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NAKAGAWA Y, ITO Y. Mannose-binding analysis and biological application of pradimicins. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:15-29. [PMID: 35013028 PMCID: PMC8795531 DOI: 10.2183/pjab.98.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Pradimicins (PRMs) are an exceptional family of natural products that specifically bind d-mannose (Man). In the past decade, their scientific significance has increased greatly, with the emergence of biological roles of Man-containing glycans. However, research into the use of PRMs has been severely limited by their inherent tendency to form water-insoluble aggregates. Recently, we have established a derivatization strategy to suppress PRM aggregation, providing an opportunity for practical application of PRMs in glycobiological research. This article first outlines the challenges in studying Man-binding mechanisms and structural modifications of PRMs, and then describes our approach to address them. We also present our recent attempts toward the development of PRM-based research tools.
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Affiliation(s)
- Yu NAKAGAWA
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yukishige ITO
- RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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Berlinck RGS, Crnkovic CM, Gubiani JR, Bernardi DI, Ióca LP, Quintana-Bulla JI. The isolation of water-soluble natural products - challenges, strategies and perspectives. Nat Prod Rep 2021; 39:596-669. [PMID: 34647117 DOI: 10.1039/d1np00037c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Covering period: up to 2019Water-soluble natural products constitute a relevant group of secondary metabolites notably known for presenting potent biological activities. Examples are aminoglycosides, β-lactam antibiotics, saponins of both terrestrial and marine origin, and marine toxins. Although extensively investigated in the past, particularly during the golden age of antibiotics, hydrophilic fractions have been less scrutinized during the last few decades. This review addresses the possible reasons on why water-soluble metabolites are now under investigated and describes approaches and strategies for the isolation of these natural compounds. It presents examples of several classes of hydrosoluble natural products and how they have been isolated. Novel stationary phases and chromatography techniques are also reviewed, providing a perspective towards a renaissance in the investigation of water-soluble natural products.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Camila M Crnkovic
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Laura P Ióca
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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Multifunctional aggregation-based fluorescent probe for visualizing intracellular calcium dynamic fluctuations. Anal Bioanal Chem 2020; 412:7187-7194. [PMID: 32767015 DOI: 10.1007/s00216-020-02851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
Abstract
Calcium ion (Ca2+) is an indispensable second messenger in living organisms. The impaired Ca2+ handling can induce many diseases. In this paper, we developed a simple and effective method to encapsulate a coumarin-based Ca2+ probe ((E)-2-hydroxy-N'-((7-hydroxy-2-oxo-2H-chromen-8-yl)methylene)-2-phenylacetohydrazide, CPM) into nanoparticles (NPs), and CPM NPs with blue fluorescence were obtained, whose maximum excitation and maximum emission wavelengths were characterized at 365 nm and 450 nm, respectively. The CPM NPs show significant fluorescence enhancement toward Ca2+ over other metal ions, with a limit of determination (LOD) of 0.04 μM. To optimize the optical property of the NPs, CPM and curcumin, which were introduced as the Förster resonance energy transfer (FRET) donor and acceptor, respectively, were co-encapsulated, and bright green CPM@Cur NPs with large stokes shift and narrow emission band width were constructed. Due to their low cytotoxicity and excellent stability, CPM NPs and CPM@Cur NPs were further successfully used to discriminate the primary aortic smooth muscle cells isolated from mice with abnormal Ca2+ homeostasis from their littermate controls. It is worth noting that CPM@Cur NPs exhibit stronger fluorescence signal and diminished background interference, which make them have great potential in the Ca2+ monitoring during biological processes. This strategy opens a new way to synthesize NPs with high brightness and has a potential application prospect in composite sensing and intracellular imaging. CPM@Cur NPs are developed and applied in biological sensing and intracellular Ca2+ imaging, as well as discriminating the cells with abnormal calcium homeostasis.
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Nakagawa Y. Paving the Way for Practical Use of Sugar-Binding Natural Products as Lectin Mimics in Glycobiological Research. Chembiochem 2020; 21:1567-1572. [PMID: 32012428 DOI: 10.1002/cbic.201900781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Indexed: 12/17/2022]
Abstract
Pradimicins (PRMs) constitute an exceptional class of natural products that show Ca2+ -dependent recognition of d-mannose (Man). In addition to therapeutic uses as antifungal drugs, the application of PRMs as lectin mimics for glycobiological research has been attracting considerable interest, since the emerging biological roles of Man-containing glycans have been highlighted. However, only a few attempts have been made to use PRMs for glycobiological purposes. The limited use of PRMs is primarily due to the early assumption that the readily modifiable carboxyl group of PRMs is involved in Ca2+ binding, and thus, not available to prepare research tools. Recently, this assumption has been disproved by structural elucidation of the Ca2+ complex of PRMs, which paves the way for designing carboxyl group modified derivatives of PRMs for research use. This article outlines studies related to Ca2+ -mediated Man binding of PRMs and discusses their application for glycobiology.
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Affiliation(s)
- Yu Nakagawa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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Reza AM, Tavakoli J, Zhou Y, Qin J, Tang Y. Synthetic fluorescent probes to apprehend calcium signalling in lipid droplet accumulation in microalgae—an updated review. Sci China Chem 2020. [DOI: 10.1007/s11426-019-9664-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Almeida LCD, Bauermeister A, Rezende-Teixeira P, Santos EAD, Moraes LABD, Machado-Neto JA, Costa-Lotufo LV. Pradimicin-IRD exhibits antineoplastic effects by inducing DNA damage in colon cancer cells. Biochem Pharmacol 2019; 168:38-47. [PMID: 31228463 DOI: 10.1016/j.bcp.2019.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
DNA-damaging agents are widely used in cancer therapy; however, their use is limited by dose-related toxicities, as well as the development of drug resistance. Drug discovery is essential to overcome these limitations and offer novel therapeutic options. In a previous study by our research group, pradimicin-IRD-a new polycyclic antibiotic produced by the actinobacteria Amycolatopsis sp.-displayed antimicrobial and potential anticancer activities. In the present study, cytotoxic activity was further confirmed in a panel of five colon cancer, including those with mutation in TP53 and KRAS, the most common ones observed in cancer colon patients. While all tested colon cancer cells were sensitive to pradimicin-IRD treatment with IC50 in micromolar range, non-tumor fibroblasts were significantly less sensitive (p < 0.05). The cellular and molecular mechanism of action of pradimicin-IRD was then investigated in the colorectal cancer cell line HCT 116. Pradimicin-IRD presented antitumor effects occurring after at least 6 h of exposure. Pradimicin-IRD induced statistically significant DNA damage (γH2AX and p21), apoptosis (PARP1 and caspase 3 cleavage) and cell cycle arrest (reduced Rb phosphorylation, cyclin A and cyclin B expression) markers. In accordance with these results, pradimicin-IRD increased cell populations in the subG1 and G0/G1 phases of the cell cycle. Additionally, mass spectrometry analysis indicated that pradimicin-IRD interacted with the DNA double strand. In summary, pradimicin-IRD exhibits multiple antineoplastic activities-including DNA damage, cell cycle arrest, reduction of clonal growth and apoptosis-in the HCT 116 cell line. Furthermore, pradimicin-IRD displays a TP53-independent regulation of p21 expression in HCT 116 TP53-/-, HT-29, SW480, and Caco-2 cells. This exploratory study identified novel targets for pradimicin-IRD and provided insights for its potential anticancer activity as a DNA-damaging agent.
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Affiliation(s)
- Larissa Costa de Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anelize Bauermeister
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Evelyne Alves Dos Santos
- Department of Cell Biology and Development, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Nakagawa Y, Doi T, Takegoshi K, Sugahara T, Akase D, Aida M, Tsuzuki K, Watanabe Y, Tomura T, Ojika M, Igarashi Y, Hashizume D, Ito Y. Molecular Basis of Mannose Recognition by Pradimicins and their Application to Microbial Cell Surface Imaging. Cell Chem Biol 2019; 26:950-959.e8. [PMID: 31031141 DOI: 10.1016/j.chembiol.2019.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/23/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022]
Abstract
Naturally occurring pradimicins (PRMs) show specific recognition of d-mannose (d-Man) in aqueous media, which has never been achieved by artificial small molecules. Although the Ca2+-mediated dimerization of PRMs is essential for their d-Man binding, the dimeric structure has yet to be elucidated, leaving the question open as to how PRMs recognize d-Man. Thus, we herein report the structural elucidation of the dimer by a combination of X-ray crystallography and solid-state NMR spectroscopy. Coupled with our previous knowledge regarding the d-Man binding geometry of PRMs, elucidation of the dimer allowed reliable estimation of the mode of d-Man binding. Based on the binding model, we further developed an azide-functionalized PRM derivative (PRM-Azide) with d-Man binding specificity. Notably, PRM-Azide stained Candida rugosa cells having mannans on their cell surface through conjugation with the tetramethylrhodamine fluorophore. The present study provides the practical demonstration that PRMs can serve as lectin mimics for use in glycobiological studies.
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Affiliation(s)
- Yu Nakagawa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Takashi Doi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - K Takegoshi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takahiro Sugahara
- Center for Quantum Life Sciences, and Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Dai Akase
- Center for Quantum Life Sciences, and Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Aida
- Center for Quantum Life Sciences, and Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Kazue Tsuzuki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasunori Watanabe
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tomohiko Tomura
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Hashizume
- RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Gao M, Li Y, Chen X, Li S, Ren L, Tang BZ. Aggregation-Induced Emission Probe for Light-Up and in Situ Detection of Calcium Ions at High Concentration. ACS APPLIED MATERIALS & INTERFACES 2018; 10:14410-14417. [PMID: 29671572 DOI: 10.1021/acsami.8b00952] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The fluorescent probe for the detection of calcium ions is an indispensable tool in the biomedical field. The millimolar order of Ca(II) ions is associated with many physiological processes and diseases, such as hypercalcemia, soft tissue calcification, and bone microcracks. However, the conventional fluorescent probes are only suitable for imaging Ca(II) ions in the nanomolar to micromolar range, which can be because of their high affinities toward Ca(II) ions and aggregation-caused quenching drawbacks. To tackle this challenge, we herein develop an aggregation-induced emission (AIE) probe SA-4CO2Na for selective and light-up detection of Ca(II) ions in the millimolar range (0.6-3.0 mM), which can efficiently distinguish between hypercalcemic (1.4-3.0 mM) and normal (1.0-1.4 mM) Ca2+ ion levels. The formation of fibrillar aggregates between SA-4CO2Na and Ca(II) ions was clearly verified by fluorescence, scanning electron microscopy, and transmission electron analysis. Moreover, this AIE-active probe can be used for wash-free and light-up imaging of a high concentration of Ca(II) ions even in the solid analytes, including calcium deposits in psammomatous meningioma slice, microcracks on bovine bone surface, and microdefects on hydroxyapatite-based scaffold. It is thus expected that this AIE-active probe would have broad biomedical applications through light-up imaging and sensing of Ca(II) ions at the millimolar level.
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Affiliation(s)
- Meng Gao
- National Engineering Research Center for Tissue Restoration and Reconstruction , South China University of Technology , Guangzhou 510006 , China
| | - Yunxia Li
- National Engineering Research Center for Tissue Restoration and Reconstruction , South China University of Technology , Guangzhou 510006 , China
| | - Xiaohui Chen
- National Engineering Research Center for Tissue Restoration and Reconstruction , South China University of Technology , Guangzhou 510006 , China
| | | | - Li Ren
- National Engineering Research Center for Tissue Restoration and Reconstruction , South China University of Technology , Guangzhou 510006 , China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , The Hong Kong University of Science & Technology , Clear Water Bay, Kowloon , Hong Kong, China
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