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Omura N, Taguchi A, Kuwahara T, Hamada K, Watanabe M, Nakakuki M, Konno S, Takayama K, Taniguchi A, Nomura T, Shuto S, Hayashi Y. Development of Conformationally Restricted Negamycin Derivatives for Potent Readthrough Activity. ACS Med Chem Lett 2023; 14:1807-1814. [PMID: 38116427 PMCID: PMC10726446 DOI: 10.1021/acsmedchemlett.3c00424] [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: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
(+)-Negamycin, which is a dipeptide-like antibiotic containing a hydrazide structure, exhibits readthrough activity, resulting in the restoration of dystrophin in the mdx mouse model of Duchenne muscular dystrophy (DMD). In our previous structure-activity relationship study of negamycin, we found that its natural analogue 3-epi-deoxynegamycin (TCP-107), without antimicrobial activity, showed a higher readthrough activity than negamycin. In this study, we designed and synthesized cyclopropane-based conformationally restricted derivatives of TCP-107 and evaluated their readthrough activity in the cell-based reporter assay against a TGA-type mutation derived from DMD. As a result, a down-cis isomer, TCP-304, showed significant readthrough activity among the four isomers. Moreover, TCP-306, a derivative acylated by l-α-aminoundecanoic acid, possessed approximately 3 times higher activity than TCP-304. These down-cis derivatives showed dose-dependent readthrough activity and were effective for not only TGA but also TAG mutations. These results suggest that the conformational restriction of negamycin derivatives by the introduction of the cyclopropane ring is effective for an exhibition of potent readthrough activity.
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Affiliation(s)
- Noriko Omura
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Taguchi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tomoki Kuwahara
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Keisuke Hamada
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Mizuki Watanabe
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Masanori Nakakuki
- Research
Center, Mochida Pharmaceutical Co., Ltd., 722 Jimba-aza-Uenohara, Gotemba, Shizuoka 412-8524, Japan
| | - Sho Konno
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kentaro Takayama
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Toshifumi Nomura
- Department
of Dermatology, Hokkaido University Graduate
School of Medicine, North
15 West 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
- Department
of Dermatology, Institute of Medicine, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Satoshi Shuto
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Yoshio Hayashi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Abstract
Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, and School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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De Roo V, Verleysen Y, Kovács B, De Vleeschouwer M, Muangkaew P, Girard L, Höfte M, De Mot R, Madder A, Geudens N, Martins JC. An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides. Microbiol Spectr 2022; 10:e0126122. [PMID: 35876524 PMCID: PMC9431178 DOI: 10.1128/spectrum.01261-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/26/2022] [Indexed: 01/21/2023] Open
Abstract
Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a 'knowledge base' at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer's lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs.
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Affiliation(s)
- Vic De Roo
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Yentl Verleysen
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Benjámin Kovács
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Matthias De Vleeschouwer
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Léa Girard
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent, Belgium
| | - René De Mot
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
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