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Vardaki MZ, Gregoriou VG, Chochos CL. Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window. RSC Chem Biol 2024; 5:273-292. [PMID: 38576725 PMCID: PMC10989507 DOI: 10.1039/d3cb00217a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024] Open
Abstract
Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.
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Affiliation(s)
- Martha Z Vardaki
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
| | - Vasilis G Gregoriou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
| | - Christos L Chochos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
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Ravindra MP, Lee M, Dimova S, Steven CF, Bluntzer MTJ, Brunton VG, Hulme AN. Stretching the Bisalkyne Raman Spectral Palette Reveals a New Electrophilic Covalent Motif. Chemistry 2023; 29:e202300953. [PMID: 37014262 PMCID: PMC10946950 DOI: 10.1002/chem.202300953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/05/2023]
Abstract
Small heteroaryl-diyne (Het-DY) tags with distinct vibrational frequencies, and physiologically relevant cLog P were designed for multiplexed bioorthogonal Raman imaging. Pd-Cu catalyzed coupling, combined with the use of Lei ligand, was shown to improve overall yields of the desired heterocoupled Het-DY tags, minimizing the production of homocoupled side-products. Spectral data were in agreement with the trends predicted by DFT calculations and systematic introduction of electron- rich/poor rings stretched the frequency limit of aryl-capped diynes (2209-2243 cm-1 ). The improved Log P of these Het-DY tags was evident from their diffuse distribution in cellular uptake studies and functionalizing tags with organelle markers allowed the acquisition of location-specific biological images. LC-MS- and NMR-based assays showed that some heteroaryl-capped internal alkynes are potential nucleophile traps with structure-dependent reactivity. These biocompatible Het-DY tags, equipped with covalent reactivity, open up new avenues for Raman bioorthogonal imaging.
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Affiliation(s)
- Manasa Punaha Ravindra
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Martin Lee
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Silviya Dimova
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Craig F. Steven
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Marie T. J. Bluntzer
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Valerie G. Brunton
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Alison N. Hulme
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
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Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases. Int J Mol Sci 2023; 24:ijms24032384. [PMID: 36768712 PMCID: PMC9917237 DOI: 10.3390/ijms24032384] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.
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Dodo K, Fujita K, Sodeoka M. Raman Spectroscopy for Chemical Biology Research. J Am Chem Soc 2022; 144:19651-19667. [PMID: 36216344 PMCID: PMC9635364 DOI: 10.1021/jacs.2c05359] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Indexed: 11/29/2022]
Abstract
In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.
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Affiliation(s)
- Kosuke Dodo
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumasa Fujita
- Department
of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute
for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- AIST-Osaka
University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science
and Technology (AIST), Suita, Osaka 565-0871, Japan
| | - Mikiko Sodeoka
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Bakthavatsalam S, Dodo K, Sodeoka M. A decade of alkyne-tag Raman imaging (ATRI): applications in biological systems. RSC Chem Biol 2021; 2:1415-1429. [PMID: 34704046 PMCID: PMC8496067 DOI: 10.1039/d1cb00116g] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
Alkyne functional groups have Raman signatures in a region (1800 cm-1 to 2800 cm-1) that is free from interference from cell components, known as the "silent region", and alkyne signals in this region were first utilized a decade ago to visualize the nuclear localization of a thymidine analogue EdU. Since then, the strategy of Raman imaging of biological samples by using alkyne functional groups, called alkyne-tag Raman imaging (ATRI), has become widely used. This article reviews the applications of ATRI in biological samples ranging from organelles to whole animal models, and briefly discusses the prospects for this technique.
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Affiliation(s)
- Subha Bakthavatsalam
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
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Fink J, Schumacher F, Schlegel J, Stenzel P, Wigger D, Sauer M, Kleuser B, Seibel J. Azidosphinganine enables metabolic labeling and detection of sphingolipid de novo synthesis. Org Biomol Chem 2021; 19:2203-2212. [PMID: 33496698 DOI: 10.1039/d0ob02592e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here were report the combination of biocompatible click chemistry of ω-azidosphinganine with fluorescence microscopy and mass spectrometry as a powerful tool to elaborate the sphingolipid metabolism. The azide probe was efficiently synthesized over 13 steps starting from l-serine in an overall yield of 20% and was used for live-cell fluorescence imaging of the endoplasmic reticulum in living cells by bioorthogonal click reaction with a DBCO-labeled fluorophore revealing that the incorporated analogue is mainly localized in the endoplasmic membrane like the endogenous species. A LC-MS(/MS)-based microsomal in vitro assay confirmed that ω-azidosphinganine mimics the natural species enabling the identification and analysis of metabolic breakdown products of sphinganine as a key starting intermediate in the complex sphingolipid biosynthetic pathways. Furthermore, the sphinganine-fluorophore conjugate after click reaction was enzymatically tolerated to form its dihydroceramide and ceramide metabolites. Thus, ω-azidosphinganine represents a useful biofunctional tool for metabolic investigations both by in vivo fluorescence imaging of the sphingolipid subcellular localization in the ER and by in vitro high-resolution mass spectrometry analysis. This should reveal novel insights of the molecular mechanisms sphingolipids and their processing enzymes have e.g. in infection.
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Affiliation(s)
- Julian Fink
- Institute of Organic Chemistry, Julius-Maximilians University Würzburg, Am Hubland C1, 97074 Würzburg, Germany.
| | - Fabian Schumacher
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany. and Institute of Nutritional Science, Department of Toxicology, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Jan Schlegel
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians University Würzburg, 97074 Würzburg, Germany.
| | - Philipp Stenzel
- Institute of Organic Chemistry, Julius-Maximilians University Würzburg, Am Hubland C1, 97074 Würzburg, Germany.
| | - Dominik Wigger
- Institute of Nutritional Science, Department of Toxicology, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians University Würzburg, 97074 Würzburg, Germany.
| | - Burkhard Kleuser
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany. and Institute of Nutritional Science, Department of Toxicology, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, Julius-Maximilians University Würzburg, Am Hubland C1, 97074 Würzburg, Germany.
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7
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Click chemistry in sphingolipid research. Chem Phys Lipids 2018; 215:71-83. [DOI: 10.1016/j.chemphyslip.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
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Kinoshita M, Suzuki KG, Murata M, Matsumori N. Evidence of lipid rafts based on the partition and dynamic behavior of sphingomyelins. Chem Phys Lipids 2018; 215:84-95. [DOI: 10.1016/j.chemphyslip.2018.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/13/2018] [Accepted: 07/10/2018] [Indexed: 01/10/2023]
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Ando J, Palonpon AF, Sodeoka M, Fujita K. High-speed Raman imaging of cellular processes. Curr Opin Chem Biol 2016; 33:16-24. [DOI: 10.1016/j.cbpa.2016.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/03/2016] [Indexed: 12/18/2022]
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Tipping WJ, Lee M, Serrels A, Brunton VG, Hulme AN. Stimulated Raman scattering microscopy: an emerging tool for drug discovery. Chem Soc Rev 2016; 45:2075-89. [PMID: 26839248 PMCID: PMC4839273 DOI: 10.1039/c5cs00693g] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 12/26/2022]
Abstract
Optical microscopy techniques have emerged as a cornerstone of biomedical research, capable of probing the cellular functions of a vast range of substrates, whilst being minimally invasive to the cells or tissues of interest. Incorporating biological imaging into the early stages of the drug discovery process can provide invaluable information about drug activity within complex disease models. Spontaneous Raman spectroscopy has been widely used as a platform for the study of cells and their components based on chemical composition; but slow acquisition rates, poor resolution and a lack of sensitivity have hampered further development. A new generation of stimulated Raman techniques is emerging which allows the imaging of cells, tissues and organisms at faster acquisition speeds, and with greater resolution and sensitivity than previously possible. This review focuses on the development of stimulated Raman scattering (SRS), and covers the use of bioorthogonal tags to enhance sample detection, and recent applications of both spontaneous Raman and SRS as novel imaging platforms to facilitate the drug discovery process.
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Affiliation(s)
- W. J. Tipping
- EaStCHEM School of Chemistry , The University of Edinburgh , Joseph Black Building , David Brewster Road , Edinburgh , EH9 3FJ , UK .
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - M. Lee
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - A. Serrels
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - V. G. Brunton
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - A. N. Hulme
- EaStCHEM School of Chemistry , The University of Edinburgh , Joseph Black Building , David Brewster Road , Edinburgh , EH9 3FJ , UK .
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Cui J, Kawatake S, Umegawa Y, Lethu S, Yamagami M, Matsuoka S, Sato F, Matsumori N, Murata M. Stereoselective synthesis of the head group of archaeal phospholipid PGP-Me to investigate bacteriorhodopsin–lipid interactions. Org Biomol Chem 2015; 13:10279-84. [DOI: 10.1039/c5ob01252j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phosphatidylglycerophosphate methyl ester (PGP-Me), a major constituent of the archaeal purple membrane, is essential for the proper proton-pump activity of bacteriorhodopsin (bR).
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Affiliation(s)
- Jin Cui
- Department of Chemistry
- Osaka University
- Toyonaka
- Japan
- JST ERATO
| | | | - Yuichi Umegawa
- Department of Chemistry
- Osaka University
- Toyonaka
- Japan
- JST ERATO
| | - Sébastien Lethu
- Department of Chemistry
- Osaka University
- Toyonaka
- Japan
- JST ERATO
| | | | | | - Fuminori Sato
- JST ERATO
- Lipid Active Structure Project
- Osaka University
- Toyonaka
- Japan
| | | | - Michio Murata
- Department of Chemistry
- Osaka University
- Toyonaka
- Japan
- JST ERATO
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