1
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Nakagawa Y, Fujii M, Ito N, Ojika M, Akase D, Aida M, Kinoshita T, Sakurai Y, Yasuda J, Igarashi Y, Ito Y. Molecular basis of N-glycan recognition by pradimicin a and its potential as a SARS-CoV-2 entry inhibitor. Bioorg Med Chem 2024; 105:117732. [PMID: 38643719 DOI: 10.1016/j.bmc.2024.117732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Virus entry inhibitors are emerging as an attractive class of therapeutics for the suppression of viral transmission. Naturally occurring pradimicin A (PRM-A) has received particular attention as the first-in-class entry inhibitor that targets N-glycans present on viral surface. Despite the uniqueness of its glycan-targeted antiviral activity, there is still limited knowledge regarding how PRM-A binds to viral N-glycans. Therefore, in this study, we performed binding analysis of PRM-A with synthetic oligosaccharides that reflect the structural motifs characteristic of viral N-glycans. Binding assays and molecular modeling collectively suggest that PRM-A preferentially binds to branched oligomannose motifs of N-glycans via simultaneous recognition of two mannose residues at the non-reducing ends. We also demonstrated, for the first time, that PRM-A can effectively inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in vitro. Significantly, the anti-SARS-CoV-2 effect of PRM-A is attenuated in the presence of the synthetic branched oligomannose, suggesting that the inhibition of SARS-CoV-2 infection is due to the interaction of PRM-A with the branched oligomannose-containing N-glycans. These data provide essential information needed to understand the antiviral mechanism of PRM-A and suggest that PRM-A could serve as a candidate SARS-CoV-2 entry inhibitor targeting N-glycans.
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Affiliation(s)
- Yu Nakagawa
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Masato Fujii
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Nanaka Ito
- 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
| | - Dai Akase
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Aida
- Office of Research and Academia-Government-Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8511, Japan
| | - Takaaki Kinoshita
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Yasuteru Sakurai
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yukishige Ito
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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2
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Milanesi F, Roelens S, Francesconi O. Towards Biomimetic Recognition of Glycans by Synthetic Receptors. Chempluschem 2024; 89:e202300598. [PMID: 37942862 DOI: 10.1002/cplu.202300598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
Carbohydrates are abundant in Nature, where they are mostly assembled within glycans as free polysaccharides or conjugated to a variety of biological molecules such as proteins and lipids. Glycans exert several functions, including protein folding, stability, solubility, resistance to proteolysis, intracellular traffic, antigenicity, and recognition by carbohydrate-binding proteins. Interestingly, misregulation of their biosynthesis that leads to changes in glycan structures is frequently recognized as a mark of a disease state. Because of glycan ubiquity, carbohydrate binding agents (CBAs) targeting glycans can lead to a deeper understanding of their function and to the development of new diagnostic and prognostic strategies. Synthetic receptors selectively recognizing specific carbohydrates of biological interest have been developed over the past three decades. In addition to the success obtained in the effective recognition of monosaccharides, synthetic receptors recognizing more complex guests have also been developed, including di- and oligosaccharide fragments of glycans, shedding light on the structural and functional requirements necessary for an effective receptor. In this review, the most relevant achievements in molecular recognition of glycans and their fragments will be summarized, highlighting potentials and future perspectives of glycan-targeting synthetic receptors.
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Affiliation(s)
- Francesco Milanesi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Stefano Roelens
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
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3
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Nakagawa Y, Oya Y, Ojika M, Igarashi Y, Ito Y. Chemical modification of pradimicin A to suppress aggregation without impairing D-mannose-binding and antifungal activities. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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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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5
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Nakagawa Y, Kakihara S, Tsuzuki K, Ojika M, Igarashi Y, Ito Y. A Pradimicin-Based Staining Dye for Glycoprotein Detection. JOURNAL OF NATURAL PRODUCTS 2021; 84:2496-2501. [PMID: 34524799 DOI: 10.1021/acs.jnatprod.1c00506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pradimicin A (PRM-A) and related compounds constitute an exceptional family of natural pigments that show Ca2+-dependent recognition of d-mannose (Man). Although these compounds hold great promise as research tools in glycobiology, their practical application has been severely limited by their inherent tendency to form water-insoluble aggregates. Here, we demonstrate that the 2-hydroxyethylamide derivative (PRM-EA) of PRM-A shows little aggregation in neutral aqueous media and retains binding specificity for Man. We also show that PRM-EA stains glycoproteins in dot blot assays, whereas PRM-A fails to do so, owing to severe aggregation. Significantly, PRM-EA is sensitive to glycoproteins carrying high mannose-type and hybrid-type N-linked glycans, but not to those carrying complex-type N-linked glycans. Such staining selectivity has never been observed in conventional dyes, suggesting that PRM-EA could serve as a unique staining agent for the selective detection of glycoproteins with terminal Man residues.
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Affiliation(s)
- Yu Nakagawa
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shintaro Kakihara
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kazue Tsuzuki
- 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
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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6
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Nakagawa Y, Yamaji F, Miyanishi W, Ojika M, Igarashi Y, Ito Y. Binding Evaluation of Pradimicins for Oligomannose Motifs from Fungal Mannans. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yu Nakagawa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Fumiya Yamaji
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Wataru Miyanishi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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7
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Bravo MF, Lema MA, Marianski M, Braunschweig AB. Flexible Synthetic Carbohydrate Receptors as Inhibitors of Viral Attachment. Biochemistry 2020; 60:999-1018. [PMID: 33094998 DOI: 10.1021/acs.biochem.0c00732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Carbohydrate-receptor interactions are often involved in the docking of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered "undruggable", meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs), small molecules that bind carbohydrates, could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of SCRs, and recent results demonstrating their ability to prevent viral infections in vitro. Common SCR design strategies based on boronic ester formation, metal chelation, and noncovalent interactions are discussed. The benefits of incorporating the idiosyncrasies of natural glycan-binding proteins-including flexibility, cooperativity, and multivalency-into SCR design to achieve nonglucosidic specificity are shown. These studies into SCR design and binding could lead to new strategies for mitigating the grave threat to human health posed by enveloped viruses, which are heavily glycosylated viroids that are the cause of some of the most pressing and untreatable diseases, including HIV, Dengue, Zika, influenza, and SARS-CoV-2.
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Affiliation(s)
- M Fernando Bravo
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Manuel A Lema
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Mateusz Marianski
- Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,The PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Adam B Braunschweig
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,The PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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8
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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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9
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10
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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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11
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Francesconi O, Roelens S. Biomimetic Carbohydrate‐Binding Agents (CBAs): Binding Affinities and Biological Activities. Chembiochem 2019; 20:1329-1346. [DOI: 10.1002/cbic.201800742] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Oscar Francesconi
- Department of Chemistry and INSTMUniversity of Florence Polo Scientifico e Tecnologico 50019 Sesto Fiorentino, Firenze Italy
| | - Stefano Roelens
- Department of Chemistry and INSTMUniversity of Florence Polo Scientifico e Tecnologico 50019 Sesto Fiorentino, Firenze Italy
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12
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Doi T, Nakagawa Y, Takegoshi K. Solid-State Nuclear Magnetic Resonance Analysis Reveals a Possible Calcium Binding Site of Pradimicin A. Biochemistry 2017; 56:468-472. [DOI: 10.1021/acs.biochem.6b01300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Takashi Doi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa
Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yu Nakagawa
- Department
of Applied Molecular Biosciences, Graduate School of Bioagricultural
Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - K. Takegoshi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa
Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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14
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Park SH, Choi YP, Park J, Share A, Francesconi O, Nativi C, Namkung W, Sessler JL, Roelens S, Shin I. Synthetic aminopyrrolic receptors have apoptosis inducing activity. Chem Sci 2015; 6:7284-7292. [PMID: 28757987 PMCID: PMC5512143 DOI: 10.1039/c5sc03200h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/25/2015] [Indexed: 12/18/2022] Open
Abstract
We report two synthetic aminopyrrolic compounds that induce apoptotic cell death. These compounds have been previously shown to act as receptors for mannosides. The extent of receptor-induced cell death is greater in cells expressing a high level of high-mannose oligosaccharides than in cells producing lower levels of high-mannose glycans. The ability of synthetic receptors to induce cell death is attenuated in the presence of external mannosides. The present results provide support for the suggestion that the observed cell death reflects an ability of the receptors to bind mannose displayed on the cell surface. Signaling pathway studies indicate that the synthetic receptors of the present study promote JNK activation, induce Bax translocation to the mitochondria, and cause cytochrome c release from the mitochondria into the cytosol, thus promoting caspase-dependent apoptosis. Such effects are also observed in cells treated with mannose-binding ConA. The present results thus serve to highlight what may be an attractive new approach to triggering apoptosis via modes of action that differ from those normally used to promote apoptosis.
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Affiliation(s)
- Seong-Hyun Park
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , 03722 Seoul , Korea .
| | - Yoon Pyo Choi
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , 03722 Seoul , Korea .
| | - Jinhong Park
- College of Pharmacy , Yonsei Institute of Pharmaceutical Sciences , Yonsei University , 21983 Incheon , Korea
| | - Andrew Share
- Department of Chemistry , The University of Texas at Austin , 78712-1224 Austin , Texas , USA
| | - Oscar Francesconi
- Department of Chemistry and INSTM , University of Florence , Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino , Firenze , Italy
| | - Cristina Nativi
- Department of Chemistry and INSTM , University of Florence , Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino , Firenze , Italy
| | - Wan Namkung
- College of Pharmacy , Yonsei Institute of Pharmaceutical Sciences , Yonsei University , 21983 Incheon , Korea
| | - Jonathan L Sessler
- Department of Chemistry , The University of Texas at Austin , 78712-1224 Austin , Texas , USA
| | - Stefano Roelens
- Istituto di Metodologie Chimiche (IMC) , Consiglio Nazionale delle Ricerche (CNR) , Department of Chemistry and INSTM , University of Florence , Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino , Firenze , Italy
| | - Injae Shin
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , 03722 Seoul , Korea .
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15
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Nakagawa Y, Watanabe Y, Igarashi Y, Ito Y, Ojika M. Pradimicin A, a D-mannose-binding antibiotic, binds pyranosides of L-fucose and L-galactose in a calcium-sensitive manner. Bioorg Med Chem Lett 2015; 25:2963-6. [PMID: 26045034 DOI: 10.1016/j.bmcl.2015.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 12/11/2022]
Abstract
Pradimicin A (PRM-A) is a unique antibiotic with a lectin-like ability to bind D-mannose (D-Man) in the presence of Ca(2+) ion. Although accumulated evidences suggest that PRM-A recognizes the 2-, 3-, and 4-hydroxyl groups of D-Man, BMY-28864, an artificial PRM-A derivative, was shown not to bind L-fucose (L-Fuc) and L-galactose (lLGal), both of which share the characteristic array of the three hydroxyl groups with D-Man. To obtain a plausible explanation for this inconsistency, we performed co-precipitation experiments of PRM-A with L-Fuc, L-Gal, and their methyl pyranosides (L-Fuc-OMe, L-Gal-OMe) by taking advantage of aggregate-forming propensity of the binary [PRM-A/Ca(2+)] complex. While L-Fuc and L-Gal were hardly incorporated into the aggregate, L-Fuc-OMe and L-Gal-OMe were found to exhibit significant binding to PRM-A. However, increased Ca(2+) concentration abolished this binding, raising the possibility that poor binding of L-Fuc and L-Gal to PRM-A is attributed to their chelation with Ca(2+) ion. This possibility was partly supported by (1)H NMR analysis that detected interaction of L-Fuc and L-Gal with Ca(2+) ion in aqueous solution. These results collectively indicate that PRM-A binds pyranosides of L-Fuc and L-Gal when Ca(2+) concentration is not excessive to trap these sugars by chelation but sufficient to form the [PRM-A/Ca(2+)] complex.
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Affiliation(s)
- Yu Nakagawa
- Department of Applied Molecular 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.
| | - Yasunori Watanabe
- Department of Applied Molecular 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
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Japan Science and Technology Agency, ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Ojika
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Enomoto M, Igarashi Y, Sasaki M, Shimizu H. A mannose-recognizable chemosensor using gold nanoparticles functionalized with pradimicin, a nonpeptidic mannose-binding natural product. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Francesconi O, Nativi C, Gabrielli G, Gentili M, Palchetti M, Bonora B, Roelens S. Pyrrolic Tripodal Receptors for the Molecular Recognition of Carbohydrates: Ditopic Receptors for Dimannosides. Chemistry 2013; 19:11742-52. [DOI: 10.1002/chem.201204298] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Indexed: 11/08/2022]
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18
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Nakagawa Y, Doi T, Taketani T, Takegoshi K, Igarashi Y, Ito Y. Mannose-Binding Geometry of Pradimicin A. Chemistry 2013; 19:10516-25. [DOI: 10.1002/chem.201301368] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Indexed: 11/12/2022]
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19
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Abstract
Lectins are proteins of non-immune origin that bind specific carbohydrates without chemical modification. Coupled with the emerging biological and pathological significance of carbohydrates, lectins have become extensively used as research tools in glycobiology. However, lectin-based drug development has been impeded by high manufacturing costs, low chemical stability, and the potential risk of initiating an unfavorable immune response. As alternatives to lectins, non-protein small molecules having carbohydrate-binding properties (lectin mimics) are currently attracting a great deal of attention because of their ease of preparation and chemical modification. Lectin mimics of synthetic origin are divided roughly into two groups, boronic acid-dependent and boronic acid-independent lectin mimics. This article outlines their representative architectures and carbohydrate-binding properties, and discusses their therapeutic potential by reviewing recent attempts to develop antiviral and antimicrobial agents using their architectures. We also focus on the naturally occurring lectin mimics, pradimicins and benanomicins. They are the only class of non-protein natural products having a C-type lectin-like ability to recognize d-mannopyranosides in the presence of Ca2 + ions. Their molecular basis of carbohydrate recognition and therapeutic potential are also discussed.
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Affiliation(s)
- Yu Nakagawa
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
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Shahzad-ul-Hussan S, Ghirlando R, Dogo-Isonagie CI, Igarashi Y, Balzarini J, Bewley CA. Characterization and carbohydrate specificity of pradimicin S. J Am Chem Soc 2012; 134:12346-9. [PMID: 22788706 DOI: 10.1021/ja303860m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The pradimicin family of antibiotics is attracting attention due to its anti-infective properties and as a model for understanding the requirements for carbohydrate recognition by small molecules. Members of the pradimicin family are unique among natural products in their ability to bind sugars in a Ca(2+)-dependent manner, but the oligomerization to insoluble aggregates that occurs upon Ca(2+) binding has prevented detailed characterization of their carbohydrate specificity and biologically relevant form. Here we take advantage of the water solubility of pradimicin S (PRM-S), a sulfated glucose-containing analogue of pradimicin A (PRM-A), to show by NMR spectroscopy and analytical ultracentrifugation that at biologically relevant concentrations, PRM-S binds Ca(2+) to form a tetrameric species that selectively binds and engulfs the trisaccharide Manα1-3(Manα1-6)Man over mannose or mannobiose. In functional HIV-1 entry assays, IC(50) values of 2-4 μM for PRM-S corrrelate with the concentrations at which oligomerization occurs as well as the affinities with which PRM-S binds the HIV surface envelope glycoprotein gp120. Together these data reveal the biologically active form of PRM-S, provide an explanation for previous speculations that PRM-A may contain a second mannose binding site, and expand our understanding of the characteristics that can engender a small molecule with the ability to function as a carbohydrate receptor.
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Affiliation(s)
- Syed Shahzad-ul-Hussan
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Nativi C, Francesconi O, Gabrielli G, De Simone I, Turchetti B, Mello T, Mannelli LDC, Ghelardini C, Buzzini P, Roelens S. Aminopyrrolic Synthetic Receptors for Monosaccharides: A Class of Carbohydrate‐Binding Agents Endowed with Antibiotic Activity versus Pathogenic Yeasts. Chemistry 2012; 18:5064-72. [DOI: 10.1002/chem.201103318] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/28/2011] [Indexed: 12/22/2022]
Affiliation(s)
- Cristina Nativi
- Dipartimento di Chimica, Università di Firenze, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy)
- FiorGen, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy)
| | - Oscar Francesconi
- Dipartimento di Chimica, Università di Firenze, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy)
| | - Gabriele Gabrielli
- Dipartimento di Chimica, Università di Firenze, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy)
| | - Irene De Simone
- Dipartimento di Chimica, Università di Firenze, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy)
| | - Benedetta Turchetti
- Dipartimento di Biologia Applicata and Industrial Yeasts, Collection DBVPG, Università di Perugia, 06121 Perugia (Italy)
| | - Tommaso Mello
- Dipartimento di Fisiopatologia Clinica, Università di Firenze, 50139 Firenze (Italy)
| | | | - Carla Ghelardini
- Dipartimento di Farmacologia Preclinica e Clinica, Università di Firenze, 50139 Firenze (Italy)
| | - Pietro Buzzini
- Dipartimento di Biologia Applicata and Industrial Yeasts, Collection DBVPG, Università di Perugia, 06121 Perugia (Italy)
| | - Stefano Roelens
- Istituto di Metodologie Chimiche (IMC), Consiglio Nazionale delle Ricerche (CNR), Dipartimento di Chimica, Polo Scientifico e Tecnologico, 50019 Sesto Fiorentino, Firenze (Italy), Fax: (+39) 055‐457‐3570
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22
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Nakagawa Y, Ito Y. Carbohydrate-Binding Molecules with Non-Peptidic Skeletons. TRENDS GLYCOSCI GLYC 2012. [DOI: 10.4052/tigg.24.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Nakagawa Y, Doi T, Takegoshi K, Igarashi Y, Ito Y. Solid-state NMR analysis of calcium and d-mannose binding of BMY-28864, a water-soluble analogue of pradimicin A. Bioorg Med Chem Lett 2012; 22:1040-3. [DOI: 10.1016/j.bmcl.2011.11.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 11/24/2011] [Accepted: 11/28/2011] [Indexed: 11/17/2022]
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24
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Nakagawa Y, Doi T, Masuda Y, Takegoshi K, Igarashi Y, Ito Y. Mapping of the Primary Mannose Binding Site of Pradimicin A. J Am Chem Soc 2011; 133:17485-93. [DOI: 10.1021/ja207816h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yu Nakagawa
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, 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
| | - Yuichi Masuda
- 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
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Science and Technology Agency, ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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