1
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Li Z, Chai L, Tang Z, Zhu H, Xue P, Sun F, Lin H, Zhou Y, Lin X. Precursor-Directed Biosynthesis of Neoantimycin Derivatives with Selective Cytotoxicity. JOURNAL OF NATURAL PRODUCTS 2024; 87:1376-1383. [PMID: 38662398 DOI: 10.1021/acs.jnatprod.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A precursor-directed biosynthesis approach led to the accumulation of seven new neoantimycin derivatives (1-7) from Streptomyces conglobatus RJ2. Structure elucidation was conducted using NMR and HRESIMS analysis, and the absolute configuration was determined by advanced Marfey's method, Mosher's analysis, and ECD analysis. The obtained compounds revealed selective and significant cytotoxicity, specifically against colorectal cancer cells bearing the K-ras mutation, with IC50 values ranging from 40 nM to 3.5 μM.
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Affiliation(s)
- Zhengyuan Li
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Ling Chai
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning 530022, People's Republic of China
| | - Zhenzhou Tang
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Hongrui Zhu
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Peiying Xue
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Fan Sun
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Houwen Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Yongjun Zhou
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Xiao Lin
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
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2
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Hu Z, Gu D, Skyrud W, Du Y, Zhai R, Wang J, Zhang W. Engineered Biosynthesis and Anticancer Studies of Ring-Expanded Antimycin-Type Depsipeptides. ACS Synth Biol 2024; 13:1562-1571. [PMID: 38679882 DOI: 10.1021/acssynbio.4c00193] [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] [Indexed: 05/01/2024]
Abstract
Respirantins are 18-membered antimycin-type depsipeptides produced by Streptomyces sp. and Kitasatospora sp. These compounds have shown extraordinary anticancer activities against a panel of cancer cell lines with nanomolar levels of IC50 values. However, further investigation has been impeded by the low titers of the natural producers and the challenging chemical synthesis due to their structural complexity. The biosynthetic gene cluster (BGC) of respirantin was previously proposed based on a bioinformatic comparison of the four members of antimycin-type depsipeptides. In this study, we report the first successful reconstitution of respirantin in Streptomyces albus using a synthetic BGC. This heterologous system serves as an accessible platform for the production and diversification of respirantins. Through polyketide synthase pathway engineering, biocatalysis, and chemical derivatization, we generated nine respirantin compounds, including six new derivatives. Cytotoxicity screening against human MCF-7 and Hela cancer cell lines revealed a unique biphasic dose-response profile of respirantin. Furthermore, a structure-activity relationship study has elucidated the essential functional groups that contribute to its remarkable cytotoxicity. This work paves the way for respirantin-based anticancer drug discovery and development.
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Affiliation(s)
- Zhijuan Hu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou 310024, China
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Will Skyrud
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Juan Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
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3
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Kawaguchi M, Yonetani Y, Mizuguchi T, Spratt SJ, Asanuma M, Shimizu H, Sasaki M, Ozeki Y. Visualization of Modified Bisarylbutadiyne-Tagged Small Molecules in Live-Cell Nuclei by Stimulated Raman Scattering Microscopy. Anal Chem 2024; 96:6643-6651. [PMID: 38626411 DOI: 10.1021/acs.analchem.3c05946] [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: 04/18/2024]
Abstract
Visualizing the distribution of small-molecule drugs in living cells is an important strategy for developing specific, effective, and minimally toxic drugs. As an alternative to fluorescence imaging using bulky fluorophores or cell fixation, stimulated Raman scattering (SRS) imaging combined with bisarylbutadiyne (BADY) tagging enables the observation of small molecules closer to their native intracellular state. However, there is evidence that the physicochemical properties of BADY-tagged analogues of small-molecule drugs differ significantly from those of their parent drugs, potentially affecting their intracellular distribution. Herein, we developed a modified BADY to reduce deviations in physicochemical properties (in particular, lipophilicity and membrane permeability) between tagged and parent drugs, while maintaining high Raman activity in live-cell SRS imaging. We highlight the practical application of this approach by revealing the nuclear distribution of a modified BADY-tagged analogue of JQ1, a bromodomain and extra-terminal motif inhibitor with applications in targeted cancer therapy, in living HeLa cells. The modified BADY, methoxypyridazyl pyrimidyl butadiyne (MPDY), revealed intranuclear JQ1, while BADY-tagged JQ1 did not show a clear nuclear signal. We anticipate that the present approach combining MPDY tagging with live-cell SRS imaging provides important insight into the behavior of intracellular drugs and represents a promising avenue for improving drug development.
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Affiliation(s)
| | - Yuki Yonetani
- Future Technology R&D Center, Canon Inc., Tokyo 146-8501, Japan
| | - Takaha Mizuguchi
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Spencer J Spratt
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
| | - Masato Asanuma
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hiroki Shimizu
- Organic & Biomolecular Chemistry Department, Daiichi Sankyo RD Novare Co., Ltd., Tokyo 134-8630, Japan
| | - Masato Sasaki
- Organic & Biomolecular Chemistry Department, Daiichi Sankyo RD Novare Co., Ltd., Tokyo 134-8630, Japan
| | - Yasuyuki Ozeki
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-8656, Japan
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4
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Zhou L, Feng RR, Zhang W, Gai F. Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences. J Phys Chem Lett 2024; 15:187-200. [PMID: 38156972 DOI: 10.1021/acs.jpclett.3c02619] [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: 01/03/2024]
Abstract
Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.
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Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Seidel J, Du Y, Devanathan R, Law R, Hu Z, Zill NA, Iavarone AT, Zhang W. Tag and Snag: A New Platform for Bioactive Natural Product Screening from Mixtures. Molecules 2023; 28:5726. [PMID: 37570695 PMCID: PMC10421080 DOI: 10.3390/molecules28155726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Natural products provide an unparalleled diversity of small molecules to fuel drug screening efforts, but deconvoluting the pharmacological activity of natural product mixtures to identify key bioactive compounds remains a vexing and labor-intensive process. Therefore, we have developed a new platform to probe the non-specific pharmacological potential of compounds present in common dietary supplements via shotgun derivatization with isotopically labeled propanoic acid, a live cell affinity assay, which was used to selectively recognize the population of compounds which bind tightly to HeLa cells in culture, and a computational LC-MS data analysis of isotopically labeled compounds from cell lysate. The data analysis showed that hundreds of compounds were successfully derivatized in each extract, and dozens of those compounds showed high affinity for HeLa cells. In total, over a thousand isotopically labeled compounds were screened for cell affinity across three separate experiments, resulting in the identification of several known bioactive compounds with specific protein targets and six previously unreported structures. The new natural products include three tulsinol compounds which were isolated from Ocimum tenuiflorum and three valeraninium alkaloids from Valeriana officinalis. The valeraninium alkaloids constitute a distinct new family of alkaloids from valerian, which may have previously undescribed bioactivity. These results collectively demonstrate the tag and snag workflow's viability as a drug discovery method.
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Affiliation(s)
- Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720-3220, USA
| | - Rohin Devanathan
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
| | - Richard Law
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
| | - Zhijuan Hu
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720-3220, USA
| | - Nicholas A. Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720-3220, USA
- QB3—Chemistry Mass Spectrometry Facility, University of California Berkeley, Berkeley, CA 94720-3220, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720-3220, USA; (J.S.)
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720-3220, USA
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6
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Shi J, Bera K, Mukherjee P, Alex A, Chaney EJ, Spencer-Dene B, Majer J, Marjanovic M, Spillman DR, Hood SR, Boppart SA. Weakly Supervised Identification and Localization of Drug Fingerprints Based on Label-Free Hyperspectral CARS Microscopy. Anal Chem 2023. [PMID: 37450658 PMCID: PMC10372874 DOI: 10.1021/acs.analchem.3c00979] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Understanding drug fingerprints in complex biological samples is essential for the development of a drug. Hyperspectral coherent anti-Stokes Raman scattering (HS-CARS) microscopy, a label-free nondestructive chemical imaging technique, can profile biological samples based on their endogenous vibrational contrast. Here, we propose a deep learning-assisted HS-CARS imaging approach for the investigation of drug fingerprints and their localization at single-cell resolution. To identify and localize drug fingerprints in complex biological systems, an attention-based deep neural network, hyperspectral attention net (HAN), was developed. By formulating the task to a multiple instance learning problem, HAN highlights informative regions through the attention mechanism when being trained on whole-image labels. Using the proposed technique, we investigated the drug fingerprints of a hepatitis B virus therapy in murine liver tissues. With the increase in drug dosage, higher classification accuracy was observed, with an average area under the curve (AUC) of 0.942 for the high-dose group. Besides, highly informative tissue structures predicted by HAN demonstrated a high degree of similarity with the drug localization shown by the in situ hybridization staining results. These results demonstrate the potential of the proposed deep learning-assisted optical imaging technique for the label-free profiling, identification, and localization of drug fingerprints in biological samples, which can be extended to nonperturbative investigations of complex biological systems under various biological conditions.
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Affiliation(s)
- Jindou Shi
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kajari Bera
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Prabuddha Mukherjee
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aneesh Alex
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- In vitro/In vivo Translation, Research, GSK, Collegeville, Pennsylvania 19426, United States
| | - Eric J Chaney
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Jan Majer
- In vitro/In vivo Translation, Research, GSK, Stevenage SG1 2NY, U.K
| | - Marina Marjanovic
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Darold R Spillman
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Steve R Hood
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- In vitro/In vivo Translation, Research, GSK, Stevenage SG1 2NY, U.K
| | - Stephen A Boppart
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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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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8
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Zill NA, Du Y, Marinkovich S, Gu D, Seidel J, Zhang W. Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening. ACS Chem Biol 2023; 18:1192-1199. [PMID: 37125845 DOI: 10.1021/acschembio.3c00083] [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: 05/02/2023]
Abstract
The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.
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Affiliation(s)
- Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Yongle Du
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Samantha Marinkovich
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China
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9
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Usuki Y, Tanaka Y, Morii M, Satoh T. Total synthesis of isoneoantimycin. Org Biomol Chem 2023; 21:2398-2404. [PMID: 36857695 DOI: 10.1039/d3ob00099k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Antimycins are one of the well-known antifungal metabolites produced by Streptomyces bacteria. Neoantimycin and its analogues, the ring-expanded antimycins featuring a 15-membered tetraester ring, have been shown to be effective regulators of the oncogenic proteins GRP78/BiP and K-Ras. Isoneoantimycin was isolated from Streptomyces fradiae IFO12773 (ISP 5063) as a minor metabolite during the fermentation of neoantimycin and is the first reported antibiotic of the antimycin family without the macrolide core. In this study, we explored the total synthesis and stereochemical assignment of isoneoantimycin as an approach to perform structure-activity studies on neoantimycins. Taking the neoantimycin biosynthesis pathway into account, we presumed that the stereochemistry of isoneoantimycin is the same as that of neoantimycin. The synthesis of our target molecule with the (1S,2R,5S,6S,14R,15R,17S) configuration has been achieved by using chiral-pool building blocks. A comparison of the spectroscopic data between the synthetic and natural samples verified our presumption of the stereochemistry of natural isoneoantimycin.
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Affiliation(s)
- Yoshinosuke Usuki
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Yuka Tanaka
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Miyu Morii
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Tetsuya Satoh
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
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10
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Tentellino C, Tipping WJ, McGee LMC, Bain LM, Wetherill C, Laing S, Tyson-Hirst I, Suckling CJ, Beveridge R, Scott FJ, Faulds K, Graham D. Ratiometric imaging of minor groove binders in mammalian cells using Raman microscopy. RSC Chem Biol 2022; 3:1403-1415. [PMID: 36544571 PMCID: PMC9709774 DOI: 10.1039/d2cb00159d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 02/02/2023] Open
Abstract
Quantitative drug imaging in live cells is a major challenge in drug discovery and development. Many drug screening techniques are performed in solution, and therefore do not consider the impact of the complex cellular environment in their result. As such, important features of drug-cell interactions may be overlooked. In this study, Raman microscopy is used as a powerful technique for semi-quantitative imaging of Strathclyde-minor groove binders (S-MGBs) in mammalian cells under biocompatible imaging conditions. Raman imaging determined the influence of the tail group of two novel minor groove binders (S-MGB-528 and S-MGB-529) in mammalian cell models. These novel S-MGBs contained alkyne moieties which enabled analysis in the cell-silent region of the Raman spectrum. The intracellular uptake concentration, distribution and mechanism were evaluated as a function of the pK a of the tail group, morpholine and amidine, for S-MGB-528 and S-MGB-529, respectively. Although S-MGB-529 had a higher binding affinity to the minor groove of DNA in solution-phase measurements, the Raman imaging data indicated that S-MGB-528 showed a greater degree of intracellular accumulation. Furthermore, using high resolution stimulated Raman scattering (SRS) microscopy, the initial localisation of S-MGB-528 was shown to be in the nucleus before accumulation in the lysosome, which was demonstrated using a multimodal imaging approach. This study highlights the potential of Raman spectroscopy for semi-quantitative drug imaging studies and highlights the importance of imaging techniques to investigate drug-cell interactions, to better inform the drug design process.
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Affiliation(s)
- Christian Tentellino
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of StrathclydeGlasgow G1 1RDUK
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Laura M. Bain
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Stacey Laing
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
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11
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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: 61] [Impact Index Per Article: 30.5] [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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12
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Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022; 61:e202204788. [PMID: 35704518 PMCID: PMC9542129 DOI: 10.1002/anie.202204788] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman‐active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native‐like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.
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Affiliation(s)
- Sam Benson
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
| | - Fabio de Moliner
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
| | - William Tipping
- Centre for Molecular Nanometrology The University of Strathclyde Glasgow G1 1RD UK
| | - Marc Vendrell
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
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13
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Abstract
As an emerging optical imaging modality, stimulated Raman scattering (SRS) microscopy provides invaluable opportunities for chemical biology studies using its rich chemical information. Through rapid progress over the past decade, the development of Raman probes harnessing the chemical biology toolbox has proven to play a key role in advancing SRS microscopy and expanding biological applications. In this perspective, we first discuss the development of biorthogonal SRS imaging using small tagging of triple bonds or isotopes and highlight their unique advantages for metabolic pathway analysis and microbiology investigations. Potential opportunities for chemical biology studies integrating small tagging with SRS imaging are also proposed. We next summarize the current designs of highly sensitive and super-multiplexed SRS probes, as well as provide future directions and considerations for next-generation functional probe design. These rationally designed SRS probes are envisioned to bridge the gap between SRS microscopy and chemical biology research and should benefit their mutual development.
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Affiliation(s)
- Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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14
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Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sam Benson
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - Fabio de Moliner
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - William Tipping
- University of Strathclyde Centre for Molecular Nanometrology UNITED KINGDOM
| | - Marc Vendrell
- University of Edinburgh Centre for Inflammation Research 47 Little France Crescent EH16 4TJ Edinburgh UNITED KINGDOM
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15
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Flores ADR, Barber CC, Narayanamoorthy M, Gu D, Shen Y, Zhang W. Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products. Annu Rev Chem Biomol Eng 2022; 13:1-24. [PMID: 35236086 PMCID: PMC9811556 DOI: 10.1146/annurev-chembioeng-092120-025140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Colin C. Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA,Chan Zuckerberg Biohub, San Francisco, California, USA
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16
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Bi X, Miao K, Wei L. Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange. J Am Chem Soc 2022; 144:8504-8514. [PMID: 35508077 DOI: 10.1021/jacs.2c01991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen-deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm-1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.
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Affiliation(s)
- Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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17
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Tipping WJ, Wilson LT, An C, Leventi AA, Wark AW, Wetherill C, Tomkinson NCO, Faulds K, Graham D. Stimulated Raman scattering microscopy with spectral phasor analysis: applications in assessing drug-cell interactions. Chem Sci 2022; 13:3468-3476. [PMID: 35432863 PMCID: PMC8943890 DOI: 10.1039/d1sc06976d] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/22/2022] [Indexed: 01/01/2023] Open
Abstract
Statins have displayed significant, although heterogeneous, anti-tumour activity in breast cancer disease progression and recurrence. They offer promise as a class of drugs, normally used for cardiovascular disease control, that could have a significant impact on the treatment of cancer. Understanding their mode of action and accurately assessing their efficacy on live cancer cells is an important and significant challenge. Stimulated Raman scattering (SRS) microscopy is a powerful, label-free imaging technique that can rapidly characterise the biochemical responses of live cell populations following drug treatment. Here, we demonstrate multi-wavelength SRS imaging together with spectral phasor analysis to characterise a panel of breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231 cells) treated with two clinically relevant statins, atorvastatin and rosuvastatin. Label-free SRS imaging within the high wavenumber region of the Raman spectrum (2800–3050 cm−1) revealed the lipid droplet distribution throughout populations of live breast cancer cells using biocompatible imaging conditions. A spectral phasor analysis of the hyperspectral dataset enables rapid differentiation of discrete cellular compartments based on their intrinsic SRS characteristics. Applying the spectral phasor method to studying statin treated cells identified a lipid accumulating phenotype in cell populations which displayed the lowest sensitivity to statin treatment, whilst a weaker lipid accumulating phenotype was associated with a potent reduction in cell viability. This study provides an insight into potential resistance mechanisms of specific cancer cells towards treatment with statins. Label-free SRS imaging provides a novel and innovative technique for phenotypic assessment of drug-induced effects across different cellular populations and enables effective analysis of drug–cell interactions at the subcellular scale. Stimulated Raman scattering microscopy with spectral phasor analysis provides a label-free approach for phenotypic evaluation of drug-induced effects.![]()
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Affiliation(s)
- William J Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Liam T Wilson
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow G1 1XL UK
| | - Connie An
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Aristea A Leventi
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Alastair W Wark
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | | | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
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18
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Gaba F, Tipping WJ, Salji M, Faulds K, Graham D, Leung HY. Raman Spectroscopy in Prostate Cancer: Techniques, Applications and Advancements. Cancers (Basel) 2022; 14:cancers14061535. [PMID: 35326686 PMCID: PMC8946151 DOI: 10.3390/cancers14061535] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 02/04/2023] Open
Abstract
Optical techniques are widely used tools in the visualisation of biological species within complex matrices, including biopsies, tissue resections and biofluids. Raman spectroscopy is an emerging analytical approach that probes the molecular signature of endogenous cellular biomolecules under biocompatible conditions with high spatial resolution. Applications of Raman spectroscopy in prostate cancer include biopsy analysis, assessment of surgical margins and monitoring of treatment efficacy. The advent of advanced Raman imaging techniques, such as stimulated Raman scattering, is creating opportunities for real-time in situ evaluation of prostate cancer. This review provides a focus on the recent preclinical and clinical achievements in implementing Raman-based techniques, highlighting remaining challenges for clinical applications. The research and clinical results achieved through in vivo and ex vivo Raman spectroscopy illustrate areas where these evolving technologies can be best translated into clinical practice.
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Affiliation(s)
- Fortis Gaba
- Department of Urology, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK; (F.G.); (M.S.)
- School of Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - William J. Tipping
- Department for Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK; (W.J.T.); (K.F.); (D.G.)
| | - Mark Salji
- Department of Urology, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK; (F.G.); (M.S.)
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow G61 1BD, UK
| | - Karen Faulds
- Department for Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK; (W.J.T.); (K.F.); (D.G.)
| | - Duncan Graham
- Department for Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK; (W.J.T.); (K.F.); (D.G.)
| | - Hing Y. Leung
- Department of Urology, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK; (F.G.); (M.S.)
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
- CRUK Beatson Institute, Bearsden, Glasgow G61 1BD, UK
- Correspondence:
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19
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Gu D, Zhang W. Engineered biosynthesis of alkyne-tagged polyketides. Methods Enzymol 2022; 665:347-373. [PMID: 35379442 PMCID: PMC9829517 DOI: 10.1016/bs.mie.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides have demonstrated their significance as therapeutics, industrial products, pesticides, and biological probes following intense study over the past decades. Tagging polyketides with a bioorthogonal functionality enables various applications such as diversification, quantification, visualization and mode-of-action elucidation. The terminal alkyne moiety, as a small, stable and highly selective clickable functionality, is widely adopted in tagging natural products. De novo biosynthesis of alkyne-tagged polyketides offers the unique advantage of reducing the background from feeding the biorthogonal moiety itself, leading to the accomplishment of in situ generation of a clickable functionality for bioorthogonal reactions. Here, we introduce several engineering strategies to apply terminal alkyne biosynthetic machinery, represented by JamABC, which produces a short terminal alkyne-bearing fatty acyl chain on a carrier protein, to functions with different downstream polyketide synthases (PKSs). Successful results in engineering type III and type I PKSs provide engineering guidelines and strategies that are applicable to additional PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications.
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Affiliation(s)
- Di Gu
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States,Corresponding author:
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20
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Tipping WJ, Merchant AS, Fearon R, Tomkinson NCO, Faulds K, Graham D. Temporal imaging of drug dynamics in live cells using stimulated Raman scattering microscopy and a perfusion cell culture system. RSC Chem Biol 2022; 3:1154-1164. [PMID: 36128503 PMCID: PMC9428671 DOI: 10.1039/d2cb00160h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Multimodal imaging of drug uptake and cell viability analysis in the same live cell population is enabled using a perfusion cell culture system.
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Affiliation(s)
- William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Andrew S. Merchant
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Rebecca Fearon
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | | | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
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21
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El-Mashtoly SF, Gerwert K. Diagnostics and Therapy Assessment Using Label-Free Raman Imaging. Anal Chem 2021; 94:120-142. [PMID: 34852454 DOI: 10.1021/acs.analchem.1c04483] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Samir F El-Mashtoly
- Center for Protein Diagnostics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Klaus Gerwert
- Center for Protein Diagnostics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
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22
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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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23
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Wilson LT, Tipping WJ, Wetherill C, Henley Z, Faulds K, Graham D, Mackay SP, Tomkinson NCO. Mitokyne: A Ratiometric Raman Probe for Mitochondrial pH. Anal Chem 2021; 93:12786-12792. [PMID: 34505518 DOI: 10.1021/acs.analchem.1c03075] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial pH (pHmito) is intimately related to mitochondrial function, and aberrant values for pHmito are linked to several disease states. We report the design, synthesis, and application of mitokyne 1-the first small molecule pHmito sensor for stimulated Raman scattering (SRS) microscopy. This ratiometric probe can determine subtle changes in pHmito in response to external stimuli and the inhibition of both the electron transport chain and ATP synthase with small molecule inhibitors. In addition, 1 was also used to monitor mitochondrial dynamics in a time-resolved manner with subcellular spatial resolution during mitophagy providing a powerful tool for dissecting the molecular and cell biology of this critical organelle.
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Affiliation(s)
- Liam T Wilson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - William J Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Zoë Henley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Simon P Mackay
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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24
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Adamczyk A, Matuszyk E, Radwan B, Rocchetti S, Chlopicki S, Baranska M. Toward Raman Subcellular Imaging of Endothelial Dysfunction. J Med Chem 2021; 64:4396-4409. [PMID: 33821652 PMCID: PMC8154563 DOI: 10.1021/acs.jmedchem.1c00051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Multiple diseases are at some point associated with altered endothelial
function, and endothelial dysfunction (ED) contributes to their pathophysiology.
Biochemical changes of the dysfunctional endothelium are linked to
various cellular organelles, including the mitochondria, endoplasmic
reticulum, and nucleus, so organelle-specific insight is needed for
better understanding of endothelial pathobiology. Raman imaging, which
combines chemical specificity with microscopic resolution, has proved
to be useful in detecting biochemical changes in ED at the cellular
level. However, the detection of spectroscopic markers associated
with specific cell organelles, while desirable, cannot easily be achieved
by Raman imaging without labeling. This critical review summarizes
the current advances in Raman-based analysis of ED, with a focus on
a new approach involving molecular Raman reporters that could facilitate
the study of biochemical changes in cellular organelles. Finally,
imaging techniques based on both conventional spontaneous Raman scattering
and the emerging technique of stimulated Raman scattering are discussed.
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Affiliation(s)
- Adriana Adamczyk
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Ewelina Matuszyk
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Basseem Radwan
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Stefano Rocchetti
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland.,Chair of Pharmacology, Jagiellonian University, 16 Grzegorzecka Str., 31-531 Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.,Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
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25
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:7715-7720. [PMID: 38505234 PMCID: PMC10946860 DOI: 10.1002/ange.202016802] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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26
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. Angew Chem Int Ed Engl 2021; 60:7637-7642. [PMID: 33491852 PMCID: PMC8048481 DOI: 10.1002/anie.202016802] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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27
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Zeng J, Zhao W, Yue S. Coherent Raman Scattering Microscopy in Oncology Pharmacokinetic Research. Front Pharmacol 2021; 12:630167. [PMID: 33613294 PMCID: PMC7887381 DOI: 10.3389/fphar.2021.630167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 11/28/2022] Open
Abstract
The high attrition rates of anti-cancer drugs during clinical development remains a bottleneck problem in pharmaceutical industry. This is partially due to the lack of quantitative, selective, and rapid readouts of anti-cancer drug activity in situ with high resolution. Although fluorescence microscopy has been commonly used in oncology pharmacological research, fluorescent labels are often too large in size for small drug molecules, and thus may disturb the function or metabolism of these molecules. Such challenge can be overcome by coherent Raman scattering microscopy, which is capable of chemically selective, highly sensitive, high spatial resolution, and high-speed imaging, without the need of any labeling. Coherent Raman scattering microscopy has tremendously improved the understanding of pharmaceutical materials in the solid state, pharmacokinetics of anti-cancer drugs and nanocarriers in vitro and in vivo. This review focuses on the latest applications of coherent Raman scattering microscopy as a new emerging platform to facilitate oncology pharmacokinetic research.
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Affiliation(s)
- Junjie Zeng
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Wenying Zhao
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shuhua Yue
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.,Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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28
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Li X, Lv JM, Hu D, Abe I. Biosynthesis of alkyne-containing natural products. RSC Chem Biol 2021; 2:166-180. [PMID: 34458779 PMCID: PMC8341276 DOI: 10.1039/d0cb00190b] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Alkyne-containing natural products are important molecules that are widely distributed in microbes and plants. Inspired by the advantages of acetylenic products used in the fields of medicinal chemistry, organic synthesis and material science, great efforts have focused on discovering the biosynthetic enzymes and pathways for alkyne formation. Here, we summarize the biosyntheses of alkyne-containing natural products and introduce de novo biosynthetic strategies for alkyne-tagged compound production.
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Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
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29
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Li Y, Shen B, Li S, Zhao Y, Qu J, Liu L. Review of Stimulated Raman Scattering Microscopy Techniques and Applications in the Biosciences. Adv Biol (Weinh) 2020; 5:e2000184. [PMID: 33724734 DOI: 10.1002/adbi.202000184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/17/2020] [Indexed: 01/10/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is a nonlinear optical imaging method for visualizing chemical content based on molecular vibrational bonds. Featuring high speed, high resolution, high sensitivity, high accuracy, and 3D sectioning, SRS microscopy has made tremendous progress toward biochemical information acquisition, cellular function investigation, and label-free medical diagnosis in the biosciences. In this review, the principle of SRS, system design, and data analysis are introduced, and the current innovations of the SRS system are reviewed. In particular, combined with various bio-orthogonal Raman tags, the applications of SRS microscopy in cell metabolism, tumor diagnosis, neuroscience, drug tracking, and microbial detection are briefly examined. The future prospects for SRS microscopy are also shared.
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Affiliation(s)
- Yanping Li
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Binglin Shen
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Shaowei Li
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Yihua Zhao
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Liwei Liu
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
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30
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Tipping WJ, Wilson LT, Blaseio SK, Tomkinson NCO, Faulds K, Graham D. Ratiometric sensing of fluoride ions using Raman spectroscopy. Chem Commun (Camb) 2020; 56:14463-14466. [PMID: 33147301 DOI: 10.1039/d0cc05939k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ratiometric Raman spectroscopy represents a novel sensing approach for the detection of fluoride anions based on alkyne desilylation chemistry. This method enables rapid, anion selective and highly sensitive detection of fluoride in a simple paper-based assay format using a portable Raman spectrometer.
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Affiliation(s)
- William J Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK.
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31
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Wilson LT, Tipping WJ, Jamieson LE, Wetherill C, Henley Z, Faulds K, Graham D, Mackay SP, Tomkinson NCO. A new class of ratiometric small molecule intracellular pH sensors for Raman microscopy. Analyst 2020; 145:5289-5298. [PMID: 32672252 DOI: 10.1039/d0an00865f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intracellular pH (pHi) homeostasis is intertwined with a myriad of normal cellular behaviors as well as pathological processes. As such, small molecule probes for the measurement of pHi are invaluable tools for chemical biology, facilitating the study of the role of pH in cellular function and disease. The field of small molecule pHi sensors has traditionally been dominated with probes based on fluorescent scaffolds. In this study, a series of low molecular weight (<260) oligoyne compounds have been developed which exhibit pH sensitive alkyne stretching frequencies (νalkyne) in Raman spectroscopy. The modular design of the compounds enabled tuneability of their pKa(H) through simple structural modification, such that continuous pH sensitivity is achieved over the range 2-10. Alkyne stretching bands reside in the 'cell-silent' region of the Raman spectrum (1800-2600 cm-1) and are readily detectable in a cellular environment with subcellular spatial resolution. This enabled the application of a pH sensitive oligoyne compound to the ratiometric sensing of pHi in prostate cancer (PC3) cells in response to drug treatment. We propose that probes based on Alkyne Tag Raman Imaging offer an entirely new platform for the sensing of pHi, complementary to fluorescence microscopy.
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Affiliation(s)
- Liam T Wilson
- Department of Pure and Applied Chemistry, WestCHEM, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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32
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Porterfield WB, Poenateetai N, Zhang W. Engineered Biosynthesis of Alkyne-Tagged Polyketides by Type I PKSs. iScience 2020; 23:100938. [PMID: 32146323 PMCID: PMC7063234 DOI: 10.1016/j.isci.2020.100938] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 01/20/2023] Open
Abstract
Polyketides produced by modular polyketide synthases (PKSs) are important small molecules widely used as drugs, pesticides, and biological probes. Tagging these polyketides with a clickable functionality enables the visualization, diversification, and mode of action study through bio-orthogonal chemistry. We report the de novo biosynthesis of alkyne-tagged polyketides by modular type I PKSs through starter unit engineering. Specifically, we use JamABC, a terminal alkyne biosynthetic machinery from the jamaicamide B biosynthetic pathway, in combination with representative modular PKSs. We demonstrate that JamABC works as a trans loading system for engineered type I PKSs to produce alkyne-tagged polyketides. In addition, the production efficiency can be improved by enhancing the interactions between the carrier protein (JamC) and PKSs using docking domains and site-directed mutagenesis of JamC. This work thus provides engineering guidelines and strategies that are applicable to additional modular type I PKSs to produce targeted alkyne-tagged metabolites for chemical and biological applications. Alkyne-tagged polyketides are de novo biosynthesized using type I PKSs Docking domains and ACP mutagenesis improve alkyne starter unit translocation Docking domains, but not ACP mutagenesis, perturb alkyne biosynthetic machinery
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Affiliation(s)
- William B Porterfield
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Nannalin Poenateetai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94709, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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33
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Yan T, Zeng Q, Wang L, Wang N, Cao H, Xu X, Chen X. Harnessing the Power of Optical Microscopic and Macroscopic Imaging for Natural Products as Cancer Therapeutics. Front Pharmacol 2019; 10:1438. [PMID: 31849680 PMCID: PMC6892944 DOI: 10.3389/fphar.2019.01438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/11/2019] [Indexed: 01/03/2023] Open
Abstract
Natural products (NPs) are an important source for new drug discovery over the past decades, which have been demonstrated to be effectively used in cancer prevention, treatment, and adjuvant therapy. Many methods, such as the genomic and metabolomic approaches, immunochemistry, mass spectrometry, and chromatography, have been used to study the effects of NPs on cancer as well as themselves. Because of the advantages in specificity, sensitivity, high throughput, and cost-effectiveness, optical imaging (OI) approaches, including optical microscopic imaging and macroscopic imaging techniques have also been applied in the studies of NPs. Optical microscopic imaging can observe NPs as cancer therapeutics at the cellular level and analyze its cytotoxicity and mechanism of action. Optical macroscopic imaging observes the distribution, metabolic pathway, and target lesions of NPs in vivo, and evaluates NPs as cancer therapeutics at the whole-body level in small living animals. This review focuses on the recent advances in NPs as cancer therapeutics, with particular emphasis on the powerful use of optical microscopic and macroscopic imaging techniques, including the studies of observation of ingestion by cells, anticancer mechanism, and in vivo delivery. Finally, we prospect the wider application and future potential of OI approaches in NPs as cancer therapeutics.
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Affiliation(s)
- Tianyu Yan
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
| | - Qi Zeng
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
| | - Lin Wang
- School of Information Sciences and Technology, Northwest University, Xi’an, China
| | - Nan Wang
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
| | - Honghao Cao
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
| | - Xinyi Xu
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
| | - Xueli Chen
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education and School of Life Science and Technology, Xidian University, Xi’an, China
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34
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Hu F, Shi L, Min W. Biological imaging of chemical bonds by stimulated Raman scattering microscopy. Nat Methods 2019; 16:830-842. [PMID: 31471618 DOI: 10.1038/s41592-019-0538-0] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022]
Abstract
All molecules consist of chemical bonds, and much can be learned from mapping the spatiotemporal dynamics of these bonds. Since its invention a decade ago, stimulated Raman scattering (SRS) microscopy has become a powerful modality for imaging chemical bonds with high sensitivity, resolution, speed and specificity. We introduce the fundamentals of SRS microscopy and review innovations in SRS microscopes and imaging probes. We highlight examples of exciting biological applications, and share our vision for potential future breakthroughs for this technology.
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Affiliation(s)
- Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA. .,Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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