101
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Chen Q, Zhang JW, Chen LL, Yang J, Yang XL, Ling Y, Yang Q. Design and synthesis of chitin synthase inhibitors as potent fungicides. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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102
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Bugg TDH. Nucleoside Natural Product Antibiotics Targetting Microbial Cell Wall Biosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/7355_2017_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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103
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Biosynthesis of 2'-Chloropentostatin and 2'-Amino-2'-Deoxyadenosine Highlights a Single Gene Cluster Responsible for Two Independent Pathways in Actinomadura sp. Strain ATCC 39365. Appl Environ Microbiol 2017; 83:AEM.00078-17. [PMID: 28258148 DOI: 10.1128/aem.00078-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/26/2017] [Indexed: 01/30/2023] Open
Abstract
2'-Chloropentostatin (2'-Cl PTN, 2'-chloro-2'-deoxycoformycin) and 2'-amino-2'-deoxyadenosine (2'-amino dA) are two adenosine-derived nucleoside antibiotics coproduced by Actinomadura sp. strain ATCC 39365. 2'-Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring, as well as a chlorination at C-2' of ribose, and 2'-amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood. Here, we report the identification of a single gene cluster (ada) essential for the biosynthesis of 2'-Cl PTN and 2'-amino dA. Further systematic genetic investigations suggest that 2'-Cl PTN and 2'-amino dA are biosynthesized by independent pathways. Moreover, we provide evidence that a predicted cation/H+ antiporter, AdaE, is involved in the chlorination step during 2'-Cl PTN biosynthesis. Notably, we demonstrate that 2'-amino dA biosynthesis is initiated by a Nudix hydrolase, AdaJ, catalyzing the hydrolysis of ATP. Finally, we reveal that the host ADA (designated ADA1), capable of converting adenosine/2'-amino dA to inosine/2'-amino dI, is not very sensitive to the powerful ADA inhibitor pentostatin. These findings provide a basis for the further rational pathway engineering of 2'-Cl PTN and 2'-amino dA production.IMPORTANCE 2'-Cl PTN/PTN and 2'-amino dA have captivated the great interests of scientists, owing to their unusual chemical structures and remarkable bioactivities. However, the precise logic for their biosynthesis has been elusive for decades. Actually, the identification and elucidation of their biosynthetic pathways not only enrich the biochemical repertoire of novel enzymatic reactions but may also lay solid foundations for the pathway engineering and combinatorial biosynthesis of this family of purine nucleoside antibiotics to generate novel hybrid analogs with improved features.
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104
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Wang SS, Zhang NN, He N, Guo WQ, Lei X, Cai Q, Hong B, Xie YY. Exploiting Substrate Diversity of NRPS Led to the Generation of New Sansanmycin Analogs. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701200524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Further exploration of substrate diversity of the sansanmycin biosynthetic pathway using available halogen- and methyl-phenylalanines led to the generation of diverse sansanmycin derivatives, either at the single C- or N-terminus alone or at both C- and N-termini. The structures of all of these derivatives were determined by MS/MS spectra, and amongst them, the structures of [2-Cl-Phe]-sansanmycin H (1) and [2-Cl-Phe]-sansanmycin A (2) were further identified by NMR. Both the C-terminal derivative 1 and the N-terminal derivative 2 were assayed for their antibacterial activities, and compound 1 exhibited moderate activity against P. aeruginosa and ΔtolC mutant E. coli.
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Affiliation(s)
- Shan-Shan Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ning-Ning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ning He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Wen-Qiang Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuan Lei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qiang Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Bin Hong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yun-Ying Xie
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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105
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Nature's combinatorial biosynthesis and recently engineered production of nucleoside antibiotics in Streptomyces. World J Microbiol Biotechnol 2017; 33:66. [PMID: 28260195 DOI: 10.1007/s11274-017-2233-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/22/2017] [Indexed: 10/20/2022]
Abstract
Modified nucleosides produced by Streptomyces and related actinomycetes are widely used in agriculture and medicine as antibacterial, antifungal, anticancer and antiviral agents. These specialized small-molecule metabolites are biosynthesized by complex enzymatic machineries encoded within gene clusters in the genome. The past decade has witnessed a burst of reports defining the key metabolic processes involved in the biosynthesis of several distinct families of nucleoside antibiotics. Furthermore, genome sequencing of various Streptomyces species has dramatically increased over recent years. Potential biosynthetic gene clusters for novel nucleoside antibiotics are now apparent by analysis of these genomes. Here we revisit strategies for production improvement of nucleoside antibiotics that have defined mechanisms of action, and are in clinical or agricultural use. We summarize the progress for genetically manipulating biosynthetic pathways for structural diversification of nucleoside antibiotics. Microorganism-based biosynthetic examples are provided and organized under genetic principles and metabolic engineering guidelines. We show perspectives on the future of combinatorial biosynthesis, and present a working model for discovery of novel nucleoside natural products in Streptomyces.
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106
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Peitsinis ZV, Mitrakas AG, Nakiou EA, Melidou DA, Kalamida D, Kakouratos C, Koukourakis MI, Koumbis AE. Trachycladines and Analogues: Synthesis and Evaluation of Anticancer Activity. ChemMedChem 2017; 12:448-455. [PMID: 28195671 DOI: 10.1002/cmdc.201600620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/14/2017] [Indexed: 02/05/2023]
Abstract
The synthesis of four new analogues of marine nucleoside trachycladine A was accomplished by direct regio- and stereoselective Vorbrüggen glycosylations of 2,6-dichloropurine and 2-chloropurine with a d-ribose-derived chiron. Naturally occurring trachycladines A and B and a series of analogues were examined for their cytotoxic activity against a number of cancer cell lines (glioblastoma, lung, and cervical cancer). Parent trachycladine A and two analogues (the diacetate of the 2,6-dichloropurine derivative and N-cyclopropyl trachycladine A) resulted in a significant decrease in cell viability, with the latter exhibiting a stronger effect. The same compounds enhanced the cytotoxic effect of docetaxel in lung cancer cell lines, whereas additional experiments revealed that their mode of action relies on mitotic catastrophe rather than DNA damage. Moreover, their activity as autophagic flux blockers was postulated.
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Affiliation(s)
- Zisis V Peitsinis
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Achilleas G Mitrakas
- Department of Radiotherapy and Oncology, Radiobiology and Radiopathology Unit, Medical School, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Eirini A Nakiou
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dafni A Melidou
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitra Kalamida
- Department of Radiotherapy and Oncology, Radiobiology and Radiopathology Unit, Medical School, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Christos Kakouratos
- Department of Radiotherapy and Oncology, Radiobiology and Radiopathology Unit, Medical School, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Michael I Koukourakis
- Department of Radiotherapy and Oncology, Radiobiology and Radiopathology Unit, Medical School, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Alexandros E Koumbis
- Laboratory of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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107
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Sansanmycin natural product analogues as potent and selective anti-mycobacterials that inhibit lipid I biosynthesis. Nat Commun 2017; 8:14414. [PMID: 28248311 PMCID: PMC5337940 DOI: 10.1038/ncomms14414] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022] Open
Abstract
Tuberculosis (TB) is responsible for enormous global morbidity and mortality, and current treatment regimens rely on the use of drugs that have been in use for more than 40 years. Owing to widespread resistance to these therapies, new drugs are desperately needed to control the TB disease burden. Herein, we describe the rapid synthesis of analogues of the sansanmycin uridylpeptide natural products that represent promising new TB drug leads. The compounds exhibit potent and selective inhibition of Mycobacterium tuberculosis, the etiological agent of TB, both in vitro and intracellularly. The natural product analogues are nanomolar inhibitors of Mtb phospho-MurNAc-pentapeptide translocase, the enzyme responsible for the synthesis of lipid I in mycobacteria. This work lays the foundation for the development of uridylpeptide natural product analogues as new TB drug candidates that operate through the inhibition of peptidoglycan biosynthesis. Drug resistant tuberculosis (TB) infections are emerging at a high rate, with only few therapeutic options currently available. Here, the authors report synthetic analogues of the natural product sansanmycin that target mycobacterial cell wall biosynthesis and represent potent leads for improved anti-TB treatments.
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108
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Goswami A, Liu X, Cai W, Wyche TP, Bugni TS, Meurillon M, Peyrottes S, Perigaud C, Nonaka K, Rohr J, Van Lanen SG. Evidence that oxidative dephosphorylation by the nonheme Fe(II), α-ketoglutarate:UMP oxygenase occurs by stereospecific hydroxylation. FEBS Lett 2017; 591:468-478. [PMID: 28074470 DOI: 10.1002/1873-3468.12554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 12/23/2016] [Accepted: 12/25/2016] [Indexed: 11/08/2022]
Abstract
LipL and Cpr19 are nonheme, mononuclear Fe(II)-dependent, α-ketoglutarate (αKG):UMP oxygenases that catalyze the formation of CO2 , succinate, phosphate, and uridine-5'-aldehyde, the last of which is a biosynthetic precursor for several nucleoside antibiotics that inhibit bacterial translocase I (MraY). To better understand the chemistry underlying this unusual oxidative dephosphorylation and establish a mechanistic framework for LipL and Cpr19, we report herein the synthesis of two biochemical probes-[1',3',4',5',5'-2 H]UMP and the phosphonate derivative of UMP-and their activity with both enzymes. The results are consistent with a reaction coordinate that proceeds through the loss of one 2 H atom of [1',3',4',5',5'-2 H]UMP and stereospecific hydroxylation geminal to the phosphoester to form a cryptic intermediate, (5'R)-5'-hydroxy-UMP. Thus, these enzyme catalysts can additionally be assigned as UMP hydroxylase-phospholyases.
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Affiliation(s)
- Anwesha Goswami
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Xiaodong Liu
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Thomas P Wyche
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, WI, USA
| | - Tim S Bugni
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, WI, USA
| | - Maïa Meurillon
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Suzanne Peyrottes
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Christian Perigaud
- Nucleosides and Phosphorylated Effectors Team, IBMM, UMR5247 CNRS University Montpellier, France
| | - Koichi Nonaka
- Biologics Technology Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Gunma, Japan
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
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109
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An Unusual Protector-Protégé Strategy for the Biosynthesis of Purine Nucleoside Antibiotics. Cell Chem Biol 2017; 24:171-181. [PMID: 28111097 DOI: 10.1016/j.chembiol.2016.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/07/2016] [Accepted: 12/19/2016] [Indexed: 01/17/2023]
Abstract
Pentostatin (PTN, deoxycoformycin) and arabinofuranosyladenine (Ara-A, vidarabine) are purine nucleoside antibiotics used clinically to treat hematological cancers and human DNA virus infections, respectively. PTN has a 1,3-diazepine ring, and Ara-A is an adenosine analog with an intriguing epimerization at the C-2' hydroxyl group. However, the logic underlying the biosynthesis of these interesting molecules has long remained elusive. Here, we report that the biosynthesis of PTN and Ara-A employs an unusual protector-protégé strategy. To our surprise, we determined that a single gene cluster governs PTN and Ara-A biosynthesis via two independent pathways. Moreover, we verified that PenB functions as a reversible oxidoreductase for the final step of PTN. Remarkably, we provided the first direct biochemical evidence that PTN can protect Ara-A from deamination by selective inhibition of the host adenosine deaminase. These findings expand our knowledge of natural product biosynthesis and open the way for target-directed genome mining of Ara-A/PTN-related antibiotics.
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110
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New tuberculosis drug leads from naturally occurring compounds. Int J Infect Dis 2017; 56:212-220. [PMID: 28062229 DOI: 10.1016/j.ijid.2016.12.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant cause of mortality and morbidity worldwide. An estimated 2 billion individuals are infected with Mycobacterium tuberculosis and annually there are approximately 10 million new cases of clinical TB and 1.5 million deaths. Currently available drugs and vaccines have had no significant impact on TB control. In addition, the emergence of drug resistant TB is considered a public health crisis, with some strains now resistant to all available drugs. Unfortunately, the growing burden of antibiotic resistance is coupled with decreased effort in the development of new antibiotics. Natural sources are attractive starting points in the search for anti-tubercular drugs because they are extremely rich in chemical diversity and have privileged antimicrobial activity. This review will discuss recent advances in the development of TB drug leads from natural products, with a particular focus on anti-mycobacterial compounds in late-stage preclinical and clinical development.
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111
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He N, Wu P, Lei Y, Xu B, Zhu X, Xu G, Gao Y, Qi J, Deng Z, Tang G, Chen W, Xiao Y. Construction of an octosyl acid backbone catalyzed by a radical S-adenosylmethionine enzyme and a phosphatase in the biosynthesis of high-carbon sugar nucleoside antibiotics. Chem Sci 2017; 8:444-451. [PMID: 28451191 PMCID: PMC5365060 DOI: 10.1039/c6sc01826b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023] Open
Abstract
Unique bicyclic octosyl uronic acid nucleosides include ezomycin, malayamycin, and octosyl acid (OA). They are structurally characterized by OA, an unusual 8-carbon furanosyl nucleoside core proposed to be the precursor to polyoxin and nikkomycin. Despite the well-known bioactivity of these nucleoside antibiotics, the biosynthesis of OA has not been elucidated yet. Here we report the two pivotal enzymatic steps in the polyoxin biosynthetic pathway leading to the identification of OA as a key intermediate. Our data suggest that this intermediate is formed via a free radical reaction catalyzed by the radical S-adenosylmethionine (SAM) enzyme, PolH, and using 3'-enolpyruvyl uridine 5'-monophosphate (3'-EUMP) as a substrate. Subsequent dephosphorylation catalyzed by phosphatase PolJ converts the resulting octosyl acid 5'-phosphate (OAP) to OA. These results provide, for the first time, significant in vitro evidence for the biosynthetic origins of the C8 backbone of OA.
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Affiliation(s)
- Nisha He
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Pan Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yongxing Lei
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Baofu Xu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Xiaochen Zhu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
| | - Gudan Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yaojie Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Jianzhao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Gongli Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
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112
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meta-Tyrosine induces modification of reactive nitrogen species level, protein nitration and nitrosoglutathione reductase in tomato roots. Nitric Oxide 2016; 68:56-67. [PMID: 27810375 DOI: 10.1016/j.niox.2016.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/26/2016] [Accepted: 10/29/2016] [Indexed: 12/12/2022]
Abstract
A non-protein amino acid (NPAA) - meta-Tyrosine (m-Tyr), is a harmful compound produced by fescue roots. Young (3-4 days old) tomato (Solanum lycopersicum L.) seedlings were supplemented for 24-72 h with m-Tyr (50 or 250 μM) inhibiting root growth by 50 or 100%, without lethal effect. Fluorescence of DAF-FM and APF derivatives was determined to show reactive nitrogen species (RNS) localization and level in roots of tomato plants. m-Tyr-induced restriction of root elongation growth was related to formation of nitrated proteins described as content of 3-nitrotyrosine. Supplementation with m-Tyr enhanced superoxide radicals generation in extracts of tomato roots and stimulated protein nitration. It correlated well to increase of fluorescence of DAF-FM derivatives, and transiently stimulated fluorescence of APF derivatives corresponding respectively to NO and ONOO- formation. Alterations in RNS formation induced by m-Tyr were linked to metabolism of nitrosoglutathione (GSNO). Activity of nitrosoglutatione reductase (GSNOR), catalyzing degradation of GSNO was enhanced by long term plant supplementation with m-Tyr, similarly as protein abundance, while transcripts level were only slightly altered by tested NPAA. We conclude, that although in animal cells m-Tyr is considered as a marker of oxidative stress, its secondary mode of action in tomato plants involves perturbation in RNS formation, alteration in GSNO metabolism and modification of protein nitration level.
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113
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Wohnig S, Spork AP, Koppermann S, Mieskes G, Gisch N, Jahn R, Ducho C. Total Synthesis of Dansylated Park's Nucleotide for High-Throughput MraY Assays. Chemistry 2016; 22:17813-17819. [PMID: 27791327 DOI: 10.1002/chem.201604279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/11/2022]
Abstract
The membrane protein translocase I (MraY) is a key enzyme in bacterial peptidoglycan biosynthesis. It is therefore frequently discussed as a target for the development of novel antibiotics. The screening of compound libraries for the identification of MraY inhibitors is enabled by an established fluorescence-based MraY assay. However, this assay requires a dansylated derivative of the bacterial biosynthetic intermediate Park's nucleotide as the MraY substrate. Isolation of Park's nucleotide from bacteria and subsequent dansylation only furnishes limited amounts of this substrate, thus hampering the high-throughput screening for MraY inhibitors. Accordingly, the efficient provision of dansylated Park's nucleotide is a major bottleneck in the exploration of this promising drug target. In this work, we present the first total synthesis of dansylated Park's nucleotide, affording an unprecedented amount of the target compound for high-throughput MraY assays.
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Affiliation(s)
- Stephanie Wohnig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Anatol P Spork
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany.,Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Gottfried Mieskes
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845, Borstel, Germany
| | - Reinhard Jahn
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
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114
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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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115
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Mitachi K, Aleiwi BA, Schneider CM, Siricilla S, Kurosu M. Stereocontrolled Total Synthesis of Muraymycin D1 Having a Dual Mode of Action against Mycobacterium tuberculosis. J Am Chem Soc 2016; 138:12975-12980. [PMID: 27617631 DOI: 10.1021/jacs.6b07395] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A stereocontrolled first total synthesis of muraymycin D1 (1) has been achieved. The synthetic route is highly stereoselective, featuring (1) selective β-ribosylation of the C2-methylated amino ribose, (2) selective Strecker reaction, and (3) ring-opening reaction of a diastereomeric mixture of a diaminolactone to synthesize muraymycidine (epi-capreomycidine). The acid-cleavable protecting groups for secondary alcohol and uridine ureido nitrogen are applied for simultaneous deprotections with the Boc and tBu groups. Muraymycin D1 (1) and its amide derivatives (2 and 3) exhibited growth inhibitory activity against Mycobacterium tuberculosis (MIC50 = 1.56-6.25 μg/mL) and strong enzyme inhibitory activities against the bacterial phosphotransferases (MurX and WecA) (IC50 = 0.096-0.69 μM).
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Bilal A Aleiwi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Christopher M Schneider
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Shajila Siricilla
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , 881 Madison Avenue, Memphis, Tennessee 38163, United States
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González-Calderón D, Mejía-Dionicio MG, Morales-Reza MA, Aguirre-de Paz JG, Ramírez-Villalva A, Morales-Rodríguez M, Fuentes-Benítes A, González-Romero C. Antifungal activity of 1'-homo-N-1,2,3-triazol-bicyclic carbonucleosides: A novel type of compound afforded by azide-enolate (3+2) cycloaddition. Bioorg Chem 2016; 69:1-6. [PMID: 27656774 DOI: 10.1016/j.bioorg.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/01/2016] [Accepted: 09/14/2016] [Indexed: 01/06/2023]
Abstract
The first report of 1'-homo-N-1,2,3-triazol-bicyclic carbonucleosides (7a and 7b) is described herein. Azide-enolate (3+2) cycloaddition afforded the synthesis of this novel type of compound. Antifungal activity was evaluated in vitro against four filamentous fungi (Aspergillus fumigatus, Trichosporon cutaneum, Rhizopus oryzae and Mucor hiemalis) as well as nine species of Candida spp. as yeast specimens. These pre-clinical studies suggest that compounds 7a and 7b are promising candidates for complementary biological studies due to their good activity against Candida spp.
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Affiliation(s)
- Davir González-Calderón
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico.
| | - María G Mejía-Dionicio
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Marco A Morales-Reza
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - José G Aguirre-de Paz
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Alejandra Ramírez-Villalva
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Macario Morales-Rodríguez
- Departamento de Microbiología, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Aydeé Fuentes-Benítes
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Carlos González-Romero
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico.
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117
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Structural Investigation of Park's Nucleotide on Bacterial Translocase MraY: Discovery of Unexpected MraY Inhibitors. Sci Rep 2016; 6:31579. [PMID: 27531195 PMCID: PMC4987650 DOI: 10.1038/srep31579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/26/2016] [Indexed: 11/17/2022] Open
Abstract
Systematic structural modifications of the muramic acid, peptide, and nucleotide moieties of Park’s nucleotide were performed to investigate the substrate specificity of B. subtilis MraY (MraYBS). It was found that the simplest analogue of Park’s nucleotide only bearing the first two amino acids, l-alanine-iso-d-glutamic acid, could function as a MraYBS substrate. Also, the acid group attached to the Cα of iso-d-glutamic acid was found to play an important role for substrate activity. Epimerization of the C4-hydroxyl group of muramic acid and modification at the 5-position of the uracil in Park’s nucleotide were both found to dramatically impair their substrate activity. Unexpectedly, structural modifications on the uracil moiety changed the parent molecule from a substrate to an inhibitor, blocking the MraYBS translocation. One unoptimized inhibitor was found to have a Ki value of 4 ± 1 μM against MraYBS, more potent than tunicamycins.
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118
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Mitachi K, Siricilla S, Yang D, Kong Y, Skorupinska-Tudek K, Swiezewska E, Franzblau SG, Kurosu M. Fluorescence-based assay for polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA) and identification of novel antimycobacterial WecA inhibitors. Anal Biochem 2016; 512:78-90. [PMID: 27530653 DOI: 10.1016/j.ab.2016.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/18/2016] [Accepted: 08/08/2016] [Indexed: 11/26/2022]
Abstract
Polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA) is an essential enzyme for the growth of Mycobacterium tuberculosis (Mtb) and some other bacteria. Mtb WecA catalyzes the transformation from UDP-GlcNAc to decaprenyl-P-P-GlcNAc, the first membrane-anchored glycophospholipid that is responsible for the biosynthesis of mycolylarabinogalactan in Mtb. Inhibition of WecA will block the entire biosynthesis of essential cell wall components of Mtb in both replicating and non-replicating states, making this enzyme a target for development of novel drugs. Here, we report a fluorescence-based method for the assay of WecA using a modified UDP-GlcNAc, UDP-Glucosamine-C6-FITC (1), a membrane fraction prepared from an M. smegmatis strain, and the E. coli B21WecA. Under the optimized conditions, UDP-Glucosamine-C6-FITC (1) can be converted to the corresponding decaprenyl-P-P-Glucosamine-C6-FITC (3) in 61.5% yield. Decaprenyl-P-P-Glucosamine-C6-FITC is readily extracted with n-butanol and can be quantified by ultraviolet-visible (UV-vis) spectrometry. Screening of the compound libraries designed for bacterial phosphotransferases resulted in the discovery of a selective WecA inhibitor, UT-01320 (12) that kills both replicating and non-replicating Mtb at low concentration. UT-01320 (12) also kills the intracellular Mtb in macrophages. We conclude that the WecA assay reported here is amenable to medium- and high-throughput screening, thus facilitating the discovery of novel WecA inhibitors.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163-0001, United States
| | - Shajila Siricilla
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163-0001, United States
| | - Dong Yang
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163-0001, United Sates
| | - Ying Kong
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163-0001, United Sates
| | - Karolina Skorupinska-Tudek
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Ewa Swiezewska
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL 60612, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163-0001, United States.
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119
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Koppermann S, Ducho C. Natural Products at Work: Structural Insights into Inhibition of the Bacterial Membrane Protein MraY. Angew Chem Int Ed Engl 2016; 55:11722-4. [DOI: 10.1002/anie.201606396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan Koppermann
- 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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120
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Koppermann S, Ducho C. Naturstoffe bei der Arbeit: strukturelle Einblicke in die Inhibition des bakteriellen Membranproteins MraY. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stefan Koppermann
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| | - Christian Ducho
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
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Liu Y, Rodrigues JPGLM, Bonvin AMJJ, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR. New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. J Biol Chem 2016; 291:15057-68. [PMID: 27226570 DOI: 10.1074/jbc.m116.717884] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/01/2023] Open
Abstract
Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide.
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Affiliation(s)
- Yao Liu
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | | | | | - Esther A Zaal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Celia R Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Michal Heger
- the Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands, and
| | - Katarzyna Gawarecka
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewa Swiezewska
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Eefjan Breukink
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands,
| | - Maarten R Egmond
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
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Shi Y, Jiang Z, Lei X, Zhang N, Cai Q, Li Q, Wang L, Si S, Xie Y, Hong B. Improving the N-terminal diversity of sansanmycin through mutasynthesis. Microb Cell Fact 2016; 15:77. [PMID: 27154005 PMCID: PMC4858918 DOI: 10.1186/s12934-016-0471-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sansanmycins are uridyl peptide antibiotics (UPAs), which are inhibitors of translocase I (MraY) and block the bacterial cell wall biosynthesis. They have good antibacterial activity against Pseudomonas aeruginosa and Mycobacterium tuberculosis strains. The biosynthetic gene cluster of sansanmycins has been characterized and the main biosynthetic pathway elucidated according to that of pacidamycins which were catalyzed by nonribosomal peptide synthetases (NRPSs). Sananmycin A is the major compound of Streptomyces sp. SS (wild type strain) and it bears a non-proteinogenic amino acid, meta-tyrosine (m-Tyr), at the N-terminus of tetrapeptide chain. RESULTS ssaX deletion mutant SS/XKO was constructed by the λ-RED mediated PCR targeting method and confirmed by PCR and southern blot. The disruption of ssaX completely abolished the production of sansanmycin A. Complementation in vivo and in vitro could both recover the production of sansanmycin A, and the overexpression of SsaX apparently increased the production of sansanmycin A by 20%. Six new compounds were identified in the fermentation culture of ssaX deletion mutant. Some more novel sansanmycin analogues were obtained by mutasynthesis, and totally ten sansanmycin analogues, MX-1 to MX-10, were purified and identified by electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR). The bioassay of these sansanmycin analogues showed that sansanmycin MX-1, MX-2, MX-4, MX-6 and MX-7 exhibited comparable potency to sansanmycin A against M. tuberculosis H37Rv, as well as multi-drug-resistant (MDR) and extensive-drug-resistant (XDR) strains. Moreover, sansanmycin MX-2 and MX-4 displayed much better stability than sansanmycin A. CONCLUSIONS We demonstrated that SsaX is responsible for the biosynthesis of m-Tyr in vivo by gene deletion and complementation. About twenty novel sansanmycin analogues were obtained by mutasynthesis in ssaX deletion mutant SS/XKO and ten of them were purified and structurally identified. Among them, MX-2 and MX-4 showed promising anti-MDR and anti-XDR tuberculosis activity and greater stability than sansanmycin A. These results indicated that ssaX deletion mutant SS/XKO was a suitable host to expand the diversity of the N-terminus of UPAs, with potential to yield more novel compounds with improved activity and/or other properties.
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Affiliation(s)
- Yuanyuan Shi
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Zhibo Jiang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Xuan Lei
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Ningning Zhang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Qiang Cai
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Qinglian Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Lifei Wang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Shuyi Si
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China
| | - Yunying Xie
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China.
| | - Bin Hong
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Tiantan Xili, Beijing, 100050, China.
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Laddomada F, Miyachiro MM, Dessen A. Structural Insights into Protein-Protein Interactions Involved in Bacterial Cell Wall Biogenesis. Antibiotics (Basel) 2016; 5:antibiotics5020014. [PMID: 27136593 PMCID: PMC4929429 DOI: 10.3390/antibiotics5020014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/15/2016] [Accepted: 04/09/2016] [Indexed: 12/30/2022] Open
Abstract
The bacterial cell wall is essential for survival, and proteins that participate in its biosynthesis have been the targets of antibiotic development efforts for decades. The biosynthesis of its main component, the peptidoglycan, involves the coordinated action of proteins that are involved in multi-member complexes which are essential for cell division (the “divisome”) and/or cell wall elongation (the “elongasome”), in the case of rod-shaped cells. Our knowledge regarding these interactions has greatly benefitted from the visualization of different aspects of the bacterial cell wall and its cytoskeleton by cryoelectron microscopy and tomography, as well as genetic and biochemical screens that have complemented information from high resolution crystal structures of protein complexes involved in divisome or elongasome formation. This review summarizes structural and functional aspects of protein complexes involved in the cytoplasmic and membrane-related steps of peptidoglycan biosynthesis, with a particular focus on protein-protein interactions whereby disruption could lead to the development of novel antibacterial strategies.
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Affiliation(s)
- Federica Laddomada
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
| | - Mayara M Miyachiro
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
| | - Andréa Dessen
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
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Wiegmann D, Koppermann S, Wirth M, Niro G, Leyerer K, Ducho C. Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents. Beilstein J Org Chem 2016; 12:769-795. [PMID: 27340469 PMCID: PMC4902027 DOI: 10.3762/bjoc.12.77] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/23/2022] Open
Abstract
Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure-activity relationship (SAR) studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.
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Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Marius Wirth
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Kristin Leyerer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
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125
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Structural insights into inhibition of lipid I production in bacterial cell wall synthesis. Nature 2016; 533:557-560. [PMID: 27088606 PMCID: PMC4882255 DOI: 10.1038/nature17636] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 03/01/2016] [Indexed: 12/30/2022]
Abstract
Antibiotic-resistant bacterial infection is a serious threat to public health. Peptidoglycan biosynthesis is a well-established target for antibiotic development. MraY (phospho-MurNAc-pentapeptide translocase) catalyzes the first and an essential membrane step of peptidoglycan biosynthesis. It is considered a very promising target for the development of new antibiotics, as many naturally occuring nucleoside inhibitors with antibacterial activity target this enzyme1-4. However, antibiotics targeting MraY have not been developed for clinical use mainly due to a lack of structural insight into inhibition of this enzyme. Here we present the crystal structure of MraY from Aquifex aeolicus (MraYAA) in complex with its naturally occurring inhibitor, muraymycin D2 (MD2). Upon binding MD2, MraYAA undergoes remarkably large conformational rearrangements near the active site, which lead to the formation of a nucleoside-binding pocket and a peptide-binding site. MD2 binds the nucleoside-binding pocket like a two-pronged plug inserting into a socket. Additional interactions it makes in the adjacent peptide-binding site anchor MD2 to and enhance its affinity for MraYAA. Surprisingly, MD2 does not interact with three acidic residues or the Mg2+ cofactor required for catalysis, suggesting that MD2 binds to MraYAA in a manner that overlaps with, but is distinct from its natural substrate, UDP-MurNAc-pentapeptide. We have deciphered the chemical logic of MD2 binding to MraYAA, including how it avoids the need for pyrophosphate and sugar moieties, which are essential features for substrate binding. The conformational plasticity of MraY could be the reason that it is the target of many structurally distinct inhibitors. These findings can inform the design of new inhibitors targeting MraY as well as its paralogs, WecA and TarO.
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126
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Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GEM, Lameira J, Lamichhane G, Kruger HG, Honarparvar B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J Biomol Struct Dyn 2016; 34:2399-417. [PMID: 26612108 DOI: 10.1080/07391102.2015.1117397] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Zeynab Fakhar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Suhashni Naiker
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Claudio N Alves
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa.,c School of Chemistry and Physics , University of KwaZulu-Natal , 4001 Durban , South Africa
| | - Jeronimo Lameira
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Gyanu Lamichhane
- d Division of Infectious Diseases, Center for Tuberculosis Research , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Bahareh Honarparvar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
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Batista D, Schwarz S, Loesche A, Csuk R, Costa PJ, Oliveira MC, Xavier NM. Synthesis of glucopyranos-6′-yl purine and pyrimidine isonucleosides as potential cholinesterase inhibitors. Access to pyrimidine-linked pseudodisaccharides through Mitsunobu reaction. PURE APPL CHEM 2016. [DOI: 10.1515/pac-2016-0102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe synthesis of new isonucleosides comprising purine and pyrimidine-derived systems linked to methyl glucopyranosidyl units at C-6 and evaluation of their cholinesterase inhibitory profiles is reported. Their access was based on the Mitsunobu coupling of partially acetylated and benzylated methyl glucopyranosides with purine and pyrimidine derivatives. While the reactions with purines and theobromine proceeded with complete regioselectivity, affording exclusively N9- or N1-linked 6′-isonucleosides, respectively, the use of pyrimidine nucleobases led to N1 and/or N3-glucopyranosid-6′-yl pyrimidines and/or to N1,N3/2-O,4-O-pyrimidine-linked pseudodisaccharides through bis-coupling, depending on the substitution pattern of the sugar precursor and on the nature of the nucleobase. From this series of compounds, four were shown to be effective and selective inhibitors of acetylcholinesterase with inhibition constants in the micromolar concentration range. A tri-O-acetylated N1-glucopyranosid-6′-yl theobromine and a benzylated N1,N3-bis-glucopyranosid-6-yl thymine were the most active molecules with Ki values of 4 μM. A tri-O-benzylated glucopyranosid-6′-yl uracil displayed good and selective inhibition of butyrylcholinesterase (Ki=8.4±1.0 μM), similar to that exhibited by the standard galantamine. Molecular docking simulations, performed with the two most effective acetylcholinesterase inhibitors, showed interactions with key amino acid residues located at the enzyme’s active site gorge, which explain the competitive component of their inhibitory activities.
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Affiliation(s)
- Daniela Batista
- 1Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016 Lisboa, Portugal
| | - Stefan Schwarz
- 2Bereich Organische Chemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Anne Loesche
- 2Bereich Organische Chemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - René Csuk
- 2Bereich Organische Chemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Paulo J. Costa
- 1Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016 Lisboa, Portugal
| | - M. Conceição Oliveira
- 3Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Nuno M. Xavier
- 1Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, 1749-016 Lisboa, Portugal
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128
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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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129
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Bugg TDH, Rodolis MT, Mihalyi A, Jamshidi S. Inhibition of phospho-MurNAc-pentapeptide translocase (MraY) by nucleoside natural product antibiotics, bacteriophage ϕX174 lysis protein E, and cationic antibacterial peptides. Bioorg Med Chem 2016; 24:6340-6347. [PMID: 27021004 DOI: 10.1016/j.bmc.2016.03.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
This review covers recent developments in the inhibition of translocase MraY and related phospho-GlcNAc transferases WecA and TagO, and insight into the inhibition and catalytic mechanism of this class of integral membrane proteins from the structure of Aquifex aeolicus MraY. Recent studies have also identified a protein-protein interaction site in Escherichia coli MraY, that is targeted by bacteriophage ϕX174 lysis protein E, and also by cationic antimicrobial peptides containing Arg-Trp close to their N- or C-termini.
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Affiliation(s)
- Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
| | - Maria T Rodolis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Agnes Mihalyi
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Shirin Jamshidi
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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130
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Affiliation(s)
- Yonglian Zhang
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
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131
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Natural and engineered biosynthesis of nucleoside antibiotics in Actinomycetes. ACTA ACUST UNITED AC 2016; 43:401-17. [DOI: 10.1007/s10295-015-1636-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/15/2015] [Indexed: 12/18/2022]
Abstract
Abstract
Nucleoside antibiotics constitute an important family of microbial natural products bearing diverse bioactivities and unusual structural features. Their biosynthetic logics are unique with involvement of complex multi-enzymatic reactions leading to the intricate molecules from simple building blocks. Understanding how nature builds this family of antibiotics in post-genomic era sets the stage for rational enhancement of their production, and also paves the way for targeted persuasion of the cell factories to make artificial designer nucleoside drugs and leads via synthetic biology approaches. In this review, we discuss the recent progress and perspectives on the natural and engineered biosynthesis of nucleoside antibiotics.
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132
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Precursor-directed biosynthesis of new sansanmycin analogs bearing para-substituted-phenylalanines with high yields. J Antibiot (Tokyo) 2016; 69:765-768. [DOI: 10.1038/ja.2016.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/23/2015] [Accepted: 01/05/2016] [Indexed: 11/09/2022]
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133
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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134
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Walvoort MTC, Lukose V, Imperiali B. A Modular Approach to Phosphoglycosyltransferase Inhibitors Inspired by Nucleoside Antibiotics. Chemistry 2015; 22:3856-64. [PMID: 26662170 DOI: 10.1002/chem.201503986] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/09/2022]
Abstract
Phosphoglycosyltransferases (PGTs) represent "gatekeeper" enzymes in complex glycan assembly pathways by catalyzing transfer of a phosphosugar from an activated nucleotide diphosphosugar to a membrane-resident polyprenol phosphate. The unique structures of selected nucleoside antibiotics, such as tunicamycin and mureidomycin A, which are known to inhibit comparable biochemical transformations, are exploited as the foundation for the development of modular synthetic inhibitors of PGTs. Herein we present the design, synthesis, and biochemical evaluation of two readily manipulatable modular scaffolds as inhibitors of monotopic bacterial PGTs. Selected compounds show IC50 values down to the 40 μm range, thereby serving as lead compounds for future development of selective and effective inhibitors of diverse PGTs of biological and medicinal interest.
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Affiliation(s)
- Marthe T C Walvoort
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Vinita Lukose
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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135
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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136
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Teo ACK, Roper DI. Core Steps of Membrane-Bound Peptidoglycan Biosynthesis: Recent Advances, Insight and Opportunities. Antibiotics (Basel) 2015; 4:495-520. [PMID: 27025638 PMCID: PMC4790310 DOI: 10.3390/antibiotics4040495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/03/2015] [Accepted: 10/26/2015] [Indexed: 11/16/2022] Open
Abstract
We are entering an era where the efficacy of current antibiotics is declining, due to the development and widespread dispersion of antibiotic resistance mechanisms. These factors highlight the need for novel antimicrobial discovery. A large number of antimicrobial natural products elicit their effect by directly targeting discrete areas of peptidoglycan metabolism. Many such natural products bind directly to the essential cell wall precursor Lipid II and its metabolites, i.e., preventing the utlisation of vital substrates by direct binding rather than inhibiting the metabolising enzymes themselves. Concurrently, there has been an increase in the knowledge surrounding the proteins essential to the metabolism of Lipid II at and across the cytoplasmic membrane. In this review, we draw these elements together and look to future antimicrobial opportunities in this area.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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137
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Gibbons GS, Showalter HD, Nikolovska-Coleska Z. Novel carboxaldehyde mediated synthetic pathway for 5'-amino adenosine analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:348-60. [PMID: 25874943 DOI: 10.1080/15257770.2014.1001074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Modifications of the 5'-position of adenosine have been prepared via a novel 5'-carboxaldehyde synthon. The described methodology should prove useful for making related compounds in which amine-derived moieties off the 5'-position of adenosine (or related nucleoside congeners) can be easily incorporated via reductive amination, especially for the incorporation of aromatic amines.
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Affiliation(s)
- Garrett S Gibbons
- a Department of Pathology, University of Michigan Medical School , Ann Arbor , MI , USA
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138
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Yao G, Zhang J, Huang Q. Conformational and vibrational analyses of meta-tyrosine: An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:111-123. [PMID: 26125991 DOI: 10.1016/j.saa.2015.06.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
M-tyrosine is one kind of positional isomer of tyrosine which is widely applied in agrichemical, medicinal chemistry, and food science. However, the structural and vibrational features of m-tyrosine have not been reported or systematically investigated. In this work, potential energy surface (PES) calculations were used for searching and determining the stable zwitterionic conformers of m-tyrosine, and the Raman spectra of m-tyrosine and deuterated m-tyrosine were measured and interpreted based on theoretical computation. For the spectral simulation, several DFT-based quantum chemistry (QC) methods were employed, and the M06-2X functional with SMD solvent model was found to be best in reproducing the Raman spectra and geometrical property. As such, this study has not only presented a detailed study of m-tyrosine's vibrational property which is lack in the literature, but also may shed some light on the optimal choice of QC methods for calculation of conformations and vibrational properties of zwitterionic amino acids.
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Affiliation(s)
- Guohua Yao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Jingjing Zhang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Qing Huang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China; University of Science & Technology of China, Hefei, Anhui 230026, PR China.
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139
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Rodolis MT, Mihalyi A, Ducho C, Eitel K, Gust B, Goss RJM, Bugg TDH. Mechanism of action of the uridyl peptide antibiotics: an unexpected link to a protein-protein interaction site in translocase MraY. Chem Commun (Camb) 2015; 50:13023-5. [PMID: 25222373 DOI: 10.1039/c4cc06516f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pacidamycin and muraymycin uridyl peptide antibiotics show some structural resemblance to an Arg-Trp-x-x-Trp sequence motif for protein-protein interaction between bacteriophage ϕX174 protein E and E. coli translocase MraY. Members of the UPA class, and a synthetic uridine-peptide analogue, were found to show reduced levels of inhibition to F288L or E287A mutant MraY enzymes, implying that the UPAs interact at this extracellular site as part of the enzyme inhibition mechanism.
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Affiliation(s)
- Maria T Rodolis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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140
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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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141
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Qi J, Liu J, Wan D, Cai YS, Wang Y, Li S, Wu P, Feng X, Qiu G, Yang SP, Chen W, Deng Z. Metabolic engineering of an industrial polyoxin producer for the targeted overproduction of designer nucleoside antibiotics. Biotechnol Bioeng 2015; 112:1865-71. [DOI: 10.1002/bit.25594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/03/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Jianzhao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Jin Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Dan Wan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - You-sheng Cai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Yinghu Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Shunying Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Pan Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Xuan Feng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Guofu Qiu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Sheng-ping Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200030 China
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142
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143
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A Modular Approach to the Total Synthesis of Tunicamycins. Angew Chem Int Ed Engl 2015; 54:6618-21. [DOI: 10.1002/anie.201501890] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/31/2023]
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144
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Niu G, Tan H. Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends Microbiol 2015; 23:110-9. [DOI: 10.1016/j.tim.2014.10.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 11/30/2022]
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145
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Ries O, Carnarius C, Steinem C, Ducho C. Membrane-interacting properties of the functionalised fatty acid moiety of muraymycin antibiotics. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00526k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simplified model system is introduced to elucidate the significance of the ω-functionalised fatty acid moiety of muraymycin nucleoside antibiotics for membrane interaction and penetration.
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Affiliation(s)
- Oliver Ries
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Christian Carnarius
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Claudia Steinem
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Christian Ducho
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
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146
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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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147
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Characterization of biosynthetic genes of ascamycin/dealanylascamycin featuring a 5'-O-sulfonamide moiety in Streptomyces sp. JCM9888. PLoS One 2014; 9:e114722. [PMID: 25479601 PMCID: PMC4257720 DOI: 10.1371/journal.pone.0114722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023] Open
Abstract
Ascamycin (ACM) and dealanylascamycin (DACM) are nucleoside antibiotics elaborated by Streptomyces sp. JCM9888. The later shows broad spectrum inhibition activity to various gram-positive and gram-negative bacteria, eukaryotic Trypanosoma and is also toxic to mice, while ascamycin is active against very limited microorganisms, such as Xanthomonas. Both compounds share an unusual 5′-O-sulfonamide moiety which is attached to an adenosine nucleoside. In this paper, we first report on the 30 kb gene cluster (23 genes, acmA to acmW) involved in the biosynthesis of these two antibiotics and a biosynthetic assembly line was proposed. Of them, six genes (AcmABGKIW) are hypothetical genes involved in 5′-O-sulfonamide formation. Two flavin adenine dinucleotide (FAD)-dependent chlorinase genes acmX and acmY were characterized which are significantly remote from acmA-W and postulated to be required for adenine C2-halogenation. Notably gene disruption of acmE resulted in a mutant which could only produce dealanylascamycin but was blocked in its ability to biosynthesize ascamycin, revealing its key role of conversion of dealanylascamycin to ascamycin.
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148
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Yan Z, Xu Y, Tian W. A new and concise way to enamides by fluoroalkanosulfonyl fluoride mediated Beckmann rearrangement of α,β-unsaturated ketoximes. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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149
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Peitsinis ZV, Melidou DA, Stefanakis JG, Evgenidou H, Koumbis AE. A Versatile Total Synthesis of Trachycladines A and B and Their Analogues. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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150
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Paszkowska J, Kral K, Bieg T, Żaba K, Węgrzyk K, Jaśkowiak N, Molinaro A, Silipo A, Wandzik I. Synthesis and biological evaluation of 5'-glycyl derivatives of uridine as inhibitors of 1,4-β-galactosyltransferase. Bioorg Chem 2014; 58:18-25. [PMID: 25462623 DOI: 10.1016/j.bioorg.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022]
Abstract
New 5'-glycyl derivatives of uridine containing fragments of varying lipophilicity were synthesized as analogues of natural peptidyl antibiotics. One of the studied compounds, 5'-O-(N-succinylglycyl)-2',3'-O-isopropylideneuridine (A4), showed moderate inhibition against 1,4-β-galactosyltransferase. However, additional studies showed that the observed inhibitory effect was due to binding to bovine serum albumin, which was used in assays as a stabilizer.
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Affiliation(s)
- Jadwiga Paszkowska
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Katarzyna Kral
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Tadeusz Bieg
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Karolina Żaba
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Katarzyna Węgrzyk
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Natalia Jaśkowiak
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Ilona Wandzik
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
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