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Sun L, Zhang S, Kou S, Yi H, Cui A, Li Z. Design, synthesis, and antibacterial activity of derivatives of Tryptophanyl-tRNA synthetase inhibitor indolmycin. Eur J Med Chem 2022; 241:114647. [PMID: 35963132 DOI: 10.1016/j.ejmech.2022.114647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/17/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022]
Abstract
In this study, indlomycin, an inhibitor of tryptophanyl-tRNA synthetase (TrpRS), and 29 racemic indolmycin derivatives were synthesized, their antibacterial activity were evaluated against methicillin-resistant Staphylococcus aureus (S. aureus) NRS384, ATCC29213, and Escherichia coli (E. coli) ATCC25922 strains. Compounds (±)-7a, (±)-7b, (±)-7c and (±)-7e exhibited minimum inhibitory concentration (MIC) values of 1-2 μg/mL against S. aureus NRS384 and ATCC29213, exhibiting significant antibacterial activity, but none of the compounds exhibited antibacterial activity against E. coli. To investigate the effect of conformation on antibacterial activity, seven racemic compounds with good antibacterial activity were separated, and the antibacterial activity of these 14 compounds was evaluated on 25 bacterial strains. This revealed that the isomers with natural conformations (1'R, 5S) had significantly better antibacterial activity than the enantiomeric isomers and racemates. Compounds 7aa, 7ba, 7ca, and 7ea exhibited good antibacterial activity against 21 strains of S. aureus and S. epidermidis with MIC values of 0.125-2 μg/mL, which were superior to that of vancomycin, used in clinical practice. The compounds 7aa, 7ba, 7ca and 7ea were moderately bound to plasma proteins and were stable in the whole blood of CD-1 mice. In conclusion, a series of new indomycin derivatives with stronger antibacterial activity against G+ bacteria were obtained.
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Affiliation(s)
- Lianqi Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Shuo Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Shibo Kou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Hong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Along Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China.
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China.
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Yang Y, Xu Y, Yue Y, Wang H, Cui Y, Pan M, Zhang X, Zhang L, Li H, Xu M, Tang Y, Chen S. Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents. ACS Chem Biol 2022; 17:39-53. [PMID: 34908399 DOI: 10.1021/acschembio.1c00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Indolmycin (IND) is a microbial natural product that selectively inhibits bacterial tryptophanyl-tRNA synthetase (TrpRS). The tryptophan biosynthesis pathway was recently shown to be an important target for developing new antibacterial agents against Mycobacterium tuberculosis (Mtb). We investigated the antibacterial activity of IND against several mycobacterial model strains. A TrpRS biochemical assay was developed to analyze a library of synthetic IND analogues. The 4″-methylated IND compound, Y-13, showed improved anti-Mtb activity with a minimum inhibitory concentration (MIC) of 1.88 μM (∼0.5 μg/mL). The MIC increased significantly when overexpression of TrpRS was induced in the genetically engineered surrogate M. bovis BCG. The cocrystal structure of Mtb TrpRS complexed with IND and ATP has revealed that the amino acid pocket is in a state between the open form of apo protein and the closed complex with the reaction intermediate. In whole-cell-based experiments, we studied the combination effect of Y-13 paired with different antibacterial agents. We evaluated the killing kinetics, the frequency of resistance to INDs, and the mode of resistance of IND-resistant mycobacteria by genome sequencing. The synergistic interaction of Y-13 with the TrpE allosteric inhibitor, indole propionic acid, suggests that prospective IND analogues could shut down tryptophan biosynthesis and protein biosynthesis in pathogens, leading to a new class of antibiotics. Finally, we discuss a strategy to expand the genome mining of antibiotic-producing microbes specifically for antimycobacterial development.
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Affiliation(s)
- Yuhong Yang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yuan Yue
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yumeng Cui
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Xi Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Lin Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Min Xu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
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Hoffarth ER, Kong S, He HY, Ryan KS. An engineered biosynthetic-synthetic platform for production of halogenated indolmycin antibiotics. Chem Sci 2021; 12:8817-8821. [PMID: 34257882 PMCID: PMC8246080 DOI: 10.1039/d0sc05843b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/15/2021] [Indexed: 11/21/2022] Open
Abstract
Indolmycin is an antibiotic from Streptomyces griseus ATCC 12648 with activity against Helicobacter pylori, Plasmodium falciparum, and methicillin-resistant Staphylococcus aureus. Here we describe the use of the indolmycin biosynthetic genes in E. coli to make indolmycenic acid, a chiral intermediate in indolmycin biosynthesis, which can then be converted to indolmycin through a three-step synthesis. To expand indolmycin structural diversity, we introduce a promiscuous tryptophanyl-tRNA synthetase gene (trpS) into our E. coli production system and feed halogenated indoles to generate the corresponding indolmycenic acids, ultimately allowing us to access indolmycin derivatives through synthesis. Bioactivity testing against methicillin-resistant Staphylococcus aureus showed modest antibiotic activity for 5-, 6-, and 7-fluoro-indolmycin.
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Affiliation(s)
- Elesha R Hoffarth
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Sunnie Kong
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Hai-Yan He
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia Vancouver Canada
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Yuan L, Palmieri A, Petrini M. Synthesis of Unsymmetrical Bisindolylmethanes by Reaction of Indolylmagnesium Bromides with Sulfonyl Indoles. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Lixia Yuan
- School of Science and Technology, Chemistry DivisionUniversity of Camerino Via S. Agostino 1 62032 Camerino Italy
- School of Chemistry and Chemical EngineeringLiaocheng University Hunan Road Liaocheng 252000 People's Republic of China
| | - Alessandro Palmieri
- School of Science and Technology, Chemistry DivisionUniversity of Camerino Via S. Agostino 1 62032 Camerino Italy
| | - Marino Petrini
- School of Science and Technology, Chemistry DivisionUniversity of Camerino Via S. Agostino 1 62032 Camerino Italy
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Ren W, Zhao Q, Yu M, Guo L, Chang H, Jiang X, Luo Y, Huang W, He G. Design and synthesis of novel spirooxindole–indenoquinoxaline derivatives as novel tryptophanyl-tRNA synthetase inhibitors. Mol Divers 2019; 24:1043-1063. [DOI: 10.1007/s11030-019-10011-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
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Docampo M, Olubu A, Wang X, Pasinetti G, Dixon RA. Glucuronidated Flavonoids in Neurological Protection: Structural Analysis and Approaches for Chemical and Biological Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7607-7623. [PMID: 28789524 PMCID: PMC5954986 DOI: 10.1021/acs.jafc.7b02633] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Both plant and mammalian cells express glucuronosyltransferases that catalyze glucuronidation of polyphenols such as flavonoids and other small molecules. Oral administration of select polyphenolic compounds leads to the accumulation of the corresponding glucuronidated metabolites at μM and sub-μM concentrations in the brain, associated with amelioration of a range of neurological symptoms. Determining the mechanisms whereby botanical extracts impact cognitive wellbeing and psychological resiliency will require investigation of the modes of action of the brain-targeted metabolites. Unfortunately, many of these compounds are not commercially available. This article describes the latest approaches for the analysis and synthesis of glucuronidated flavonoids. Synthetic schemes include both standard organic synthesis, semisynthesis, enzymatic synthesis and use of synthetic biology utilizing heterologous enzymes in microbial platform organisms.
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Affiliation(s)
- Maite Docampo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Adiji Olubu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Xiaoqiang Wang
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Giulio Pasinetti
- Department of Psychiatry, The Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1230, New York, NY 10029, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
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Spectrophotometric assays for monitoring tRNA aminoacylation and aminoacyl-tRNA hydrolysis reactions. Methods 2016; 113:3-12. [PMID: 27780756 DOI: 10.1016/j.ymeth.2016.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases play a central role in protein synthesis, catalyzing the attachment of amino acids to their cognate tRNAs. Here, we describe a spectrophotometric assay for tyrosyl-tRNA synthetase in which the Tyr-tRNA product is cleaved, regenerating the tRNA substrate. As tRNA is the limiting substrate in the assay, recycling it substantially increases the sensitivity of the assay while simultaneously reducing its cost. The tRNA aminoacylation reaction is monitored spectrophotometrically by coupling the production of AMP to the conversion of NAD+ to NADH. We have adapted the tyrosyl-tRNA synthetase assay to monitor: (1) aminoacylation of tRNA by l- or d-tyrosine, (2) cyclodipeptide formation by cyclodipeptide synthases, (3) hydrolysis of d-aminoacyl-tRNAs by d-tyrosyl-tRNA deacylase, and (4) post-transfer editing by aminoacyl-tRNA synthetases. All of these assays are continuous and homogenous, making them amenable for use in high-throughput screens of chemical libraries. In the case of the cyclodipeptide synthase, d-tyrosyl-tRNA deacylase, and post-transfer editing assays, the aminoacyl-tRNAs are generated in situ, avoiding the need to synthesize and purify aminoacyl-tRNA substrates prior to performing the assays. Lastly, we describe how the tyrosyl-tRNA synthetase assay can be adapted to monitor the activity of other aminoacyl-tRNA synthetases and how the approach to regenerating the tRNA substrate can be used to increase the sensitivity and decrease the cost of commercially available aminoacyl-tRNA synthetase assays.
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Jiang M, Xiang H, Zhu F, Xu X, Deng L, Yang C. Efficient Pd-catalyzed domino synthesis of 1-phenyl-1H-indol-2-amine and 5-amino-indolo[1,2-a]quinazoline derivatives. Org Biomol Chem 2015; 13:10122-6. [PMID: 26377704 DOI: 10.1039/c5ob01642h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient and practical one-pot domino synthesis of 1-phenyl-1H-indol-2-amine and 5-amino-indolo[1,2-a]quinazoline derivatives from readily available 2-(2-bromophenyl)acetonitriles was developed. The overall protocol involves a Buchwald-Hartwig type coupling and a base-promoted intramolecular nucleophilic reaction. The reaction scope, advantages and limitations are discussed.
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Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, P. R. China.
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In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly. Proc Natl Acad Sci U S A 2015; 112:2717-22. [PMID: 25730866 DOI: 10.1073/pnas.1419964112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial tryptophanyl-tRNA synthetase inhibitor indolmycin features a unique oxazolinone heterocycle whose biogenetic origins have remained obscure for over 50 years. Here we identify and characterize the indolmycin biosynthetic pathway, using systematic in vivo gene inactivation, in vitro biochemical assays, and total enzymatic synthesis. Our work reveals that a phenylacetate-CoA ligase-like enzyme Ind3 catalyzes an unusual ATP-dependent condensation of indolmycenic acid and dehydroarginine, driving oxazolinone ring assembly. We find that Ind6, which also has chaperone-like properties, acts as a gatekeeper to direct the outcome of this reaction. With Ind6 present, the normal pathway ensues. Without Ind6, the pathway derails to an unusual shunt product. Our work reveals the complete pathway for indolmycin formation and sets the stage for using genetic and chemoenzymatic methods to generate indolmycin derivatives as potential therapeutic agents.
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Özdemir A, Altintop MD, Kaplancıklı ZA, Turan-Zitouni G, Karaca H, Tunalı Y. Synthesis and Biological Evaluation of Pyrazoline Derivatives Bearing an Indole Moiety as New Antimicrobial Agents. Arch Pharm (Weinheim) 2013; 346:463-9. [DOI: 10.1002/ardp.201200479] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 03/04/2013] [Accepted: 03/08/2013] [Indexed: 11/11/2022]
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11
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Ekholm FS, Eklund P, Leino R. A short semi-synthesis and complete NMR-spectroscopic characterization of the naturally occurring lignan glycoside matairesinol 4,4′-di-O-β-d-diglucoside. Carbohydr Res 2010; 345:1963-7. [DOI: 10.1016/j.carres.2010.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/09/2010] [Accepted: 06/15/2010] [Indexed: 10/19/2022]
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12
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Regulation of an auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene via ribosome-mediated transcriptional attenuation. J Bacteriol 2010; 192:3565-73. [PMID: 20453096 DOI: 10.1128/jb.00290-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
cis-Acting RNA elements in the leaders of bacterial mRNA often regulate gene transcription, especially in the context of amino acid metabolism. We determined that the transcription of the auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene (trpRS1) in Streptomyces coelicolor is regulated by a ribosome-mediated attenuator in the 5' leader of its mRNA region. This regulatory element controls gene transcription in response to the physiological effects of indolmycin and chuangxinmycin, two antibiotics that inhibit bacterial tryptophanyl-tRNA synthetases. By mining streptomycete genome sequences, we found several orthologs of trpRS1 that share this regulatory element; we predict that they are regulated in a similar fashion. The validity of this prediction was established through the analysis of a trpRS1 ortholog (SAV4725) in Streptomyces avermitilis. We conclude that the trpRS1 locus is a widely distributed and self-regulating antibiotic resistance cassette. This study provides insights into how auxiliary aminoacyl-tRNA synthetase genes are regulated in bacteria.
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A novel tryptophanyl-tRNA synthetase gene confers high-level resistance to indolmycin. Antimicrob Agents Chemother 2009; 53:3972-80. [PMID: 19546369 DOI: 10.1128/aac.00723-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Indolmycin, a potential antibacterial drug, competitively inhibits bacterial tryptophanyl-tRNA synthetases. An effort to identify indolmycin resistance genes led to the discovery of a gene encoding an indolmycin-resistant isoform of tryptophanyl-tRNA synthetase. Overexpression of this gene in an indolmycin-sensitive strain increased the indolmycin MIC 60-fold. Its transcription and distribution in various bacterial genera were assessed. The level of resistance conferred by this gene was compared to that of a known indolmycin resistance gene and to those of genes with resistance-conferring point mutations.
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Sutou N, Kato K, Akita H. A concise synthesis of (−)-indolmycin and (−)-5-methoxyindolmycin. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.07.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jacobsson M, Malmberg J, Ellervik U. Aromatic O-glycosylation. Carbohydr Res 2006; 341:1266-81. [PMID: 16650391 DOI: 10.1016/j.carres.2006.04.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/20/2006] [Accepted: 04/02/2006] [Indexed: 10/24/2022]
Abstract
Carbohydrates carrying an aromatic aglycon are important natural products and thus key synthetic targets. However, due to the electron-withdrawing properties of aromatic rings, phenols are difficult to glycosylate. This review covers the most common carbohydrate donors used for aromatic O-glycosylation (anomeric acetates, halides, trichloroacetimidates and thioglycosides) as well as some less common donors. The scope of the review is to give practical examples of aromatic O-glycosylations and to offer guidelines for glycosylation of typical aromatic residues. Anomeric acetates or trichloroacetimidates, activated under acidic conditions, are preferred for electron rich aromatic aglycons, while glycosyl halides, activated using basic conditions, are preferred for electron deficient aromatic residues.
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Affiliation(s)
- Mårten Jacobsson
- Organic Chemistry, Lund University, PO Box 124, SE-221 00 Lund, Sweden
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Wang P, Zhang Z, Yu B. Total synthesis of CRM646-A and -B, two fungal glucuronides with potent heparinase inhibition activities. J Org Chem 2006; 70:8884-9. [PMID: 16238322 DOI: 10.1021/jo051384k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] CRM646-A (1) and -B (2), two fungal glucuronides with a dimeric 2,4-dihydroxy-6-alkylbenzoic acid (orcinol p-depside) aglycone showing significant heparinase and telomerase inhibition activities, were synthesized for the first time. The successful approach involved construction of the phenol glucuronidic linkage, via coupling of the orsellinate derivative 27 with glucuronate bromide 7, before assembly of the phenolic ester linkage in the depside aglycone. Attempts via direct glycosylation of the depside aglycone derivatives were not successful.
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Affiliation(s)
- Ping Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences
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