing for profiling of the glycoproteome as an important modulator of cellular function.
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Affiliation(s)
- Anna Cioce
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Beatriz Calle
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Tatiana Rizou
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah C Lowery
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Victoria L Bridgeman
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Andrea Marchesi
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ganka Bineva-Todd
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Zhen Li
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Omur Y Tastan
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Pablo Soro-Barrio
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Thomas M Wood
- Sarafan ChEM-H, Department of Chemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tessa Keenan
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Peter Both
- School of Chemistry & Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
- R&D Department, Axxence Slovakia s.r.o., 81107, Bratislava, Slovakia
| | - Kun Huang
- School of Chemistry & Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Fabio Parmeggian
- School of Chemistry & Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milano, Italy
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Carolyn R Bertozzi
- Sarafan ChEM-H, Department of Chemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sabine L Flitsch
- School of Chemistry & Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Benjamin Schumann
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK.
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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27
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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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28
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Ko JH, Forsythe NL, Gelb MB, Messina KMM, Lau UY, Bhattacharya A, Olafsen T, Lee JT, Kelly KA, Maynard HD. Safety and Biodistribution Profile of Poly(styrenyl acetal trehalose) and Its Granulocyte Colony Stimulating Factor Conjugate. Biomacromolecules 2022; 23:3383-3395. [PMID: 35767465 DOI: 10.1021/acs.biomac.2c00511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Poly(styrenyl acetal trehalose) (pSAT), composed of trehalose side chains linked to a polystyrene backbone via acetals, stabilizes a variety of proteins and enzymes against fluctuations in temperature. A promising application of pSAT is conjugation of the polymer to therapeutic proteins to reduce renal clearance. To explore this possibility, the safety of the polymer was first studied. Investigation of acute toxicity of pSAT in mice showed that there were no adverse effects of the polymer at a high (10 mg/kg) concentration. The immune response (antipolymer antibody and cytokine production) in mice was also studied. No significant antipolymer IgG was detected for pSAT, and only a transient and low level of IgM was elicited. pSAT was also safe in terms of cytokine response. The polymer was then conjugated to a granulocyte colony stimulating factor (GCSF), a therapeutic protein that is approved by the Federal Drug Administration, in order to study the biodistribution of a pSAT conjugate. A site-selective, two-step synthesis approach was developed for efficient conjugate preparation for the biodistribution study resulting in 90% conjugation efficiency. The organ distribution of GCSF-pSAT was measured by positron emission tomography and compared to controls GCSF and GCSF-poly(ethylene glycol), which confirmed that the trehalose polymer conjugate improved the in vivo half-life of the protein by reducing renal clearance. These findings suggest that trehalose styrenyl polymers are promising for use in therapeutic protein-polymer conjugates for reduced renal clearance of the biomolecule.
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Affiliation(s)
- Jeong Hoon Ko
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Neil L Forsythe
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Madeline B Gelb
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Kathryn M M Messina
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Uland Y Lau
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Arvind Bhattacharya
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Tove Olafsen
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Jason T Lee
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Kathleen A Kelly
- Department of Pathology and Lab Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Heather D Maynard
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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29
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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30
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Xi Z, Kong H, Chen Y, Deng J, Xu W, Liang Y, Zhang Y. Metal- and Strain-Free Bioorthogonal Cycloaddition of o-Diones with Furan-2(3H)-one as Anionic Cycloaddend. Angew Chem Int Ed Engl 2022; 61:e202200239. [PMID: 35304810 DOI: 10.1002/anie.202200239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 12/18/2022]
Abstract
The development of new bioorthogonal reactions with mutual orthogonality to classic bioorthogonal reactions such as the strain-promoted azide-alkyne click reaction and the inverse-electron-demand Diels-Alder reaction is of great importance in providing chemical tools for multiplex labelling of live cells. Here we report the first anionic cycloaddend-promoted bioorthogonal cycloaddition reaction between phenanthrene-9,10-dione and furan-2(3H)-one derivatives, where the high polarity of water is exploited to stabilize the highly electron-rich anionic cycloaddend. The reaction is metal- and strain-free, which proceeds rapidly in aqueous solution and on live cells with a second-order rate constant up to 119 M-1 s-1 . The combined utilization of this reaction together with the two other widely used bioorthogonal reactions allows for mutually orthogonal labelling of three types of proteins or three groups of living cells in one batch without cross-talking. Such results highlight the great potential for multiplex labelling of different biomolecules in live cells.
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Affiliation(s)
- Ziwei Xi
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hao Kong
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jiafang Deng
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Wenyuan Xu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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31
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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32
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In situ identification of cellular drug targets in mammalian tissue. Cell 2022; 185:1793-1805.e17. [PMID: 35483372 PMCID: PMC9106931 DOI: 10.1016/j.cell.2022.03.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/01/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022]
Abstract
The lack of tools to observe drug-target interactions at cellular resolution in intact tissue has been a major barrier to understanding in vivo drug actions. Here, we develop clearing-assisted tissue click chemistry (CATCH) to optically image covalent drug targets in intact mammalian tissues. CATCH permits specific and robust in situ fluorescence imaging of target-bound drug molecules at subcellular resolution and enables the identification of target cell types. Using well-established inhibitors of endocannabinoid hydrolases and monoamine oxidases, direct or competitive CATCH not only reveals distinct anatomical distributions and predominant cell targets of different drug compounds in the mouse brain but also uncovers unexpected differences in drug engagement across and within brain regions, reflecting rare cell types, as well as dose-dependent target shifts across tissue, cellular, and subcellular compartments that are not accessible by conventional methods. CATCH represents a valuable platform for visualizing in vivo interactions of small molecules in tissue.
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33
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Wang F, Kong H, Meng X, Tian X, Wang C, Xu L, Zhang X, Wang L, Xie R. A light-initiated chemical reporter strategy for spatiotemporal labeling of biomolecules. RSC Chem Biol 2022; 3:539-545. [PMID: 35656482 PMCID: PMC9092362 DOI: 10.1039/d2cb00072e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The emergence of optochemical approaches has had a diverse impact over a broad range of biological research due to spatiotemporal regulation. Herein, we integrate this feature into the bioorthogonal chemical reporter strategy, which enables visible light-controlled spatiotemporal labeling of cell-surface glycans, lipids, and proteins. The metabolic precursors were first incorporated into live cells, and next the bioorthogonal reaction converted the azide/alkyne into a photo-active functional group, which allowed for subsequent photo-click reaction. We demonstrated this strategy by specifically labeling sialome, mucin-type O-glycome, phospholipids and newly-synthesized membrane proteins, respectively. The sequential photoirradiation-orthogonal reporter tagging (SPORT) should facilitate the probing of biomolecules in complex biological systems with high spatiotemporal precision.
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Affiliation(s)
- Feifei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hao Kong
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Lei Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Xiang Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
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34
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Engineering Proteins Containing Noncanonical Amino Acids on the Yeast Surface. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2491:491-559. [PMID: 35482204 DOI: 10.1007/978-1-0716-2285-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Yeast display has been used to advance many critical research areas, including the discovery of unique protein binders and biological therapeutics. In parallel, noncanonical amino acids (ncAAs) have been used to tailor antibody-drug conjugates and enable discovery of therapeutic leads. Together, these two technologies have allowed for generation of synthetic antibody libraries, where the introduction of ncAAs in yeast-displayed proteins allows for library screening for therapeutically relevant targets. The combination of yeast display with genetically encoded ncAAs increases the available chemistry in proteins and advances applications that require high-throughput strategies. In this chapter, we discuss methods for displaying proteins containing ncAAs on the yeast surface, generating and screening libraries of proteins containing ncAAs, preparing bioconjugates on the yeast surface in large scale, generating and screening libraries of aminoacyl-tRNA synthetases (aaRSs) for encoding ncAAs by using reporter constructs, and characterizing ncAA-containing proteins secreted from yeast. The experimental designs laid out in this chapter are generalizable for discovery of protein binders to a variety of targets and aaRS evolution to continue expanding the genetic code beyond what is currently available in yeast.
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35
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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36
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Incorporating, Quantifying, and Leveraging Noncanonical Amino Acids in Yeast. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:377-432. [PMID: 35094338 DOI: 10.1007/978-1-0716-1811-0_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic code expansion has allowed for extraordinary advances in enhancing protein chemical diversity and functionality, but there remains a critical need for understanding and engineering genetic code expansion systems for improved efficiency. Incorporation of noncanonical amino acids (ncAAs) at stop codons provides a site-specific method for introducing unique chemistry into proteins, though often at reduced yields compared to wild-type proteins. A powerful platform for ncAA incorporation supports both the expression and evaluation of chemically diverse proteins for a broad range of applications. In yeast, ncAAs have been used to study dynamic cellular processes such as protein-protein interactions and also allow for exploration of eukaryotic-specific biology such as epigenetics. Furthermore, yeast display is an advantageous technology for engineering and screening the properties of proteins in high throughput. The protocols presented in this chapter describe detailed methods for the yeast-based genetic encoding of ncAAs in proteins intracellularly or on the yeast surface. In addition, methods are presented for modifying proteins on the yeast surface using bioorthogonal chemical reactions and evaluating reaction efficiency. Finally, protocols are included for the preparation of libraries that involve genetic code expansion. Libraries of proteins that contain ncAAs or libraries of the cellular machinery required to encode ncAAs can be constructed and screened in high throughput for many biological and chemical applications. Efficient incorporation of ncAAs facilitates elucidation of fundamental eukaryotic biology and advances tools for enzyme and genome engineering to evolve host cells that are better able to accommodate alternative genetic codes.
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37
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Xi Z, Kong H, Chen Y, Deng J, Xu W, Liang Y, Zhang Y. Metal‐ and Strain‐free Bioorthogonal Cycloaddition of o‐Diones with Furan‐2(3H)‐one as Anionic Cycloaddend. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ziwei Xi
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Hao Kong
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Yu Chen
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Jiafang Deng
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Wenyuan Xu
- Nanjing University School of Chemistry and Chemical Engineering CHINA
| | - Yong Liang
- Nanjing University Chemistry 163 Xianlin Ave 210023 Nanjing CHINA
| | - Yan Zhang
- Nanjing University School of Chemistry and Chemical Engineering CHINA
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38
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Wu Q, Ye J, Chao Y, Dong S, Niu M, Wang Y, Liu Z, Chen W, Ge N, Lu S, Wang PG, Chen M. Chemoenzymatic Labeling Pathogens Containing Terminal N-Acetylneuraminic Acid-α(2-3)-Galactose Glycans. ACS Infect Dis 2022; 8:657-664. [PMID: 35179863 DOI: 10.1021/acsinfecdis.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N-acetylneuraminic acid-α(2-3)-galactose epitope is often located at the nonreducing terminal ends of glycans on the envelopes of many pathogens, and it is believed that this structure mimics a host's oligosaccharide so as to circumvent and/or counteract the host's immune responses. A chemoenzymatic method for the rapid and sensitive detection of N-acetylneuraminic acid-α(2-3)-galactose has been built, so we planned to examine whether the chemoenzymatic method could be applied on the detection of N-acetylneuraminic acid-α(2-3)-galactose on pathogens. Our results revealed that the chemoenzymatic method was rapid and sensitive for labeling live or dead Gram-positive Streptococcus agalactiae A909 and Gram-negative Campylobacter jejuni MK104 with N-acetylneuraminic acid-α(2-3)-galactose. This study suggested that the chemoenzymatic method was a new strategy for labeling pathogens and had potential for the diagnosis of or therapeutics for pathogenic infection.
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Affiliation(s)
- Qizheng Wu
- The State Key Laboratory of Microbial Technology and National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Jinfeng Ye
- The State Key Laboratory of Microbial Technology and National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Yicong Chao
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Shuchen Dong
- Department of Gastroenterology, Qingdao Municipal Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266000, China
| | - Min Niu
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Yaqian Wang
- The State Key Laboratory of Microbial Technology and National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Zhaoxi Liu
- The State Key Laboratory of Microbial Technology and National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Wang Chen
- Department of Neurology, Linyi People’s Hospital, Linyi 276000, China
| | - Ningning Ge
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Shuhua Lu
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Peng George Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Min Chen
- The State Key Laboratory of Microbial Technology and National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
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39
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40
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Synthesis and Fluorescent Properties of Aminopyridines and the Application in "Click and Probing". Molecules 2022; 27:molecules27051596. [PMID: 35268697 PMCID: PMC8912075 DOI: 10.3390/molecules27051596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Unsubstituted pyridin-2-amine has a high quantum yield and is a potential scaffold for a fluorescent probe. However, the facile access to conjugated highly substituted aminopyridines and the study of their fluorescent properties is scarce. In this paper, synthesis and fluorescent properties of multisubstituted aminopyridines were studied based on a recently developed Rh-catalyzed coupling of vinyl azide with isonitrile to form a vinyl carbodiimide intermediate, following tandem cyclization with an alkyne. An aminopyridine substituted with an azide group as a potential probe was further designed, synthesized, and evaluated. The “clicking-and-probing” experiment of it on BSA protein showed the potential of aminopyridine as a scaffold of a biological probe.
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41
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Liu J, Xing Y, Xue B, Zhou X. Nanozyme enhanced paper-based biochip with a smartphone readout system for rapid detection of cyanotoxins in water. Biosens Bioelectron 2022; 205:114099. [PMID: 35217255 DOI: 10.1016/j.bios.2022.114099] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/02/2022]
Abstract
Cyanobacterial harmful algal blooms in freshwater systems can produce cyanotoxins, such as microcystins (MCs) and nodularins (NODs), presenting serious threats to human health and ecosystems. Required routine monitoring of cyanotoxins in water samples, as posed by U.S. EPA drinking water contaminant candidate list 5 (CCL5), demands for cost-effective, reliable and sensitive MCs/NODs detection methods. We report the development of a colorimetric paper-based immunochip assisted by nanozyme catalysis with a smartphone readout system for rapid detection of cyanotoxins in water. We show that the introduction of biorthogonal click reaction enables in situ facile self-assembly of multi-layers of peroxidase-like nanozyme onto the anti-MCs/NODs monoclonal antibody. We can detect 13 variants of MCs/NODs even in the sub-microgram per liter range with detection limit of below 0.7 μg/L and satisfactory recovery percentages between 88 and 120% in different water matrices. Our technology shows a good correlation with the well-developed ELISA technology, demonstrating its great potential applications in resource-limited or less-developed regions for on-site and large-scale screening of cyanotoxins in water environment.
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Affiliation(s)
- Jinchuan Liu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunpeng Xing
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Boyuan Xue
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China.
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42
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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43
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Cheng B, Wan Y, Tang Q, Du Y, Xu F, Huang Z, Qin W, Chen X. A Photocaged Azidosugar for
Light‐Controlled
Metabolic Labeling of
Cell‐Surface
Sialoglycans. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bo Cheng
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Yi Wan
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Qi Tang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Yifei Du
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Feiyang Xu
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Zhimin Huang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Wei Qin
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Xing Chen
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
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44
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Xiong H, Liu L, Wang Y, Jiang H, Wang X. Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104341. [PMID: 34622570 DOI: 10.1002/smll.202104341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.
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Affiliation(s)
- Hongjie Xiong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yihan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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45
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Xiong TM, Garcia ES, Chen J, Zhu L, Alzona AJ, Zimmerman SC. Enzyme-like catalysis by single chain nanoparticles that use transition metal cofactors. Chem Commun (Camb) 2021; 58:985-988. [PMID: 34935784 DOI: 10.1039/d1cc05578j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a modular approach in which a noncovalently cross-linked single chain nanoparticle (SCNP) selectively binds catalyst "cofactors" and substrates to increase both the catalytic activity of a Cu-catalyzed alkyne-azide cycloaddition reaction and the Ru-catalyzed cleavage of allylcarbamate groups compared to the free catalysts.
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Affiliation(s)
- Thao M Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Edzna S Garcia
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Junfeng Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Lingyang Zhu
- NMR Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Ariale J Alzona
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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46
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Sapienza PJ, Currie MM, Lancaster NM, Li K, Aubé J, Goldfarb D, Cloer EW, Major MB, Lee AL. Visualizing an Allosteric Intermediate Using CuAAC Stabilization of an NMR Mixed Labeled Dimer. ACS Chem Biol 2021; 16:2766-2775. [PMID: 34784173 DOI: 10.1021/acschembio.1c00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homodimers are the most abundant type of enzyme in cells, and as such, they represent the most elemental system for studying the phenomenon of allostery. In these systems, in which the allosteric features are manifest by the effect of the first binding event on a similar event at the second site, the most informative state is the asymmetric singly bound (lig1) form, yet it tends to be thermodynamically elusive. Here we obtain milligram quantities of lig1 of the allosteric homodimer, chorismate mutase, in the form of a mixed isotopically labeled dimer stabilized by Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) between the subunits. Below, we outline several critical steps required to generate high yields of both types of unnatural amino acid-containing proteins and overcome multiple pitfalls intrinsic to CuAAC to obtain high yields of a highly purified, fully intact, active mixed labeled dimer, which provides the first glimpse of the lig1 intermediate. These data not only will make possible NMR-based investigations of allostery envisioned by us but also should facilitate other structural applications in which specific linkage of proteins is helpful.
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Affiliation(s)
- Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michelle M. Currie
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Noah M. Lancaster
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dennis Goldfarb
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Michael B. Major
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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47
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Abstract
Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.
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Affiliation(s)
- Robert E Bird
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Steven A Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xiang Yu
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
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48
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Cioce A, Bineva-Todd G, Agbay AJ, Choi J, Wood TM, Debets MF, Browne WM, Douglas HL, Roustan C, Tastan OY, Kjaer S, Bush JT, Bertozzi CR, Schumann B. Optimization of Metabolic Oligosaccharide Engineering with Ac 4GalNAlk and Ac 4GlcNAlk by an Engineered Pyrophosphorylase. ACS Chem Biol 2021. [PMID: 33835779 DOI: 10.1021/acschem-bio.1c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Metabolic oligosaccharide engineering (MOE) has fundamentally contributed to our understanding of protein glycosylation. Efficient MOE reagents are activated into nucleotide-sugars by cellular biosynthetic machineries, introduced into glycoproteins and traceable by bioorthogonal chemistry. Despite their widespread use, the metabolic fate of many MOE reagents is only beginning to be mapped. While metabolic interconnectivity can affect probe specificity, poor uptake by biosynthetic salvage pathways may impact probe sensitivity and trigger side reactions. Here, we use metabolic engineering to turn the weak alkyne-tagged MOE reagents Ac4GalNAlk and Ac4GlcNAlk into efficient chemical tools to probe protein glycosylation. We find that bypassing a metabolic bottleneck with an engineered version of the pyrophosphorylase AGX1 boosts nucleotide-sugar biosynthesis and increases bioorthogonal cell surface labeling by up to two orders of magnitude. A comparison with known azide-tagged MOE reagents reveals major differences in glycoprotein labeling, substantially expanding the toolbox of chemical glycobiology.
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Affiliation(s)
- Anna Cioce
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Anthony J Agbay
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas M Wood
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Marjoke F Debets
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - William M Browne
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Holly L Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Omur Y Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Jacob T Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY United Kingdom
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, 380 Roth Way, Stanford, California 94305, United States
| | - Benjamin Schumann
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
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49
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Liu J, Hao Y, He Y, Li X, Sun DE, Zhang Y, Yang PY, Chen X. Quantitative and Site-Specific Chemoproteomic Profiling of Protein O-GlcNAcylation in the Cell Cycle. ACS Chem Biol 2021; 16:1917-1923. [PMID: 34161081 DOI: 10.1021/acschembio.1c00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mammalian cell cycle is a central process for tissue growth and maintenance. Protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification has been found to occur on several important cell cycle regulators. However, the O-GlcNAcylated proteome has not been extensively profiled during cell cycle progression. Herein, we report a quantitative profiling of protein O-GlcNAcylation sites in cell proliferation, by using an O-GlcNAc chemoproteomic strategy. In HeLa cells, a total of 902, 439, and 872 high-confidence O-GlcNAcylation sites distributed on 414, 265, and 425 proteins are identified in the interphase, early mitosis, and mitotic exit stages, respectively. The identified O-GlcNAcylation events occur on a variety of important regulators, which are involved in the processes of cell division, DNA repair, and cell death. Furthermore, we show that O-GlcNAcylation is dynamically regulated in a cell cycle stage-dependent manner. Our results provide a valuable resource for investigating the functional roles of O-GlcNAc in the mammalian cell cycle.
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Affiliation(s)
- Jialin Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yi Hao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yanwen He
- College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Xiang Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - De-en Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yang Zhang
- Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Peng-Yuan Yang
- Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
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50
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Cioce A, Bineva-Todd G, Agbay AJ, Choi J, Wood TM, Debets MF, Browne WM, Douglas HL, Roustan C, Tastan OY, Kjaer S, Bush JT, Bertozzi CR, Schumann B. Optimization of Metabolic Oligosaccharide Engineering with Ac 4GalNAlk and Ac 4GlcNAlk by an Engineered Pyrophosphorylase. ACS Chem Biol 2021; 16:1961-1967. [PMID: 33835779 PMCID: PMC8501146 DOI: 10.1021/acschembio.1c00034] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Metabolic oligosaccharide
engineering (MOE) has fundamentally contributed
to our understanding of protein glycosylation. Efficient MOE reagents
are activated into nucleotide-sugars by cellular biosynthetic machineries,
introduced into glycoproteins and traceable by bioorthogonal chemistry.
Despite their widespread use, the metabolic fate of many MOE reagents
is only beginning to be mapped. While metabolic interconnectivity
can affect probe specificity, poor uptake by biosynthetic salvage
pathways may impact probe sensitivity and trigger side reactions.
Here, we use metabolic engineering to turn the weak alkyne-tagged
MOE reagents Ac4GalNAlk and Ac4GlcNAlk into
efficient chemical tools to probe protein glycosylation. We find that
bypassing a metabolic bottleneck with an engineered version of the
pyrophosphorylase AGX1 boosts nucleotide-sugar biosynthesis and increases
bioorthogonal cell surface labeling by up to two orders of magnitude.
A comparison with known azide-tagged MOE reagents reveals major differences
in glycoprotein labeling, substantially expanding the toolbox of chemical
glycobiology.
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Affiliation(s)
- Anna Cioce
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Anthony J. Agbay
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas M. Wood
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Marjoke F. Debets
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - William M. Browne
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Holly L. Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Omur Y. Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY United Kingdom
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, 380 Roth Way, Stanford, California 94305, United States
| | - Benjamin Schumann
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ London, United Kingdom
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
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