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Chemla Y, Kaufman F, Amiram M, Alfonta L. Expanding the Genetic Code of Bioelectrocatalysis and Biomaterials. Chem Rev 2024. [PMID: 39377473 DOI: 10.1021/acs.chemrev.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
Genetic code expansion is a promising genetic engineering technology that incorporates noncanonical amino acids into proteins alongside the natural set of 20 amino acids. This enables the precise encoding of non-natural chemical groups in proteins. This review focuses on the applications of genetic code expansion in bioelectrocatalysis and biomaterials. In bioelectrocatalysis, this technique enhances the efficiency and selectivity of bioelectrocatalysts for use in sensors, biofuel cells, and enzymatic electrodes. In biomaterials, incorporating non-natural chemical groups into protein-based polymers facilitates the modification, fine-tuning, or the engineering of new biomaterial properties. The review provides an overview of relevant technologies, discusses applications, and highlights achievements, challenges, and prospects in these fields.
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [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: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A. Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [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: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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4
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Fox A, Leonard GD, Adzibolosu N, Wong T, Tedja R, Sharma S, Gogoi R, Morris R, Mor G, Fehl C, Alvero AB. Adipose microenvironment promotes hypersialylation of ovarian cancer cells. Front Oncol 2024; 14:1432333. [PMID: 39104719 PMCID: PMC11299042 DOI: 10.3389/fonc.2024.1432333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
Introduction Ovarian and other peritoneal cancers have a strong tendency to metastasize into the surrounding adipose tissue. This study describes an effect of the adipose microenvironment on upregulation of sialic acid-containing glycans in ovarian cancer (OC). Heterogeneous populations of glycosylated OC tumors converged to a highly sialylated cell state that regulates tumorigenesis in an immune-dependent manner. Methods We modeled the adipose microenvironment by conditioning growth media with human patient-derived adipose tissue. OC cell lines grown in the presence vs. absence of adipose conditioned media (ACM) were characterized by transcriptomics, western blotting, and chemical biology glycan labeling methods. Fluorescence-activated cell sorting was used to separate adipose-driven upregulation of hypersialylated ("SNA-high") vs. hyposialylated ("SNA-low") OC subpopulations. The two subpopulations were characterized by further transcriptomic and quantitative polymerase chain reaction analyses, then injected into a syngeneic mouse model. Immune system involvement was implicated using wild type and athymic nude mice with a primary endpoint of overall survival. Results Adipose conditioning resulted in upregulation of sialyltransferases ST3GAL1, ST6GAL1, ST6GALNAC3, and ST8Sia1. In culture, OC cells displayed two distinct sialylated subpopulations that were stable for up to 9 passages, suggesting inherent heterogeneity in sialylation that is maintained throughout cell division and media changes. OC tumors that implanted in the omental adipose tissue exclusively reprogrammed to the highly sialylated subpopulation. In wild type C57BL/6 mice, only the hypersialylated SNA-high subpopulation implanted in the adipose, whereas the hyposialylated SNA-low subpopulation failed to be tumorigenic (p=0.023, n=5). In the single case where SNA-low established a tumor, post-mortem analysis revealed reprogramming of the tumor to the SNA-high state in vivo. In athymic nude mice, both subpopulations rapidly formed tumors, implicating a role of the adaptive immune system. Conclusions These findings suggest a model of glycan-dependent tumor evolution wherein the adipose microenvironment reprograms OC to a tumorigenic state that resists the adaptive immune system. Mechanistically, adipose factors upregulate sialyltransferases. To our knowledge, this is the first demonstration of the effect of adipose microenvironment on OC tumor sialylation. Our results set the stage for translational applications targeting sialic acid pathways in OC and other peritoneal cancer tumorigenesis and metastasis.
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Affiliation(s)
- Alexandra Fox
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Garry D. Leonard
- Department of Chemistry, Wayne State University, Detroit, MI, United States
| | - Nicholas Adzibolosu
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Terrence Wong
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Roslyn Tedja
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Sapna Sharma
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Radhika Gogoi
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Robert Morris
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Gil Mor
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
| | - Ayesha B. Alvero
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Detroit, MI, United States
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5
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Laomeephol C, Tawinwung S, Suppipat K, Arunmanee W, Wang Q, Amie Luckanagul J. Surface functionalization of virus-like particles via bioorthogonal click reactions for enhanced cell-specific targeting. Int J Pharm 2024; 660:124332. [PMID: 38866085 DOI: 10.1016/j.ijpharm.2024.124332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
Surface functionalization of nano drug carriers allows for precise delivery of therapeutic molecules to the target site. This technique involves attaching targeting molecules to the nanoparticle surface, facilitating selective interaction. In this study, we engineered virus-like particles (VLPs) to enhance their targeting capabilities. Azide groups incorporated on the lipid membranes of VLPs enabled bioorthogonal click reactions for conjugation with cycloalkyne-bearing molecules, providing efficient conjugation with high specificity. HIV-1 Gag VLPs were chosen due to their envelope, which allows host membrane component incorporation, and the Gag protein, which serves as a recognition motif for human T cells. This combination, along with antibody-mediated targeting, addresses the limitations of intracellular delivery to T cells, which typically exhibit low uptake of exogenous materials. The selective uptake of azide VLPs by CD3-positive T cells was evaluated in a co-culture system. Even without antibody conjugation, VLP uptake was enhanced in T cells, indicating their intrinsic targeting potential. Antibody conjugation further amplified this effect, demonstrating the synergistic benefits of the combined targeting approach. Our study shows that recombinant production of azide functionalized VLPs results in engineered nanoparticles that can be easily modified using bioorthogonal click reactions, providing high specificity and versatility for conjugation with various molecules, making it applicable to a wide range of biological products.
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Affiliation(s)
- Chavee Laomeephol
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Biomaterial Engineering in Medical and Health, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supannikar Tawinwung
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Cellular Immunotherapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Koramit Suppipat
- Cellular Immunotherapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Department of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wanatchaporn Arunmanee
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Jittima Amie Luckanagul
- Center of Excellence in Biomaterial Engineering in Medical and Health, Chulalongkorn University, Bangkok 10330, Thailand; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand.
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6
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Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
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Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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7
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Wang B, Li C, He D, Ding K, Tian Q, Feng G, Qin A, Tang BZ. Bioconjugation and Reaction-Induced Tumor Therapy via Alkynamide-Based Thiol-Yne Click Reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307309. [PMID: 38150611 DOI: 10.1002/smll.202307309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/23/2023] [Indexed: 12/29/2023]
Abstract
Ferroptosis is associated with the occurrence and development of many diseases, which is the result of an imbalance in cellular metabolism and oxidation-reduction balance. Therefore, it is an effective therapeutic strategy that simultaneously regulating the intracellular oxidation-reduction system. Herein, a click reaction of alkynylamide with thiol groups in the presence of amine or in PBS (pH = 7.4) is developed, which can react efficiently with thiol substances, such as cysteine (Cys), glutathione (GSH), and bovine serum albumin (BSA). Notably, MBTB-PA, an aggregation-induced emission (AIE) photosensitizer with an alkynylamide unit, is synthesized and its intracellular behavior is visualized in situ by fluorescence imaging, demonstrating its excellent ability to target the endoplasmic reticulum. Furthermore, MBTB-PA reacted with proteins in tumor cells, consumed reducing substances, and triggered intracellular oxidative stress, resulting in cell death. Based on this reaction therapy strategy, click reaction is combined with photodynamic therapy to achieve effective killing of tumor cells by simultaneously raising the intracellular oxidative state and reducing the reductive state. This work not only develops an application of click reaction of alkynamide with thiol in bioconjugation and anti-tumor therapy, but also provides feasible ideas for organic reactions in the exploration of organisms.
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Affiliation(s)
- Bingnan Wang
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, China
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
| | - Chunyang Li
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, China
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
| | - Dong He
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Keke Ding
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Qi Tian
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, China
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
| | - Guangxue Feng
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, China
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
| | - Anjun Qin
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, China
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
| | - Ben Zhong Tang
- Center for Aggregation-Induced Emission, AIE Institute, South China University of Technology, Guangzhou, 510640, China
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen(CUHK-Shenzhen), Guangdong, 518172, China
- Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
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8
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [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: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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9
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Fox A, Leonard GD, Adzibolosu N, Wong T, Tedja R, Sharma S, Gogoi R, Morris R, Mor G, Fehl C, Alvero AB. Adipose microenvironment promotes hypersialylation of ovarian cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593990. [PMID: 38798490 PMCID: PMC11118282 DOI: 10.1101/2024.05.13.593990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Sialylation, the addition of negatively charged sialic acid sugars to terminal ends of glycans, is upregulated in most cancers. Hypersialylation supports multiple pro-tumor mechanisms such as enhanced migration and invasion, resistance to apoptosis and immune evasion. A current gap in knowledge is the lack of understanding on how the tumor microenvironment regulates cancer cell sialylation. The adipose niche is a main component of most peritoneal cancers' microenvironment. This includes ovarian cancer (OC), which causes most deaths from all gynecologic cancers. In this report, we demonstrate that the adipose microenvironment is a critical regulator of OC cell sialylation. In vitro adipose conditioning led to an increase in both ⍺2,3- and ⍺2,6-linked cell surface sialic acids in both human and mouse models of OC. Adipose-induced sialylation reprogramming was also observed in vivo from intra-peritoneal OC tumors seeded in the adipose-rich omentum. Mechanistically, we observed upregulation of at least three sialyltransferases, ST3GAL1, ST6GAL1 and ST3GALNAC3. Hypersialylated OC cells consistently formed intra-peritoneal tumors in both immune-competent mice and immune-compromised athymic nude mice. In contrast, hyposiaylated OC cells persistently formed tumors only in athymic nude mice demonstrating that sialylation impacts OC tumor formation in an immune dependent manner. To our knowledge, this is the first demonstration of the effect of adipose microenvironment on OC tumor sialylation. Our results set the stage for translational applications targeting sialic acid pathways in OC and other peritoneal cancers.
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10
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Huang W, Laughlin ST. Cell-selective bioorthogonal labeling. Cell Chem Biol 2024; 31:409-427. [PMID: 37837964 DOI: 10.1016/j.chembiol.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/25/2023] [Accepted: 09/19/2023] [Indexed: 10/16/2023]
Abstract
In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Scott T Laughlin
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA.
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11
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Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
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Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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12
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Lightle HE, Kafley P, Lewis TR, Wang RE. Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging. Methods 2023; 219:95-101. [PMID: 37804961 PMCID: PMC10841489 DOI: 10.1016/j.ymeth.2023.10.001] [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: 08/10/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
This work features the use of amber suppression-mediated unnatural amino acid (UAA) incorporation into proteins for various imaging purposes. The site-specific incorporation of the UAA, p-azido-L-phenylalanine (pAzF), provides an azide handle that can be used to complete the strain promoted azide-alkyne click cycloaddition (SPAAC) reaction to introduce an imaging modality such as a fluorophore or a positron emission tomography (PET) tracer on the protein of interest (POI). Such methodology can be pursued directly in mammalian cell lines or on proteins expressed in vitro, thereby conferring a homogeneous pool of protein conjugates. A general procedure for UAA incorporation to use with a site-specific protein labeling method is provided allowing for in vitro and in vivo imaging applications based on the representative proteins PTEN and PD-L1. This approach would help elucidate the cellular or in vivo biological activities of the POI.
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Affiliation(s)
- Hailey E Lightle
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Todd R Lewis
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA.
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13
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Mandler MD, Degnan AP, Zhang S, Aulakh D, Georges K, Sandhu B, Sarjeant A, Zhu Y, Traeger SC, Cheng PT, Ellsworth BA, Regueiro-Ren A. Structural and Thermal Characterization of Halogenated Azidopyridines: Under-Reported Synthons for Medicinal Chemistry. Org Lett 2022; 24:799-803. [PMID: 34714083 DOI: 10.1021/acs.orglett.1c03201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Owing to their participation in Click reactions, bifunctional azides are valuable intermediates in the preparation of medicines and biochemical tool compounds. Despite the privileged nature of pyridines among pharmaceutical scaffolds, reports of the synthesis and characterization of azidopyridines bearing a halogen substituent for further elaboration are almost completely unknown in the literature. As azidopyridines carry nearly equal numbers of nitrogen and carbon atoms, we hypothesized that safety concerns limited the application of these useful bifunctional building blocks in medicinal and biological chemistry. To address this concern, we prepared and characterized nine azidopyridines bearing a single fluorine, chlorine, or bromine atom. All were examined by differential scanning calorimetry (DSC), in which they demonstrated exotherms of 228-326 kJ/mol and onset temperatures between 119 and 135 °C. Selected azidopyridines were advanced to mechanical stress testing, in which impact sensitivity was noted for one regioisomer of C5H3FN4. The utility of these versatile intermediates was demonstrated through their use in a variety of Click reactions and the diversification of the halogen handles.
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Affiliation(s)
- Michael D Mandler
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew P Degnan
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Shasha Zhang
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Darpandeep Aulakh
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Ketleine Georges
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Bhupinder Sandhu
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Yeheng Zhu
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Sarah C Traeger
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Peter T Cheng
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Bruce A Ellsworth
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Alicia Regueiro-Ren
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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14
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Wu D, Yang K, Zhang Z, Feng Y, Rao L, Chen X, Yu G. Metal-free bioorthogonal click chemistry in cancer theranostics. Chem Soc Rev 2022; 51:1336-1376. [PMID: 35050284 DOI: 10.1039/d1cs00451d] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry is a powerful tool to site-specifically activate drugs in living systems. Bioorthogonal reactions between a pair of biologically reactive groups can rapidly and specifically take place in a mild physiological milieu without perturbing inherent biochemical processes. Attributed to their high selectivity and efficiency, bioorthogonal reactions can significantly decrease background signals in bioimaging. Compared with metal-catalyzed bioorthogonal click reactions, metal-free click reactions are more biocompatible without the metal catalyst-induced cytotoxicity. Although a great number of bioorthogonal chemistry-based strategies have been reported for cancer theranostics, a comprehensive review is scarce to highlight the advantages of these strategies. In this review, recent progress in cancer theranostics guided by metal-free bioorthogonal click chemistry will be depicted in detail. The elaborate design as well as the advantages of bioorthogonal chemistry in tumor theranostics are summarized and future prospects in this emerging field are emphasized.
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Affiliation(s)
- Dan Wu
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China.
| | - Kuikun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Zhankui Zhang
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China.
| | - Yunxuan Feng
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Lang Rao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, P. R. China.
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 117597, Singapore.
| | - Guocan Yu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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15
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Meineke B, Heimgärtner J, Craig AJ, Landreh M, Moodie LWK, Elsässer SJ. A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling. Front Chem 2021; 9:768535. [PMID: 34858945 PMCID: PMC8632528 DOI: 10.3389/fchem.2021.768535] [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: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Bioorthogonal chemistry allows rapid and highly selective reactivity in biological environments. The copper-catalyzed azide–alkyne cycloaddition (CuAAC) is a classic bioorthogonal reaction routinely used to modify azides or alkynes that have been introduced into biomolecules. Amber suppression is an efficient method for incorporating such chemical handles into proteins on the ribosome, in which noncanonical amino acids (ncAAs) are site specifically introduced into the polypeptide in response to an amber (UAG) stop codon. A variety of ncAA structures containing azides or alkynes have been proven useful for performing CuAAC chemistry on proteins. To improve CuAAC efficiency, biologically incorporated alkyne groups can be reacted with azide substrates that contain copper-chelating groups. However, the direct incorporation of copper-chelating azides into proteins has not been explored. To remedy this, we prepared the ncAA paz-lysine (PazK), which contains a picolyl azide motif. We show that PazK is efficiently incorporated into proteins by amber suppression in mammalian cells. Furthermore, PazK-labeled proteins show improved reactivity with alkyne reagents in CuAAC.
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Affiliation(s)
- Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Alexander J Craig
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lindon W K Moodie
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden.,Uppsala Antibiotic Centre, Uppsala University, Uppsala, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
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16
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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17
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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18
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Alamudi SH, Liu X, Chang YT. Azide-based bioorthogonal chemistry: Reactions and its advances in cellular and biomolecular imaging. BIOPHYSICS REVIEWS 2021; 2:021301. [PMID: 38505123 PMCID: PMC10903415 DOI: 10.1063/5.0050850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/29/2021] [Indexed: 03/21/2024]
Abstract
Since the term "bioorthogonal" was first demonstrated in 2003, new tools for bioorthogonal chemistry have been rapidly developed. Bioorthogonal chemistry has now been widely utilized for applications in imaging various biomolecules, such as proteins, glycoconjugates, nucleic acids, and lipids. Contrasting the chemical reactions or synthesis that are typically executed in vitro with organic solvents, bioorthogonal reactions can occur inside cells under physiological conditions. Functional groups or chemical reporters for bioorthogonal chemistry are highly selective and will not perturb the native functions of biological systems. Advances in azide-based bioorthogonal chemical reporters make it possible to perform chemical reactions in living systems for wide-ranging applications. This review discusses the milestones of azide-based bioorthogonal reactions, from Staudinger ligation and copper(I)-catalyzed azide-alkyne cycloaddition to strain-promoted azide-alkyne cycloaddition. The development of bioorthogonal reporters and their capability of being built into biomolecules in vivo have been extensively applied in cellular imaging. We focus on strategies used for metabolic incorporation of chemically tagged molecular building blocks (e.g., amino acids, carbohydrates, nucleotides, and lipids) into cells via cellular machinery systems. With the aid of exogenous bioorthogonally compatible small fluorescent probes, we can selectively visualize intracellular architectures, such as protein, glycans, nucleic acids, and lipids, with high specificity to help in answering complex biological problems.
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Affiliation(s)
- Samira Husen Alamudi
- Institute of Bioengineering and Nanotechnology, Agency for Science, Technology and Research (ASTAR), 31 Biopolis Way, #07‐01, Singapore 138669
| | - Xiao Liu
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, South Korea
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19
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Welling MM, Duszenko N, van Willigen DM, Hensbergen AW, Buckle T, Rietbergen DDD, Roestenberg M, van Leeuwen FWB. Interventional nuclear medicine: "click" chemistry as an in vivo targeting strategy for imaging microspheres and bacteria. Biomater Sci 2021; 9:1683-1690. [PMID: 33410436 DOI: 10.1039/d0bm01823f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIM Pre-targeting is a proven strategy for in vivo delivery of a diagnostic or therapeutic payload. The pre-targeting concept can be realized through various conjugation strategies, one of which is based on copper-free "click" chemistry. Copper-free click reactions have shown in vivo potential for imaging and radionuclide therapy, but this conjugation strategy has not yet been explored in combination with microspheres or unicellular organisms. This study aims to evaluate the in vivo efficacy of strain-promoted azide-alkyne cycloaddition (SPAAC) reactions to achieve imaging and targeting of azide-functionalized macro-aggregated albumin (MAA) microspheres and Staphylococcus aureus bacteria. METHODS MAA microspheres (diameter 10-90 μm) were functionalized with a biorthogonal Cy5 fluorophore, bearing an azide functionality (N3), to generate MAA-Cy5-N3. S. aureus (diameter ∼1 μm) were functionalized with 99mTc-UBI29-41-Cy5-N3, generating S. aureus-99mTc-UBI29-41-Cy5-N3. In situ and in vitro click conjugation on the -N3 moieties was studied for 20 h using a radioactivity-based assay and fluorescence microscopy. For in vivo validation, both primary entities, radiolabeled with 99mTc, were deposited into the microvasculature of the liver via intrasplenic injections. Secondary targeting was realized following the intravenous administration of indium-111-radiolabeled diethylenetriaminepentaacetic acid-dibenzocyclooctyne (111In-DTPA-DBCO). To assess click reaction efficiency in vivo, 99mTc and 111In-biodistributions were measured (SPECT and %ID g-1). Use of 111In-DTPA-DBCO in mice without MAA deposits or mice infected with non-functionalized S. aureus served as controls. Ex vivo confocal fluorescence imaging was carried out in excised tissues to confirm the presence of functionalized MAA and bacteria. RESULTS In vitro data confirmed effective click reactions on both the MAA particles and the bacterial membrane. SPECT imaging and biodistribution studies revealed significantly (p < 0.05) increased accumulation of 111In-DTPA-DBCO at the sites where MAA-Cy5-N3 (7.5 ± 1.5%ID g-1vs. 3.5 ± 0.5%ID g-1 in control mice) and S. aureus-99mTc-UBI29-41-Cy5-N3 (9.3 ± 1.3%ID g-1vs. 6.0 ± 0.5%ID g-1 in control mice) resided. Ex vivo fluorescence imaging confirmed the presence of either functionalized MAA or S. aureus in excised spleens and livers of mice. CONCLUSION Copper-free click chemistry between a DBCO moiety and Cy5-N3-functionalized microspheres or bacterial entities in the liver can be used to realize in vivo imaging and targeting.
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Affiliation(s)
- M M Welling
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands.
| | - N Duszenko
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands. and Departments of Parasitology and Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - D M van Willigen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands.
| | - A W Hensbergen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands.
| | - T Buckle
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands.
| | - D D D Rietbergen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands. and Section of Nuclear Medicine, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - M Roestenberg
- Departments of Parasitology and Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - F W B van Leeuwen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, Netherlands.
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20
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Li K, Fong D, Meichsner E, Adronov A. A Survey of Strain-Promoted Azide-Alkyne Cycloaddition in Polymer Chemistry. Chemistry 2021; 27:5057-5073. [PMID: 33017499 DOI: 10.1002/chem.202003386] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Indexed: 02/06/2023]
Abstract
Highly efficient reactions that enable the assembly of molecules into complex structures have driven extensive progress in synthetic chemistry. In particular, reactions that occur under mild conditions and in benign solvents, while producing no by-products and rapidly reach completion are attracting significant attention. Amongst these, the strain-promoted azide-alkyne cycloaddition, involving various cyclooctyne derivatives reacting with azide-bearing molecules, has gained extensive popularity in organic synthesis and bioorthogonal chemistry. This reaction has also recently gained momentum in polymer chemistry, where it has been used to decorate, link, crosslink, and even prepare polymer chains. This survey highlights key achievements in the use of this reaction to produce a variety of polymeric constructs for disparate applications.
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Affiliation(s)
- Kelvin Li
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4M1, Canada
| | - Darryl Fong
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4M1, Canada
| | - Eric Meichsner
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4M1, Canada
| | - Alex Adronov
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4M1, Canada
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21
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Evans HT, Blackmore D, Götz J, Bodea LG. De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory. Brain Res Bull 2021; 169:94-103. [PMID: 33465403 DOI: 10.1016/j.brainresbull.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023]
Abstract
Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Daniel Blackmore
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
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22
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Ganz D, Harijan D, Wagenknecht HA. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. RSC Chem Biol 2020; 1:86-97. [PMID: 34458750 PMCID: PMC8341813 DOI: 10.1039/d0cb00047g] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Dennis Harijan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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23
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Luo W, Legge SM, Luo J, Lagugné-Labarthet F, Workentin MS. Investigation of Au SAMs Photoclick Derivatization by PM-IRRAS. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1014-1022. [PMID: 31922420 DOI: 10.1021/acs.langmuir.9b03782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, we present a clean one-step process for modifying headgroups of self-assembled monolayers (SAMs) on gold using photo-enabled click chemistry. A thiolated, cyclopropenone-caged strained alkyne precursor was first functionalized onto a flat gold substrate through self-assembly. Exposure of the cyclopropenone SAM to UVA light initiated the efficient photochemical decarbonylation of the cyclopropenone moiety, revealing the strained alkyne capable of undergoing the interfacial strain-promoted alkyne-azide cycloaddition (SPAAC). Irradiated SAMs were derivatized with a series of model azides with varied hydrophobicity to demonstrate the generality of this chemical system for the modification and fine-tuning of the surface chemistry on gold substrates. SAMs were characterized at each step with polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) to confirm the successful functionalization and reactivity. Furthermore, to showcase the compatibility of this approach with biochemical applications, cyclopropenone SAMs were irradiated and modified with azide-bearing cell adhesion peptides to promote human fibroblast cell adhesion, and then imaged by live-cell fluorescence microscopy. Thus, the "photoclick" methodology reported here represents an improved, versatile, catalyst-free protocol that allows for a high degree of control over the modification of material surfaces, with applicability in materials science as well as biochemistry.
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Affiliation(s)
- Wilson Luo
- Department of Chemistry and the Centre for Materials and Biomaterials Research , Western University , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Sydney M Legge
- Department of Chemistry and the Centre for Materials and Biomaterials Research , Western University , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Johnny Luo
- Department of Biochemistry , Western University , London , Ontario N6A 5C1 , Canada
- Lawson Health Research Institute , London , Ontario N6C 2R5 , Canada
| | - François Lagugné-Labarthet
- Department of Chemistry and the Centre for Materials and Biomaterials Research , Western University , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
| | - Mark S Workentin
- Department of Chemistry and the Centre for Materials and Biomaterials Research , Western University , 1151 Richmond Street , London , Ontario N6A 5B7 , Canada
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24
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Evans HT, Bodea LG, Götz J. Cell-specific non-canonical amino acid labelling identifies changes in the de novo proteome during memory formation. eLife 2020; 9:e52990. [PMID: 31904341 PMCID: PMC6944461 DOI: 10.7554/elife.52990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022] Open
Abstract
The formation of spatial long-term memory (LTM) requires the de novo synthesis of distinct sets of proteins; however, a non-biased examination of the de novo proteome in this process is lacking. Here, we generated a novel mouse strain, which enables cell-type-specific labelling of newly synthesised proteins with non-canonical amino acids (NCAAs) by genetically restricting the expression of the mutant tRNA synthetase, NLL-MetRS, to hippocampal neurons. By combining this labelling technique with an accelerated version of the active place avoidance task and bio-orthogonal non-canonical amino acid tagging (BONCAT) followed by SWATH quantitative mass spectrometry, we identified 156 proteins that were altered in synthesis in hippocampal neurons during spatial memory formation. In addition to observing increased synthesis of known proteins important in memory-related processes, such as glutamate receptor recycling, we also identified altered synthesis of proteins associated with mRNA splicing as a potential mechanism involved in spatial LTM formation.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
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25
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Gupta K, Toombes GE, Swartz KJ. Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis. eLife 2019; 8:50776. [PMID: 31714877 PMCID: PMC6850778 DOI: 10.7554/elife.50776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells. Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins. Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins. Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein. This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
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Anhäuser L, Hüwel S, Zobel T, Rentmeister A. Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells. Nucleic Acids Res 2019; 47:e42. [PMID: 30726958 PMCID: PMC6468298 DOI: 10.1093/nar/gkz084] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
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Affiliation(s)
- Lea Anhäuser
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Thomas Zobel
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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28
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Serwa RA, Sekine E, Brown J, Teo SHC, Tate EW, O’Hare P. Analysis of a fully infectious bio-orthogonally modified human virus reveals novel features of virus cell entry. PLoS Pathog 2019; 15:e1007956. [PMID: 31589653 PMCID: PMC6797222 DOI: 10.1371/journal.ppat.1007956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/17/2019] [Accepted: 09/12/2019] [Indexed: 12/28/2022] Open
Abstract
We report the analysis of a complex enveloped human virus, herpes simplex virus (HSV), assembled after in vivo incorporation of bio-orthogonal methionine analogues homopropargylglycine (HPG) or azidohomoalanine (AHA). We optimised protocols for the production of virions incorporating AHA (termed HSVAHA), identifying conditions which resulted in normal yields of HSV and normal particle/pfu ratios. Moreover we show that essentially every single HSVAHA capsid-containing particle was detectable at the individual particle level by chemical ligation of azide-linked fluorochromes to AHA-containing structural proteins. This was a completely specific chemical ligation, with no capsids assembled under normal methionine-containing conditions detected in parallel. We demonstrate by quantitative mass spectrometric analysis that HSVAHA virions exhibit no qualitative or quantitative differences in the repertoires of structural proteins compared to virions assembled under normal conditions. Individual proteins and AHA incorporation sites were identified in capsid, tegument and envelope compartments, including major essential structural proteins. Finally we reveal novel aspects of entry pathways using HSVAHA and chemical fluorochrome ligation that were not apparent from conventional immunofluorescence. Since ligation targets total AHA-containing protein and peptides, our results demonstrate the presence of abundant AHA-labelled products in cytoplasmic macrodomains and tubules which no longer contain intact particles detectable by immunofluorescence. Although these do not co-localise with lysosomal markers, we propose they may represent sites of proteolytic virion processing. Analysis of HSVAHA also enabled the discrimination from primary entering from secondary assembling virions, demonstrating assembly and second round infection within 6 hrs of initial infection and dual infections of primary and secondary virus in spatially restricted cytoplasmic areas of the same cell. Together with other demonstrated applications e.g., in genome biology, lipid and protein trafficking, this work further exemplifies the utility and potential of bio-orthogonal chemistry for studies in many aspects of virus-host interactions.
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Affiliation(s)
- Remigiusz A. Serwa
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, London, United Kingdom
| | - Eiki Sekine
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jonathan Brown
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Su Hui Catherine Teo
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
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Prasher P, Sharma M. Tailored therapeutics based on 1,2,3-1 H-triazoles: a mini review. MEDCHEMCOMM 2019; 10:1302-1328. [PMID: 31534652 PMCID: PMC6748286 DOI: 10.1039/c9md00218a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Contemporary drug discovery approaches rely on library synthesis coupled with combinatorial methods and high-throughput screening to identify leads. However, due to the multitude of components involved, a majority of optimization techniques face persistent challenges related to the efficiency of synthetic processes and the purity of compound libraries. These methods have recently found an upgradation as fragment-based approaches for target-guided synthesis of lead molecules with active involvement of their biological target. The click chemistry approach serves as a promising tool for tailoring the therapeutically relevant biomolecules of interest, improving their bioavailability and bioactivity and redirecting them as efficacious drugs. 1,2,3-1H-Triazole nucleus, being a planar and biologically acceptable scaffold, plays a crucial role in the design of biomolecular mimetics and tailor-made molecules with therapeutic relevance. This versatile scaffold also forms an integral part of the current fragment-based approaches for drug design, kinetic target guided synthesis and bioorthogonal methodologies.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
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30
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Evans HT, Benetatos J, van Roijen M, Bodea L, Götz J. Decreased synthesis of ribosomal proteins in tauopathy revealed by non-canonical amino acid labelling. EMBO J 2019; 38:e101174. [PMID: 31268600 PMCID: PMC6600635 DOI: 10.15252/embj.2018101174] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
Tau is a scaffolding protein that serves multiple cellular functions that are perturbed in neurodegenerative diseases, including Alzheimer's disease (AD) and frontotemporal dementia (FTD). We have recently shown that amyloid-β, the second hallmark of AD, induces de novo protein synthesis of tau. Importantly, this activation was found to be tau-dependent, raising the question of whether FTD-tau by itself affects protein synthesis. We therefore applied non-canonical amino acid labelling to visualise and identify newly synthesised proteins in the K369I tau transgenic K3 mouse model of FTD. This revealed massively decreased protein synthesis in neurons containing pathologically phosphorylated tau, a finding confirmed in P301L mutant tau transgenic rTg4510 mice. Using quantitative SWATH-MS proteomics, we identified changes in 247 proteins of the de novo proteome of K3 mice. These included decreased synthesis of the ribosomal proteins RPL23, RPLP0, RPL19 and RPS16, a finding that was validated in both K3 and rTg4510 mice. Together, our findings present a potential pathomechanism by which pathological tau interferes with cellular functions through the dysregulation of ribosomal protein synthesis.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Joseph Benetatos
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | | | - Liviu‐Gabriel Bodea
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
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31
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Cheng MSQ, Su MXX, Wang MXN, Sun MZY, Ou TM. Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions. Methods 2019; 167:124-133. [PMID: 31185274 DOI: 10.1016/j.ymeth.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.
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Affiliation(s)
- Miss Sui-Qi Cheng
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Xiao-Xuan Su
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China.
| | - Miss Xiao-Na Wang
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Zhi-Yin Sun
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Tian-Miao Ou
- Sun Yat-Sen University, School of Pharmaceutical Sciences, 132 Waihuan East Road, Guangzhou University City, Guangzhou, Guangdong, China.
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32
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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33
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF-Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019; 58:6987-6992. [PMID: 30888728 DOI: 10.1002/anie.201901760] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Indexed: 01/05/2023]
Abstract
As a typical bioorthogonal reaction, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) has been used for drug design and synthesis. However, for localized drug synthesis, it is important to be able to determine where the CuAAC reaction occurs in living cells. In this study, we constructed a heterogeneous copper catalyst on a metal-organic framework that could preferentially accumulate in the mitochondria of living cells. Our system enabled the localized synthesis of drugs through a site-specific CuAAC reaction in mitochondria with good biocompatibility. Importantly, the subcellular catalytic process for localized drug synthesis avoided the problems of the delivery and distribution of toxic molecules. In vivo tumor therapy experiments indicated that the localized synthesis of resveratrol-derived drugs led to greater antitumor efficacy and minimized side effects usually associated with drug delivery and distribution.
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Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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34
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF–Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901760] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
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35
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Szymczak LC, Mrksich M. Using Peptide Arrays To Discover the Sequence-Specific Acetylation of the Histidine-Tyrosine Dyad. Biochemistry 2019; 58:1810-1817. [PMID: 30817132 DOI: 10.1021/acs.biochem.9b00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions that can selectively modify amino acid sequences within peptides and proteins are important for preparing protein reagents, immobilizing proteins, and making antibody-drug conjugates. The development of new reactions often begins with known chemistries and optimizes yields using a small set of peptide reactants. This article describes the use of peptide arrays and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to discover and characterize unanticipated sequence-selective reactions of peptides. This work reports the selective acetylation of HY (histidine-tyrosine) and YH (tyrosine-histidine) dyads when treated with acetic anhydride in aqueous conditions. More broadly, this example illustrates the benefits of using peptide arrays and a label-free analysis method to discover peptide-modifying reactions and gain mechanistic insight into their sequence specificity.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Milan Mrksich
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Biomedical Engineering , Northwestern University , Evanston , Illinois 60208 , United States
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36
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Shi Y, Meng X, Yang H, Song L, Liu S, Xu A, Chen Z, Huang W, Zhao Q. Lysosome-specific sensing and imaging of pH variations in vitro and in vivo utilizing a near-infrared boron complex. J Mater Chem B 2019. [DOI: 10.1039/c8tb03353f] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A NIR lysosome-targeting boron complex has been developed based on hemicyanine for monitoring pH variations in vitro and in vivo.
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Affiliation(s)
- Yuxiang Shi
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Xiangchun Meng
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Huiran Yang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Linna Song
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Shujuan Liu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Aqiang Xu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Zejing Chen
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
| | - Qiang Zhao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
- P. R. China
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37
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Yoshida S. Controlled Reactive Intermediates Enabling Facile Molecular Conjugation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180104] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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38
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Silantyeva EA, Nasir W, Carpenter J, Manahan O, Becker ML, Willits RK. Accelerated neural differentiation of mouse embryonic stem cells on aligned GYIGSR-functionalized nanofibers. Acta Biomater 2018; 75:129-139. [PMID: 29879551 PMCID: PMC6774047 DOI: 10.1016/j.actbio.2018.05.052] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/09/2022]
Abstract
Substrates for embryonic stem cell culture are typified by poorly defined xenogenic, whole proteins or cellular components that are difficult and expensive to generate, characterize, and recapitulate. Herein, the generation of well-defined scaffolds of Gly-Tyr-Ile-Gly-Ser-Arg (GYIGSR) peptide-functionalized poly(ε-caprolactone) (PCL) aligned nanofibers are used to accelerate the neural lineage commitment and differentiation of D3 mouse embryonic stem cells (mESCs). Gene expression trends and immunocytochemistry analysis were similar to laminin-coated glass, and indicated an earlier differentiation progression than D3 mESCs on laminin. Further, GYIGSR-functionalized nanofiber substrates yielded an increased gene expression of Sox1, a neural progenitor cell marker, and Tubb3, Cdh2, Syp, neuronal cell markers, at early time points. In addition, guidance of neurites was found to parallel the fiber direction. We demonstrate the fabrication of a well-defined, xeno-free functional nanofiber scaffold and demonstrates its use as a surrogate for xenogenic and complex matrixes currently used for the neural differentiation of stem cells ex vivo. STATEMENT OF SIGNIFICANCE In this paper, we report the use of GYIGSR-functionalized poly(ε-caprolactone) aligned nanofibers as a tool to accelerate the neural lineage commitment and differentiation of D3 mouse embryonic stem cells. The results indicate that functional nanofiber substrates promote faster differentiation than laminin coated substrates. The data suggest that aligned nanofibers and post-electrospinning surface modification with bioactive species can be combined to produce translationally relevant xeno-free substrates for stem cell therapy. Future development efforts are focused on additional bioactive species that are able to function as surrogates for other xenogenic factors found in differentiation media.
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Affiliation(s)
- Elena A Silantyeva
- Department of Polymer Science, The University of Akron, Akron, OH 44325, United States
| | - Wafaa Nasir
- Biomedical Engineering, The University of Akron, Akron, OH 44325, United States
| | | | - Olivia Manahan
- Department of Polymer Science, The University of Akron, Akron, OH 44325, United States
| | - Matthew L Becker
- Department of Polymer Science, The University of Akron, Akron, OH 44325, United States; Biomedical Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Rebecca K Willits
- Biomedical Engineering, The University of Akron, Akron, OH 44325, United States
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39
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Teo CSH, O’Hare P. A bimodal switch in global protein translation coupled to eIF4H relocalisation during advancing cell-cell transmission of herpes simplex virus. PLoS Pathog 2018; 14:e1007196. [PMID: 30028874 PMCID: PMC6070287 DOI: 10.1371/journal.ppat.1007196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/01/2018] [Accepted: 07/02/2018] [Indexed: 12/28/2022] Open
Abstract
We used the bioorthogonal protein precursor, homopropargylglycine (HPG) and chemical ligation to fluorescent capture agents, to define spatiotemporal regulation of global translation during herpes simplex virus (HSV) cell-to-cell spread at single cell resolution. Translational activity was spatially stratified during advancing infection, with distal uninfected cells showing normal levels of translation, surrounding zones at the earliest stages of infection with profound global shutoff. These cells further surround previously infected cells with restored translation close to levels in uninfected cells, reflecting a very early biphasic switch in translational control. While this process was dependent on the virion host shutoff (vhs) function, in certain cell types we also observed temporally altered efficiency of shutoff whereby during early transmission, naïve cells initially exhibited resistance to shutoff but as infection advanced, naïve target cells succumbed to more extensive translational suppression. This may reflect spatiotemporal variation in the balance of oscillating suppression-recovery phases. Our results also strongly indicate that a single particle of HSV-2, can promote pronounced global shutoff. We also demonstrate that the vhs interacting factor, eIF4H, an RNA helicase accessory factor, switches from cytoplasmic to nuclear localisation precisely correlating with the initial shutdown of translation. However translational recovery occurs despite sustained eIF4H nuclear accumulation, indicating a qualitative change in the translational apparatus before and after suppression. Modelling simulations of high multiplicity infection reveal limitations in assessing translational activity due to sampling frequency in population studies and how analysis at the single cell level overcomes such limitations. The work reveals new insight and a revised model of translational manipulation during advancing infection which has important implications both mechanistically and with regards to the physiological role of translational control during virus propagation. The work also demonstrates the potential of bioorthogonal chemistry for single cell analysis of cellular metabolic processes during advancing infections in other virus systems.
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Affiliation(s)
- Catherine Su Hui Teo
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, London, United Kingdom
| | - Peter O’Hare
- Section of Virology, Faculty of Medicine, Imperial College London, St Mary’s Medical School, London, United Kingdom
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40
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Bakkum T, van Leeuwen T, Sarris AJC, van Elsland DM, Poulcharidis D, Overkleeft HS, van Kasteren SI. Quantification of Bioorthogonal Stability in Immune Phagocytes Using Flow Cytometry Reveals Rapid Degradation of Strained Alkynes. ACS Chem Biol 2018; 13:1173-1179. [PMID: 29693370 PMCID: PMC5962927 DOI: 10.1021/acschembio.8b00355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
One of the areas
in which bioorthogonal chemistry—chemistry
performed inside a cell or organism—has become of pivotal importance
is in the study of host–pathogen interactions. The incorporation
of bioorthogonal groups into the cell wall or proteome of intracellular
pathogens has allowed study within the endolysosomal system. However,
for the approach to be successful, the incorporated bioorthogonal
groups must be stable to chemical conditions found within these organelles,
which are some of the harshest found in metazoans: the groups are
exposed to oxidizing species, acidic conditions, and reactive thiols.
Here we present an assay that allows the assessment of the stability
of bioorthogonal groups within host cell phagosomes. Using a flow
cytometry-based assay, we have quantified the relative label stability
inside dendritic cell phagosomes of strained and unstrained alkynes.
We show that groups that were shown to be stable in other systems
were degraded by as much as 79% after maturation of the phagosome.
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Affiliation(s)
- Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daphne M. van Elsland
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dimitrios Poulcharidis
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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41
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Iyer S, Le D, Park BR, Kim M. Distinct mechanisms coordinate transcription and translation under carbon and nitrogen starvation in Escherichia coli. Nat Microbiol 2018; 3:741-748. [PMID: 29760462 DOI: 10.1038/s41564-018-0161-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 04/16/2018] [Indexed: 11/09/2022]
Abstract
Bacteria adapt to environmental stress by producing proteins that provide stress protection. However, stress can severely perturb the kinetics of gene expression, disrupting protein production. Here, we characterized how Escherichia coli mitigates such perturbations under nutrient stress through the kinetic coordination of transcription and translation. We observed that, when translation became limiting under nitrogen starvation, transcription elongation slowed accordingly. This slowdown was mediated by (p)ppGpp, the alarmone whose primary role is thought to be promoter regulation. This kinetic coordination by (p)ppGpp was critical for the robust synthesis of gene products. Surprisingly, under carbon starvation, (p)ppGpp was dispensable for robust synthesis. Characterization of the underlying kinetics revealed that under carbon starvation, transcription became limiting, and translation aided transcription elongation. This mechanism naturally coordinated transcription with translation, alleviating the need for (p)ppGpp as a mediator. These contrasting mechanisms for coordination resulted in the condition-dependent effects of (p)ppGpp on global protein synthesis and starvation survival. Our findings reveal a kinetic aspect of gene expression plasticity, establishing (p)ppGpp as a condition-dependent global effector of gene expression.
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Affiliation(s)
- Sukanya Iyer
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Dai Le
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Bo Ryoung Park
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, USA. .,Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA. .,Emory Antibiotic Resistance Center, Emory University, Atlanta, GA, USA.
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42
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Umlauf BJ, Mix KA, Grosskopf VA, Raines RT, Shusta EV. Site-Specific Antibody Functionalization Using Tetrazine-Styrene Cycloaddition. Bioconjug Chem 2018; 29:1605-1613. [PMID: 29694034 DOI: 10.1021/acs.bioconjchem.8b00114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biologics, such as antibody-drug conjugates, are becoming mainstream therapeutics. Consequently, methods to functionalize biologics without disrupting their native properties are essential for identifying, characterizing, and translating candidate biologics from the bench to clinical practice. Here, we present a method for site-specific, carboxy-terminal modification of single-chain antibody fragments (scFvs). ScFvs displayed on the surface of yeast were isolated and functionalized by combining intein-mediated expressed protein ligation (EPL) with inverse electron-demand Diels-Alder (IEDDA) cycloaddition using a styrene-tetrazine pair. The high thiol concentration required to trigger EPL can hinder the subsequent chemoselective ligation reactions; therefore, the EPL reaction was used to append styrene to the scFv, limiting tetrazine exposure to damaging thiols. Subsequently, the styrene-functionalized scFv was reacted with tetrazine-conjugated compounds in an IEDDA cycloaddition to generate functionalized scFvs that retain their native binding activity. Rapid functionalization of yeast surface-derived scFv in a site-directed manner could find utility in many downstream laboratory and preclinical applications.
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43
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Schmitt MA, Biddle W, Fisk JD. Mapping the Plasticity of the Escherichia coli Genetic Code with Orthogonal Pair-Directed Sense Codon Reassignment. Biochemistry 2018; 57:2762-2774. [PMID: 29668270 DOI: 10.1021/acs.biochem.8b00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in Escherichia coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8 to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.
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Affiliation(s)
- Margaret A Schmitt
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Wil Biddle
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - John D Fisk
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,School of Biomedical Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
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44
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site-Selective Cysteine-Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018; 57:6459-6463. [PMID: 29575377 DOI: 10.1002/anie.201800860] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2018] [Indexed: 11/06/2022]
Abstract
We report a site-selective cysteine-cyclooctyne conjugation reaction between a seven-residue peptide tag (DBCO-tag, Leu-Cys-Tyr-Pro-Trp-Val-Tyr) at the N or C terminus of a peptide or protein and various aza-dibenzocyclooctyne (DBCO) reagents. Compared to a cysteine peptide control, the DBCO-tag increases the rate of the thiol-yne reaction 220-fold, thereby enabling selective conjugation of DBCO-tag to DBCO-linked fluorescent probes, affinity tags, and cytotoxic drug molecules. Fusion of DBCO-tag with the protein of interest enables regioselective cysteine modification on proteins that contain multiple endogenous cysteines; these examples include green fluorescent protein and the antibody trastuzumab. This study demonstrates that short peptide tags can aid in accelerating bond-forming reactions that are often slow to non-existent in water.
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Affiliation(s)
- Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Alexander A Vinogradov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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45
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site‐Selective Cysteine–Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Chi Zhang
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Peng Dai
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Alexander A. Vinogradov
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Zachary P. Gates
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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46
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Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 655] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
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Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
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47
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Adelmund SM, Ruskowitz ER, Farahani PE, Wolfe JV, DeForest CA. Light-Activated Proteomic Labeling via Photocaged Bioorthogonal Non-Canonical Amino Acids. ACS Chem Biol 2018; 13:573-577. [PMID: 29419281 DOI: 10.1021/acschembio.7b01023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work introduces light-activated bioorthogonal noncanonical amino acid tagging (laBONCAT) as a method to selectively label, isolate, and identify proteins newly synthesized at user-defined regions in tissue culture. By photocaging l-azidohomoalanine (Aha), metabolic incorporation into proteins is prevented. The caged compound remains stable for many hours in culture, but can be photochemically liberated rapidly and on demand with spatial control. Upon directed light exposure, the uncaged amino acid is available for local translation, enabling downstream proteomic interrogation via bioorthogonal conjugation. Exploiting the reactive azide moiety present on Aha's amino acid side chain, we demonstrate that newly synthesized proteins can be purified for quantitative proteomics or visualized in synthetic tissues with a new level of spatiotemporal control. Shedding light on when and where proteins are translated within living samples, we anticipate that laBONCAT will aid in understanding the progression of complex protein-related disorders.
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Affiliation(s)
- Steven M. Adelmund
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Emily R. Ruskowitz
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Payam E. Farahani
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Julie V. Wolfe
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
| | - Cole A. DeForest
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, Washington 98195, United States
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, Washington 98105, United States
- Institute for Stem Cell & Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular Engineering & Sciences Institute, University of Washington, 3946 W Stevens Way NE, Seattle, Washington 98105, United States
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48
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Fong D, Yeung J, McNelles SA, Adronov A. Decoration of Polyfluorene-Wrapped Carbon Nanotubes via Strain-Promoted Azide–Alkyne Cycloaddition. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Darryl Fong
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S
4M1, Canada
| | - Jason Yeung
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S
4M1, Canada
| | - Stuart A. McNelles
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S
4M1, Canada
| | - Alex Adronov
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S
4M1, Canada
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49
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Moghaddam-Taaheri P, Karlsson AJ. Protein Labeling in Live Cells for Immunological Applications. Bioconjug Chem 2018; 29:680-685. [DOI: 10.1021/acs.bioconjchem.7b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Fong D, Andrews GM, Adronov A. Functionalization of polyfluorene-wrapped carbon nanotubes via copper-mediated azide–alkyne cycloaddition. Polym Chem 2018. [DOI: 10.1039/c8py00377g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Copper-mediated azide–alkyne cycloaddition enables quantitative functionalization of polymer-nanotube complexes containing azide moieties in the polymer side chains.
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Affiliation(s)
- Darryl Fong
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
| | | | - Alex Adronov
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
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