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Weigert Muñoz A, Zhao W, Sieber SA. Monitoring host-pathogen interactions using chemical proteomics. RSC Chem Biol 2024; 5:73-89. [PMID: 38333198 PMCID: PMC10849124 DOI: 10.1039/d3cb00135k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 02/10/2024] Open
Abstract
With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.
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Affiliation(s)
- Angela Weigert Muñoz
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University Shenzhen 518118 China
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Germany
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2
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Pelgrom LR, Davis GM, O'Shaughnessy S, Wezenberg EJM, Van Kasteren SI, Finlay DK, Sinclair LV. QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations. Cell Rep 2023; 42:112828. [PMID: 37478011 DOI: 10.1016/j.celrep.2023.112828] [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: 10/26/2022] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.
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Affiliation(s)
- Leonard R Pelgrom
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Gavin M Davis
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Simon O'Shaughnessy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Emilie J M Wezenberg
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander I Van Kasteren
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland.
| | - Linda V Sinclair
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
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van Kasteren S, Rozen DE. Using click chemistry to study microbial ecology and evolution. ISME COMMUNICATIONS 2023; 3:9. [PMID: 36721064 PMCID: PMC9889756 DOI: 10.1038/s43705-022-00205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.
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Affiliation(s)
- Sander van Kasteren
- Leiden Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden, 2300 RA, The Netherlands.
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2300 RA, The Netherlands.
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Qi YK, Tang X, Wei NN, Pang CJ, Du SS, Wang KW. Discovery, synthesis, and optimization of teixobactin, a novel antibiotic without detectable bacterial resistance. J Pept Sci 2022; 28:e3428. [PMID: 35610021 DOI: 10.1002/psc.3428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Discovering new antibiotics with novel chemical scaffolds and antibacterial mechanisms presents a challenge for medicinal scientists worldwide as the ever-increasing bacterial resistance poses a serious threat to human health. A new cyclic peptide-based antibiotic termed teixobactin was discovered from a screen of uncultured soil bacteria through iChip technology in 2015. Teixobactin exhibits excellent antibacterial activity against all the tested gram-positive pathogens and Mycobacterium tuberculosis, including drug-resistant strains. Given that teixobactin targets the highly conserved lipid II and lipid III, which induces the simultaneous inhibition of both peptidoglycan and teichoic acid synthesis, the emergence of resistance is considered to be rather difficult. The novel structure, potent antibacterial activity, and highly conservative targets make teixobactin a promising lead compound for further antibiotic development. This review provides a comprehensive treatise on the advances of teixobactin in the areas of discovery processes, antibacterial activity, mechanisms of action, chemical synthesis, and structural optimizations. The synthetic methods for the key building block l-allo-End, natural teixobactin, representative teixobactin analogues, as well as the structure-activity relationship studies will be highlighted and discussed in details. Finally, some insights into new trends for the generation of novel teixobactin analogues and tips for future work and directions will be commented.
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Affiliation(s)
- Yun-Kun Qi
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China.,State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaowen Tang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Ning-Ning Wei
- Institute of Innovative Drugs, Qingdao University, Qingdao, China
| | - Cheng-Jian Pang
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shan-Shan Du
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Ke Wei Wang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China
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Kong Y, Du Q, Li J, Xing H. Engineering bacterial surface interactions using DNA as a programmable material. Chem Commun (Camb) 2022; 58:3086-3100. [PMID: 35077527 DOI: 10.1039/d1cc06138k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.
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Affiliation(s)
- Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Qi Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Juan Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
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Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, United States
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, United States
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Greco V, Sciuto S, Rizzarelli E. Mono- and dialdehyde of trehalose: new synthons to prepare trehalose bio-conjugates. Org Biomol Chem 2021; 19:9427-9432. [PMID: 34668911 DOI: 10.1039/d1ob01816g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trehalose, a non-reducing disaccharide of glucose, is a natural bioactive and non-toxic sugar. It is found in many organisms that synthesise it when their cells are exposed to stress conditions. While not produced by mammalian cells, this disaccharide and also some of its derivatives have been shown to have a number of interesting properties that indicate their importance in the treatment of certain human diseases. Differentiating the two glucosyl moieties in the trehalose molecule has often been a synthetic challenge. We report here an easy way to obtain the monoaldehyde of trehalose, as well as the relevant symmetrical dialdehyde. The reactivity of the aldehyde functionalities involved in the molecular structure of these synthons allows the easy preparation of the corresponding amino or carboxy derivatives of trehalose, as well the synthesis of some new trehalose conjugates useful for diagnostic or therapeutic purposes.
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Affiliation(s)
- Valentina Greco
- Department of Chemical Sciences, University of Catania, viale A. Doria 6, 95125, Catania, Italy.
| | - Sebastiano Sciuto
- Department of Chemical Sciences, University of Catania, viale A. Doria 6, 95125, Catania, Italy.
| | - Enrico Rizzarelli
- Department of Chemical Sciences, University of Catania, viale A. Doria 6, 95125, Catania, Italy. .,Institute of Crystallography, CNR, P. Gaifami 18, 95126 Catania, Italy
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