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Bär D, Konetschny B, Kulik A, Xu H, Paccagnella D, Beller P, Ziemert N, Dickschat JS, Gust B. Origin of the 3-methylglutaryl moiety in caprazamycin biosynthesis. Microb Cell Fact 2022; 21:232. [PMID: 36335365 PMCID: PMC9636800 DOI: 10.1186/s12934-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Caprazamycins are liponucleoside antibiotics showing bioactivity against Gram-positive bacteria including clinically relevant Mycobacterium tuberculosis by targeting the bacterial MraY-translocase. Their chemical structure contains a unique 3-methylglutaryl moiety which they only share with the closely related liposidomycins. Although the biosynthesis of caprazamycin is understood to some extent, the origin of 3-methylglutaryl-CoA for caprazamycin biosynthesis remains elusive. RESULTS In this work, we demonstrate two pathways of the heterologous producer Streptomyces coelicolor M1154 capable of supplying 3-methylglutaryl-CoA: One is encoded by the caprazamycin gene cluster itself including the 3-hydroxy-3-methylglutaryl-CoA synthase Cpz5. The second pathway is part of primary metabolism of the host cell and encodes for the leucine/isovalerate utilization pathway (Liu-pathway). We could identify the liu cluster in S. coelicolor M1154 and gene deletions showed that the intermediate 3-methylglutaconyl-CoA is used for 3-methylglutaryl-CoA biosynthesis. This is the first report of this intermediate being hijacked for secondary metabolite biosynthesis. Furthermore, Cpz20 and Cpz25 from the caprazamycin gene cluster were found to be part of a common route after both individual pathways are merged together. CONCLUSIONS The unique 3-methylglutaryl moiety in caprazamycin originates both from the caprazamycin gene cluster and the leucine/isovalerate utilization pathway of the heterologous host. Our study enhanced the knowledge on the caprazamycin biosynthesis and points out the importance of primary metabolism of the host cell for biosynthesis of natural products.
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Affiliation(s)
- Daniel Bär
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Benjamin Konetschny
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Davide Paccagnella
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Patrick Beller
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bertolt Gust
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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2
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Muramatsu W, Yamamoto H. An economical approach for peptide synthesis via regioselective C-N bond cleavage of lactams. Chem Sci 2022; 13:6309-6315. [PMID: 35733900 PMCID: PMC9159104 DOI: 10.1039/d2sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022] Open
Abstract
An economical, solvent-free, and metal-free method for peptide synthesis via C-N bond cleavage using lactams has been developed. The method not only eliminates the need for condensation agents and their auxiliaries, which are essential for conventional peptide synthesis, but also exhibits high atom economy. The reaction is versatile because it can tolerate side chains bearing a range of functional groups, affording up to >99% yields of the corresponding peptides without racemisation or polymerisation. Moreover, the developed strategy enables peptide segment coupling, providing access to a hexapeptide that occurs as a repeat sequence in spider silk proteins.
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Affiliation(s)
- Wataru Muramatsu
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Hisashi Yamamoto
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
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3
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Okamoto K, Ishikawa A, Okawa R, Yamamoto K, Sato T, Yokota SI, Chiba K, Ichikawa S. Design, synthesis and biological evaluation of simplified analogues of MraY inhibitory natural product with rigid scaffold. Bioorg Med Chem 2022; 55:116556. [PMID: 35016115 DOI: 10.1016/j.bmc.2021.116556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Muraymycins and caprazamycins are strong inhibitors of MraY, which is responsible for peptidoglycan biosynthesis. Although they are promising antibacterial agents with a novel mode of action, their chemical structures are rather complex. This study investigated the simplification of these natural products by structure-based drug design, synthesis, and biological evaluation. We developed a simplified rigid scaffold with an arylalkyne moiety, which shows sub-micromolar MraY inhibitory activity. The scaffold is suitable for further investigating the structure-activity relationship by virtue of our synthetic strategy, where the substituent of interest is installed in the last stage of synthesis. This scaffold shows the potential for further use in optimizing MraY inhibitory and antibacterial activities.
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Affiliation(s)
- Kazuhiro Okamoto
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Aoi Ishikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Ryotaro Okawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan; Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Kazuhiro Chiba
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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4
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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5
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Patel B, Grant G, Zunk M, Rudrawar S. Stereoselective Approaches toward the Synthesis of Nucleoside Antibiotic Core Aminoribosyl Glycyluridine. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Bhautikkumar Patel
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Gary Grant
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Matthew Zunk
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
| | - Santosh Rudrawar
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
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6
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Mashalidis EH, Kaeser B, Terasawa Y, Katsuyama A, Kwon DY, Lee K, Hong J, Ichikawa S, Lee SY. Chemical logic of MraY inhibition by antibacterial nucleoside natural products. Nat Commun 2019; 10:2917. [PMID: 31266949 PMCID: PMC6606608 DOI: 10.1038/s41467-019-10957-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Novel antibacterial agents are needed to address the emergence of global antibiotic resistance. MraY is a promising candidate for antibiotic development because it is the target of five classes of naturally occurring nucleoside inhibitors with potent antibacterial activity. Although these natural products share a common uridine moiety, their core structures vary substantially and they exhibit different activity profiles. An incomplete understanding of the structural and mechanistic basis of MraY inhibition has hindered the translation of these compounds to the clinic. Here we present crystal structures of MraY in complex with representative members of the liposidomycin/caprazamycin, capuramycin, and mureidomycin classes of nucleoside inhibitors. Our structures reveal cryptic druggable hot spots in the shallow inhibitor binding site of MraY that were not previously appreciated. Structural analyses of nucleoside inhibitor binding provide insights into the chemical logic of MraY inhibition, which can guide novel approaches to MraY-targeted antibiotic design.
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Affiliation(s)
- Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Benjamin Kaeser
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Yuma Terasawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Kiyoun Lee
- Department of Chemistry, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
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7
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Patel B, Ryan P, Makwana V, Zunk M, Rudrawar S, Grant G. Caprazamycins: Promising lead structures acting on a novel antibacterial target MraY. Eur J Med Chem 2019; 171:462-474. [DOI: 10.1016/j.ejmech.2019.01.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/29/2022]
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8
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Wiker F, Hauck N, Grond S, Gust B. Caprazamycins: Biosynthesis and structure activity relationship studies. Int J Med Microbiol 2019; 309:319-324. [PMID: 31138496 DOI: 10.1016/j.ijmm.2019.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 11/28/2022] Open
Abstract
Cell wall biosynthesis represents a valid target for antibacterial action but only a limited number of chemical structure classes selectively interact with specific enzymes or protein structures like transporters of the cell envelope. The integral membrane protein MraY translocase is essential for peptidoglycan biosynthesis catalysing the transfer of the peptidoglycan precursor phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl phosphate, thereby generating the cell wall intermediate lipid I. Not present in eukaryotic cells, MraY is a member of the superfamily of yet not well-understood integral membrane enzymes which involve proteins for bacterial lipopolysaccharide and teichoic acid or eukaryotic N-linked saccharides biosynthesis. Different natural nucleoside antibiotics as inhibitors of MraY translocase have been discovered comprising a glycosylated heterocyclic pyrimidin base among other potential lipid-, peptidic- or sugar moieties. Caprazamycins are liponucleoside antibiotics isolated from Streptomyces sp. MK730-62F2. They possess activity in vitro against Gram-positive bacteria, in particular against the genus Mycobacterium including M. intracellulare, M. avium and M. tuberculosis. Structural elucidation revealed the (+)-caprazol core skeleton as a unique moiety, the caprazamycins share with other MraY inhibitors such as the liposidomycins, A-90289 and the muraminomicins. They also share structural features such as uridyl-, aminoribosyl- and fatty acyl-moieties with other MraY translocase inhibitors like FR-900493 and the muraymycins. Intensive studies on their biosynthesis during the last decade identified not only common initial biosynthetic steps, but also revealed possible branching points towards individual biosynthesis of the respective compound. Structural diversity of caprazamycins was generated by feeding experiments, genetic engineering of the biosynthetic gene clusters and chemical synthesis for structure activity relationship studies with its target, MraY translocase.
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Affiliation(s)
- Franziska Wiker
- Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, 72076 Tübingen, Germany
| | - Nils Hauck
- Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, 72076 Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, 72076 Tübingen, Germany.
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9
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Linder R, Ducho C. Unified Synthesis of Densely Functionalized Amino Acid Building Blocks for the Preparation of Caprazamycin Nucleoside Antibiotics. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ruth Linder
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
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10
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Katsuyama A, Ichikawa S. Synthesis and Medicinal Chemistry of Muraymycins, Nucleoside Antibiotics. Chem Pharm Bull (Tokyo) 2018; 66:123-131. [PMID: 29386462 DOI: 10.1248/cpb.c17-00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Muraymycins, isolated from a culture broth of Streptomyces sp., are members of a class of naturally occurring nucleoside antibiotics. They are strong inhibitors of the phospho-MurNAc-pentapeptide translocase (MraY), which is responsible for the peptidoglycan biosynthesis. Since MraY is an essential enzyme among bacteria, muraymycins are expected to be a novel antibacterial agent. In this review, our efforts to synthesize muraymycin D2, simplify the chemical structure, improve antibacterial spectrum, and solve the X-ray crystal structure of the muraymycin D2/MraY complex are described.
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Affiliation(s)
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Science, Hokkaido University.,Center for Research and Education on Drug Discovery, Hokkaido University
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11
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Ying J, Lin R, Xu P, Wu Y, Liu Y, Zhao Y. Prebiotic formation of cyclic dipeptides under potentially early Earth conditions. Sci Rep 2018; 8:936. [PMID: 29343792 PMCID: PMC5772641 DOI: 10.1038/s41598-018-19335-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/27/2017] [Indexed: 11/26/2022] Open
Abstract
Cyclic dipeptides, also known as 2,5-diketopiperazines (DKPs), represent the simplest peptides that were first completely characterized. DKPs can catalyze the chiral selection of reactions and are considered as peptide precursors. The origin of biochemical chirality and synthesis of peptides remains abstruse problem believed to be essential precondition to origin of life. Therefore, it is reasonable to believe that the DKPs could have played a key role in the origin of life. How the formation of the DKPs through the condensation of unprotected amino acids in simulated prebiotic conditions has been unclear. Herein, it was found that cyclo-Pro-Pro could be formed directly from unprotected proline in the aqueous solution of trimetaphosphate (P3m) under mild condition with the yield up to 97%. Other amino acids were found to form proline-containing DKPs under the same conditions in spite of lower yield. During the formation process of these DKPs, P3m promotes the formation of linear dipeptides in the first step of the mechanism. The above findings are helpful and significant for understanding the formation of DKPs in the process of chemical evolution of life.
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Affiliation(s)
- Jianxi Ying
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Rongcan Lin
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Pengxiang Xu
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Yile Wu
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Yan Liu
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China.
| | - Yufen Zhao
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China. .,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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12
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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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13
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Ichikawa S. Function-Oriented Synthesis: How to Design Simplified Analogues of Antibacterial Nucleoside Natural Products? CHEM REC 2016; 16:1106-15. [DOI: 10.1002/tcr.201500247] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Satoshi Ichikawa
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences Hokkaido University; Kita-12 Nishi-6 Kita-ku Sapporo 060-0812 Japan
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14
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Fer MJ, Bouhss A, Patrão M, Le Corre L, Pietrancosta N, Amoroso A, Joris B, Mengin-Lecreulx D, Calvet-Vitale S, Gravier-Pelletier C. 5'-Methylene-triazole-substituted-aminoribosyl uridines as MraY inhibitors: synthesis, biological evaluation and molecular modeling. Org Biomol Chem 2015; 13:7193-222. [PMID: 26008868 DOI: 10.1039/c5ob00707k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The straightforward synthesis of 5'-methylene-[1,4]-triazole-substituted aminoribosyl uridines is described. Two families of compounds were synthesized from a unique epoxide which was regioselectively opened by acetylide ions (for compounds II) or azide ions (for compounds III). Sequential diastereoselective glycosylation with a ribosyl fluoride derivative, Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) with various complementary azide and alkyne partners afforded the targeted compounds after final deprotection. The biological activity of the 16 resulting compounds together with that of 14 previously reported compounds I, lacking the 5' methylene group, was evaluated on the MraY transferase activity. Out of the 30 tested compounds, 18 compounds revealed MraY inhibition with IC50 ranging from 15 to 150 μM. A molecular modeling study was performed to rationalize the observed structure-activity relationships (SAR), which allowed us to correlate the activity of the most potent compounds with an interaction involving Leu191 of MraYAA. The antibacterial activity was also evaluated and seven compounds exhibited a good activity against Gram-positive bacterial pathogens with MIC ranging from 8 to 32 μg mL(-1), including the methicillin resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Mickaël J Fer
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, CICB-Paris (Centre Interdisciplinaire Chimie Biologie-Paris), 45 rue des Saints Pères, 75270 Paris 06, France.
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15
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Ichikawa S, Yamaguchi M, Hsuan LS, Kato Y, Matsuda A. Carbacaprazamycins: Chemically Stable Analogues of the Caprazamycin Nucleoside Antibiotics. ACS Infect Dis 2015; 1:151-6. [PMID: 27622529 DOI: 10.1021/id5000376] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbacaprazamycins, which are chemically stable analogues of caprazamycins, were designed and synthesized. These analogues were active against drug-resistant bacterial pathogens such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, and their activities were comparable to those of the parent caprazamycins. The effect of treatment with carbacaprazamycin on morphological changes in S. aureus indicated that the mode of action was completely different from those of existing peptidoglycan inhibitors.
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Affiliation(s)
- Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences and ‡Center for Research
and Education on Drug Discovery, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Mayumi Yamaguchi
- Faculty of Pharmaceutical Sciences and ‡Center for Research
and Education on Drug Discovery, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Lee Shang Hsuan
- Faculty of Pharmaceutical Sciences and ‡Center for Research
and Education on Drug Discovery, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuta Kato
- Faculty of Pharmaceutical Sciences and ‡Center for Research
and Education on Drug Discovery, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences and ‡Center for Research
and Education on Drug Discovery, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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16
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17
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Nakaya T, Matsuda A, Ichikawa S. Design, synthesis and biological evaluation of 5′-C-piperidinyl-5′-O-aminoribosyluridines as potential antibacterial agents. Org Biomol Chem 2015; 13:7720-35. [DOI: 10.1039/c5ob01037c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Caprazamycin analogues, which were designed and synthesized via an aza-Prins–Ritter reaction, exhibit a good MraY and antibacterial activity without cytotoxicity against human cells.
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Affiliation(s)
- Takeshi Nakaya
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
- Center for Research and Education on Drug Discovery
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
- Center for Research and Education on Drug Discovery
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18
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Yamaguchi M, Matsuda A, Ichikawa S. Synthesis of isoxazolidine-containing uridine derivatives as caprazamycin analogues. Org Biomol Chem 2015; 13:1187-97. [DOI: 10.1039/c4ob02142h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Simplification of caprazamycins was conducted by scaffold-hopping of the structurally complex diazepanone moiety to the isoxazolidine scaffold.
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Affiliation(s)
- Mayumi Yamaguchi
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Sapporo 060-0812
- Japan
- Center for Research and Education on Drug Discovery
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19
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Gopinath P, Wang L, Abe H, Ravi G, Masuda T, Watanabe T, Shibasaki M. Catalytic asymmetric total synthesis of (+)-caprazol. Org Lett 2014; 16:3364-7. [PMID: 24897294 DOI: 10.1021/ol501397b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Catalytic asymmetric total synthesis of caprazol, a lipo-nucleoside antibiotic, has been accomplished employing two of the stereoselective C-C bond forming reactions as key transformations. The stereochemistries of the β-hydroxy-α-aminoester moiety at the juncture of the uridine part and diazepanone part, and of the β-hydroxy-α-amino acid moiety embedded in the diazepanone system, were constructed using a diastereoselective isocyanoacetate aldol reaction (dr = 88:12) and an enantioselective anti-nitroaldol reaction catalyzed by a Nd/Na-chiral amide ligand (dr = 12:1, 95% ee), respectively.
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Affiliation(s)
- Purushothaman Gopinath
- Institute of Microbial Chemistry (BIKAKEN), Tokyo , 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
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20
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Miyaoka H, Wada J, Kawashima E. Synthesis of the Diazepanone-Nucleoside Core Structure of Liposidomycins and Caprazamycins Based on 7-Exo Cyclization of Epoxyamine. HETEROCYCLES 2014. [DOI: 10.3987/com-13-s(s)34] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Fer MJ, Olatunji S, Bouhss A, Calvet-Vitale S, Gravier-Pelletier C. Toward Analogues of MraY Natural Inhibitors: Synthesis of 5′-Triazole-Substituted-Aminoribosyl Uridines Through a Cu-Catalyzed Azide–Alkyne Cycloaddition. J Org Chem 2013; 78:10088-105. [DOI: 10.1021/jo4014035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mickaël J. Fer
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Samir Olatunji
- Laboratoire
des
Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie
et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 11, UMR 8619 CNRS, Orsay F-91405, France
| | - Ahmed Bouhss
- Laboratoire
des
Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie
et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 11, UMR 8619 CNRS, Orsay F-91405, France
| | - Sandrine Calvet-Vitale
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Christine Gravier-Pelletier
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
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22
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Schitter G, Wrodnigg TM. Update on carbohydrate-containing antibacterial agents. Expert Opin Drug Discov 2013; 4:315-56. [PMID: 23489128 DOI: 10.1517/17460440902778725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Since the first known use of antibiotics > 2,500 years ago, a research field with immense importance for the welfare of mankind has been developed. After a decrease in interest in this topic by the end of the 20th century the occurrence of (poly-)resistant strains of bacteria induced a revival of antibiotics research. Health systems have been seeking viable and reliable solutions to this dangerous and expansive threat. OBJECTIVE This review will focus on carbohydrate-containing antibiotics and will give an outline of recently published novel isolated, semisynthetic as well as synthetic structures, their mechanism of action, if known, and the strategies for the design of compounds with potential by improved antibacterial properties. METHODS The literature between 2000 and 2008 was screened with main focus on recent examples of novel structures and strategies for the lead finding of exclusively antibacterial agents. RESULTS/CONCLUSION With the explanation of the role of the carbohydrate moieties in the respective antibacterial agents together with better synthetic strategies in carbohydrate chemistry as well as improvements in assay development for high throughput screening methods, carbohydrate-containing antibiotics can be used for the finding of potential drug leads that contribute to the fight against infections and diseases caused by (resistant) bacterial pathogens.
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Affiliation(s)
- Georg Schitter
- Technical University Graz, Institute of Organic Chemistry, Univ.-Doz. TMW, Dip.-Ing. GS, Glycogroup, A-8010 Graz, Austria +43 316 873 8744 ; +43 316 873 8740 ;
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23
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Sarabia F, Vivar-García C, García-Ruiz C, Martín-Ortiz L, Romero-Carrasco A. Exploring the Chemistry of Epoxy Amides for the Synthesis of the 2′′-epi-Diazepanone Core of Liposidomycins and Caprazamycins. J Org Chem 2012; 77:1328-39. [DOI: 10.1021/jo202061t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francisco Sarabia
- Department of Organic Chemistry, Faculty
of Sciences, University of Malaga, 29071
Malaga, Spain
| | - Carlos Vivar-García
- Department of Organic Chemistry, Faculty
of Sciences, University of Malaga, 29071
Malaga, Spain
| | - Cristina García-Ruiz
- Department of Organic Chemistry, Faculty
of Sciences, University of Malaga, 29071
Malaga, Spain
| | - Laura Martín-Ortiz
- Department of Organic Chemistry, Faculty
of Sciences, University of Malaga, 29071
Malaga, Spain
| | - Antonio Romero-Carrasco
- Department of Organic Chemistry, Faculty
of Sciences, University of Malaga, 29071
Malaga, Spain
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24
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Kirst HA. Recent derivatives from smaller classes of fermentation-derived antibacterials. Expert Opin Ther Pat 2011; 22:15-35. [DOI: 10.1517/13543776.2012.642370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Spork AP, Wiegmann D, Granitzka M, Stalke D, Ducho C. Stereoselective synthesis of uridine-derived nucleosyl amino acids. J Org Chem 2011; 76:10083-98. [PMID: 22059552 DOI: 10.1021/jo201935w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Novel hybrid structures of 5'-deoxyuridine and glycine were conceived and synthesized. Such nucleosyl amino acids (NAAs) represent simplified analogues of the core structure of muraymycin nucleoside antibiotics, making them useful synthetic building blocks for structure-activity relationship (SAR) studies. The key step of the developed synthetic route was the efficient and highly diastereoselective asymmetric hydrogenation of didehydro amino acid precursors toward protected NAAs. It was anticipated that the synthesis of unprotected muraymycin derivatives via this route would require a suitable intermediate protecting group at the N-3 of the uracil base. After initial attempts using PMB- and BOM-N-3 protection, both of which resulted in problematic deprotection steps, an N-3 protecting group-free route was envisaged. In spite of the pronounced acidity of the uracil-3-NH, this route worked equally efficient and with identical stereoselectivities as the initial strategies involving N-3 protection. The obtained NAA building blocks were employed for the synthesis of truncated 5'-deoxymuraymycin analogues.
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Affiliation(s)
- Anatol P Spork
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37 077 Göttingen, Germany
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26
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Tanino T, Al-Dabbagh B, Mengin-Lecreulx D, Bouhss A, Oyama H, Ichikawa S, Matsuda A. Mechanistic Analysis of Muraymycin Analogues: A Guide to the Design of MraY Inhibitors. J Med Chem 2011; 54:8421-39. [DOI: 10.1021/jm200906r] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tetsuya Tanino
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Bayan Al-Dabbagh
- Laboratoire
des Enveloppes Bactériennes
et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire
et Cellulaire, UMR 8619 CNRS, Université Paris-Sud, Bâtiment 430, Orsay F-91405, France
| | - Dominique Mengin-Lecreulx
- Laboratoire
des Enveloppes Bactériennes
et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire
et Cellulaire, UMR 8619 CNRS, Université Paris-Sud, Bâtiment 430, Orsay F-91405, France
| | - Ahmed Bouhss
- Laboratoire
des Enveloppes Bactériennes
et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire
et Cellulaire, UMR 8619 CNRS, Université Paris-Sud, Bâtiment 430, Orsay F-91405, France
| | - Hiroshi Oyama
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21, Nishi-11, Kita-ku, Sapporo 001-0021, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
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27
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Mravljak J, Monasson O, Al-Dabbagh B, Crouvoisier M, Bouhss A, Gravier-Pelletier C, Le Merrer Y. Synthesis and biological evaluation of a diazepanone-based library of liposidomycins analogs as MraY inhibitors. Eur J Med Chem 2011; 46:1582-92. [DOI: 10.1016/j.ejmech.2011.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 02/01/2011] [Accepted: 02/03/2011] [Indexed: 11/29/2022]
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28
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Ichikawa S, Tanino T, Ii K, Matsuda A. Development of Antibacterial Agents Active against Drug-resistant Bacterial Pathogens Based on Total Synthesis of Nucleoside Natural Products. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.1020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Spork AP, Ducho C. Novel 5'-deoxy nucleosyl amino acid scaffolds for the synthesis of muraymycin analogues. Org Biomol Chem 2010; 8:2323-6. [PMID: 20386790 DOI: 10.1039/c003092a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naturally occurring nucleoside antibiotics such as muraymycins represent promising lead structures for the development of novel antibacterial agents. A concise synthesis of 5'-deoxy muraymycin derivatives has been developed. The key step was the highly stereoselective asymmetric hydrogenation of suitable didehydro amino acid precursors, providing unique nucleosyl amino acid structures.
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Affiliation(s)
- Anatol P Spork
- Georg-August-University Göttingen, Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Tammannstr. 2, 37077 Göttingen, Germany
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30
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Ii K, Ichikawa S, Al-Dabbagh B, Bouhss A, Matsuda A. Function-oriented synthesis of simplified caprazamycins: discovery of oxazolidine-containing uridine derivatives as antibacterial agents against drug-resistant bacteria. J Med Chem 2010; 53:3793-813. [PMID: 20405928 DOI: 10.1021/jm100243n] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rational simplification of the caprazamycin (CPZ) class of nucleoside natural products was carried out to address their molecular complexity. First, analogues 6-8, where the diazepanone ring of the CPZ was removed and a lipophilic side chain was attached to either the C-7' or N(6') atom, were used to investigate the conformation-activity relationship. On the basis of this relationship, we designed the oxazolidine-containing uridine derivatives 18-21 by restricting the conformation of 6-8. As a result, the (t)Bu ester derivatives 20 were found to be the most active against a range of bacterial strains containing VRE with a potency similar to that of the parent CPZs. This study provides a novel strategy for the development of a new type of antibacterial agent effective against drug-resistant bacteria.
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Affiliation(s)
- Kensuke Ii
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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31
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32
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Kaysser L, Eitel K, Tanino T, Siebenberg S, Matsuda A, Ichikawa S, Gust B. A new arylsulfate sulfotransferase involved in liponucleoside antibiotic biosynthesis in streptomycetes. J Biol Chem 2010; 285:12684-94. [PMID: 20157116 DOI: 10.1074/jbc.m109.094490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sulfotransferases are involved in a variety of physiological processes and typically use 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as the sulfate donor substrate. In contrast, microbial arylsulfate sulfotransferases (ASSTs) are PAPS-independent and utilize arylsulfates as sulfate donors. Yet, their genuine acceptor substrates are unknown. In this study we demonstrate that Cpz4 from Streptomyces sp. MK730-62F2 is an ASST-type sulfotransferase responsible for the formation of sulfated liponucleoside antibiotics. Gene deletion mutants showed that cpz4 is required for the production of sulfated caprazamycin derivatives. Cloning, overproduction, and purification of Cpz4 resulted in a 58-kDa soluble protein. The enzyme catalyzed the transfer of a sulfate group from p-nitrophenol sulfate (K(m) 48.1 microM, k(cat) 0.14 s(-1)) and methyl umbelliferone sulfate (K(m) 34.5 microM, k(cat) 0.15 s(-1)) onto phenol (K(m) 25.9 and 29.7 mM, respectively). The Cpz4 reaction proceeds by a ping pong bi-bi mechanism. Several structural analogs of intermediates of the caprazamycin biosynthetic pathway were synthesized and tested as substrates of Cpz4. Des-N-methyl-acyl-caprazol was converted with highest efficiency 100 times faster than phenol. The fatty acyl side chain and the uridyl moiety seem to be important for substrate recognition by Cpz4. Liponucleosides, partially purified from various mutant strains, were readily sulfated by Cpz4 using p-nitrophenol sulfate. No product formation could be observed with PAPS as the donor substrate. Sequence homology of Cpz4 to the previously examined ASSTs is low. However, numerous orthologs are encoded in microbial genomes and represent interesting subjects for future investigations.
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Affiliation(s)
- Leonard Kaysser
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
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33
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Tanino T, Ichikawa S, Shiro M, Matsuda A. Total Synthesis of (−)-Muraymycin D2 and Its Epimer. J Org Chem 2010; 75:1366-77. [DOI: 10.1021/jo9027193] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tetsuya Tanino
- Faculty of Pharmaceutical Sciences, Hokkaido University Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, Rigaku Corporation, 3-9-12 Matsubara, Akishima, Tokyo 196-0003, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, Rigaku Corporation, 3-9-12 Matsubara, Akishima, Tokyo 196-0003, Japan
| | - Motoo Shiro
- Faculty of Pharmaceutical Sciences, Hokkaido University Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, Rigaku Corporation, 3-9-12 Matsubara, Akishima, Tokyo 196-0003, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, Rigaku Corporation, 3-9-12 Matsubara, Akishima, Tokyo 196-0003, Japan
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34
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Winn M, Goss RJM, Kimura KI, Bugg TDH. Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis. Nat Prod Rep 2009; 27:279-304. [PMID: 20111805 DOI: 10.1039/b816215h] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quest for new antibiotics, especially those with activity against Gram-negative bacteria, is urgent; however, very few new antibiotics have been marketed in the last 40 years, with this limited number falling into only four new structural classes. Several nucleoside natural product antibiotics target bacterial translocase MraY, involved in the lipid-linked cycle of peptidoglycan biosynthesis, and fungal chitin synthase. Biosynthetic studies on the nikkomycin, caprazamycin and pacidamycin/mureidomycin families are also reviewed.
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Affiliation(s)
- Michael Winn
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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35
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Monasson O, Ginisty M, Mravljak J, Bertho G, Gravier-Pelletier C, Le Merrer Y. Synthetic studies towards diazepanone scaffolds. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Raman K, Yeturu K, Chandra N. targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC SYSTEMS BIOLOGY 2008; 2:109. [PMID: 19099550 PMCID: PMC2651862 DOI: 10.1186/1752-0509-2-109] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Accepted: 12/19/2008] [Indexed: 01/19/2023]
Abstract
Background Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.
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Affiliation(s)
- Karthik Raman
- Supercomputer Education and Research Centre and Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.
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37
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Ichikawa S. [Medicinal chemistry targeting nucleosides and nucleic acids based on fine synthetic chemistry]. YAKUGAKU ZASSHI 2008; 128:1403-30. [PMID: 18827462 DOI: 10.1248/yakushi.128.1403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleosides and nucleotides are one of the most important elements for cells by the fact that they are components of DNAs and RNAs. In addition, they play important roles in most fundamental cellular metabolic pathways such as energy donors, second messengers, and cofactors for various enzymes. Therefore, there exists a rich source in drug discovery targeting nucleosides and nucleotides. In order to utilize nucleosides and nucleic acids on the drug development, it is very important to develop reactions and methods, by which the highly coordinating and labile nucleoside intermediates can be used. With these in mind, we have been working on synthetic nucleoside and nucleic acid chemistry. First, branched sugar nucleoside derivatives, which are potential antitumor agents, have been synthesized utilizing samarium diiodide (SmI(2)) mediated Reformatsky reaction or aldol reaction. 3'-beta-Carbamoylmethylcytidine (CAMC) was found to exhibit potent cytotoxicity against various human tumor cell lines. Synthetic methodology of the caprazamycins, which are promising antibacterial nucleoside natural products, was also developed by the strategy including beta-selective ribosylation without using a neighboring group participation. Our synthetic route provided a range of key analogues with partial structures to define the pharmacophore. Simplification of the caprazamycins was further pursued to develop diketopiperazine analogs. Medicinal chemistry of oligodeoxynucleotides has been conducted. Thus, novel triazole-linked dumbbell oligodeoxynucleotides and modular bent oligodeoxynucleotides were synthesized. They exhibit excellent binding affinity to NF-kappaB or HMGB1 A-box protein, which are important therapeutic targets. Therefore, the results obtained conclusively demonstrated these oligodeoxynucleotides could be proposed as powerful decoy molecules.
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Hirano S, Ichikawa S, Matsuda A. Structure-activity relationship of truncated analogs of caprazamycins as potential anti-tuberculosis agents. Bioorg Med Chem 2008; 16:5123-33. [PMID: 18375127 DOI: 10.1016/j.bmc.2008.03.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 11/29/2022]
Abstract
Systematic structure-activity relationship studies of caprazamycin (CPZ) analogs, including the aminoribose-truncated 5 and the uridine-truncated 6, have been carried out. Both 5 and 6 were synthesized efficiently via diazepanone ring construction by intramolecular reductive alkylation of aminoaldehyde derivatives. The antibacterial activity of a range of analogs, including 5 and 6, against Mycobacteriumosis was evaluated, and it was found that the uridine, the aminoribose, and the fatty acyl side chains are crucial for antibacterial activity. This study would be a guide for designing novel anti-tuberculosis agents based on the 6'-N-alkyl-5'-beta-O-aminoribosyl-glycyluridine class of antibiotics including the CPZs.
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Affiliation(s)
- Shinpei Hirano
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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Ichikawa S. Fine Synthetic Nucleoside Chemistry Based on Nucleoside Natural Products Synthesis. Chem Pharm Bull (Tokyo) 2008; 56:1059-72. [DOI: 10.1248/cpb.56.1059] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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