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Sato S, Fan PH, Yeh YC, Liu HW. Complete In Vitro Reconstitution of the Apramycin Biosynthetic Pathway Demonstrates the Unusual Incorporation of a β-d-Sugar Nucleotide in the Final Glycosylation Step. J Am Chem Soc 2024; 146:10103-10114. [PMID: 38546392 PMCID: PMC11317085 DOI: 10.1021/jacs.4c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Apramycin is a widely used aminoglycoside antibiotic with applications in veterinary medicine. It is composed of a 4-amino-4-deoxy-d-glucose moiety and the pseudodisaccharide aprosamine, which is an adduct of 2-deoxystreptamine and an unusual eight-carbon bicyclic dialdose. Despite its extensive study and relevance to medical practice, the biosynthetic pathway of this complex aminoglycoside nevertheless remains incomplete. Herein, the remaining unknown steps of apramycin biosynthesis are reconstituted in vitro, thereby leading to a comprehensive picture of its biological assembly. In particular, phosphomutase AprJ and nucleotide transferase AprK are found to catalyze the conversion of glucose 6-phosphate to NDP-β-d-glucose as a critical biosynthetic intermediate. Moreover, the dehydrogenase AprD5 and transaminase AprL are identified as modifying this intermediate via introduction of an amino group at the 4″ position without requiring prior 6″-deoxygenation as is typically encountered in aminosugar biosynthesis. Finally, the glycoside hydrolase family 65 protein AprO is shown to utilize NDP-β-d-glucose or NDP-4"-amino-4"-deoxy-β-d-glucose to form the 8',1″-O-glycosidic linkage of saccharocin or apramycin, respectively. As the activated sugar nucleotides in all known natural glycosylation reactions involve either NDP-α-d-hexoses or NDP-β-l-hexoses, the reported chemistry expands the scope of known biological glycosylation reactions to NDP-β-d-hexoses, with important implications for the understanding and repurposing of aminoglycoside biosynthesis.
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2
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Mohamad-Ramshan R, Ande C, Matsushita T, Haldimann K, Vasella A, Hobbie SN, Crich D. Synthesis of 4- O-(4-Amino-4-deoxy-β-D-xylopyranosyl)paromomycin and 4- S-(β-D-Xylopyranosyl)-4-deoxy-4'-thio-paromomycin and Evaluation of their Antiribosomal and Antibacterial Activity. Tetrahedron 2023; 135:133330. [PMID: 37035443 PMCID: PMC10081503 DOI: 10.1016/j.tet.2023.133330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The design, synthesis and antiribosomal and antibacterial activity of two novel glycosides of the aminoglycoside antibiotic paromomycin are described. The first carries of 4-amino-4-deoxy-β-D-xylopyranosyl moiety at the paromomycin 4'-position and is approximately two-fold more active than the corresponding β-D-xylopyranosyl derivative. The second is a 4'-(β-D-xylopyranosylthio) derivative of 4'-deoxyparomomycin that is unexpectedly less active than the simple β-D-xylopyranosyl derivative, perhaps because of the insertion of the conformationally more mobile thioglycosidic linkage.
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Affiliation(s)
| | - Chennaiah Ande
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
| | - Takahiko Matsushita
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30, 8006 Zürich, Switzerland
| | - Andrea Vasella
- Organic Chemistry Laboratory, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30, 8006 Zürich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 302 East Campus Road, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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3
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Quirke JCK, Rajasekaran P, Sarpe VA, Sonousi A, Osinnii I, Gysin M, Haldimann K, Fang QJ, Shcherbakov D, Hobbie SN, Sha SH, Schacht J, Vasella A, Böttger EC, Crich D. Apralogs: Apramycin 5- O-Glycosides and Ethers with Improved Antibacterial Activity and Ribosomal Selectivity and Reduced Susceptibility to the Aminoacyltranserferase (3)-IV Resistance Determinant. J Am Chem Soc 2019; 142:530-544. [PMID: 31790244 DOI: 10.1021/jacs.9b11601] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Apramycin is a structurally unique member of the 2-deoxystreptamine class of aminoglycoside antibiotics characterized by a monosubstituted 2-deoxystreptamine ring that carries an unusual bicyclic eight-carbon dialdose moiety. Because of its unusual structure, apramycin is not susceptible to the most prevalent mechanisms of aminoglycoside resistance including the aminoglycoside-modifying enzymes and the ribosomal methyltransferases whose widespread presence severely compromises all aminoglycosides in current clinical practice. These attributes coupled with minimal ototoxocity in animal models combine to make apramycin an excellent starting point for the development of next-generation aminoglycoside antibiotics for the treatment of multidrug-resistant bacterial infections, particularly the ESKAPE pathogens. With this in mind, we describe the design, synthesis, and evaluation of three series of apramycin derivatives, all functionalized at the 5-position, with the goals of increasing the antibacterial potency without sacrificing selectivity between bacterial and eukaryotic ribosomes and of overcoming the rare aminoglycoside acetyltransferase (3)-IV class of aminoglycoside-modifying enzymes that constitutes the only documented mechanism of antimicrobial resistance to apramycin. We show that several apramycin-5-O-β-d-ribofuranosides, 5-O-β-d-eryrthofuranosides, and even simple 5-O-aminoalkyl ethers are effective in this respect through the use of cell-free translation assays with wild-type bacterial and humanized bacterial ribosomes and of extensive antibacterial assays with wild-type and resistant Gram negative bacteria carrying either single or multiple resistance determinants. Ex vivo studies with mouse cochlear explants confirm the low levels of ototoxicity predicted on the basis of selectivity at the target level, while the mouse thigh infection model was used to demonstrate the superiority of an apramycin-5-O-glycoside in reducing the bacterial burden in vivo.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Parasuraman Rajasekaran
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Vikram A Sarpe
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Amr Sonousi
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Ivan Osinnii
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Marina Gysin
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Qiao-Jun Fang
- Department of Pathology and Laboratory Medicine , Medical University of South Carolina , Walton Research Building, Room 403-E, 39 Sabin Street , Charleston , South Carolina 29425 , United States
| | - Dimitri Shcherbakov
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Su-Hua Sha
- Department of Pathology and Laboratory Medicine , Medical University of South Carolina , Walton Research Building, Room 403-E, 39 Sabin Street , Charleston , South Carolina 29425 , United States
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology , University of Michigan , 1150 West Medical Center Drive , Ann Arbor , Michigan 48109 , United States
| | - Andrea Vasella
- Organic Chemistry Laboratory , ETH Zürich , Vladimir-Prelog-Weg 1-5/10 , 8093 Zürich , Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
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4
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Sarpe VA, Pirrone MG, Haldimann K, Hobbie SN, Vasella A, Crich D. Synthesis of saccharocin from apramycin and evaluation of its ribosomal selectivity. MEDCHEMCOMM 2019; 10:554-558. [PMID: 31057735 PMCID: PMC6482888 DOI: 10.1039/c9md00093c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/08/2019] [Indexed: 12/25/2022]
Abstract
We describe a straightforward synthesis of the apramycin biosynthetic precursor saccharocin from apramycin by regioselective partial azidation followed by stereoretentive oxidative deamination. Saccharocin was found to exhibit excellent selectivity for inhibition of the bacterial ribosome over the eukaryotic ribosomes indicating that its presence as a minor impurity in apramycin itself should not be problematic in the development of the latter as a clinical candidate.
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Affiliation(s)
- Vikram A Sarpe
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , MI 48202 , USA . ;
| | - Michael G Pirrone
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , MI 48202 , USA . ;
| | - Klara Haldimann
- Institut für Medizinische Mikrobiologie , Universität Zürich , Gloriastrasse 30 , 8006 Zürich , Switzerland
| | - Sven N Hobbie
- Institut für Medizinische Mikrobiologie , Universität Zürich , Gloriastrasse 30 , 8006 Zürich , Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 1-5/10 , 8093 Zürich , Switzerland
| | - David Crich
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , MI 48202 , USA . ;
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5
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Lv M, Ji X, Zhao J, Li Y, Zhang C, Su L, Ding W, Deng Z, Yu Y, Zhang Q. Characterization of a C3 Deoxygenation Pathway Reveals a Key Branch Point in Aminoglycoside Biosynthesis. J Am Chem Soc 2016; 138:6427-35. [PMID: 27120352 DOI: 10.1021/jacs.6b02221] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Apramycin is a clinically interesting aminoglycoside antibiotic (AGA) containing a highly unique bicyclic octose moiety, and this octose is deoxygenated at the C3 position. Although the biosynthetic pathways for most 2-deoxystreptamine-containing AGAs have been well characterized, the pathway for apramycin biosynthesis, including the C3 deoxygenation process, has long remained unknown. Here we report detailed investigation of apramycin biosynthesis by a series of genetic, biochemical and bioinformatical studies. We show that AprD4 is a novel radical S-adenosyl-l-methionine (SAM) enzyme, which uses a noncanonical CX3CX3C motif for binding of a [4Fe-4S] cluster and catalyzes the dehydration of paromamine, a pseudodisaccharide intermediate in apramycin biosynthesis. We also show that AprD3 is an NADPH-dependent reductase that catalyzes the reduction of the dehydrated product from AprD4-catalyzed reaction to generate lividamine, a C3' deoxygenated product of paromamine. AprD4 and AprD3 do not form a tight catalytic complex, as shown by protein complex immunoprecipitation and other assays. The AprD4/AprD3 enzyme system acts on different pseudodisaccharide substrates but does not catalyze the deoxygenation of oxyapramycin, an apramycin analogue containing a C3 hydroxyl group on the octose moiety, suggesting that oxyapramycin and apramycin are partitioned into two parallel pathways at an early biosynthetic stage. Functional dissection of the C6 dehydrogenase AprQ shows the crosstalk between different AGA biosynthetic gene clusters from the apramycin producer Streptomyces tenebrarius, and reveals the remarkable catalytic versatility of AprQ. Our study highlights the intriguing chemistry in apramycin biosynthesis and nature's ingenuity in combinatorial biosynthesis of natural products.
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Affiliation(s)
- Meinan Lv
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Junfeng Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.,Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Chen Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Li Su
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Wei Ding
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Qi Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
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6
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Mandhapati AR, Shcherbakov D, Duscha S, Vasella A, Böttger EC, Crich D. Importance of the 6'-hydroxy group and its configuration for apramycin activity. ChemMedChem 2014; 9:2074-83. [PMID: 25045149 DOI: 10.1002/cmdc.201402146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 01/08/2023]
Abstract
A series of apramycin derivatives was prepared and investigated for antibacterial activity and the ability to inhibit protein synthesis in cell-free translation assays. The effect of various modifications at the 6'- and N7'-positions on antiribosomal activity is discussed in terms of their influence on drug binding to specific residues in the decoding A-site. These studies contribute to the development of a structure-activity relationship for the antibacterial activity of the apramycin class of aminoglycosides and to the future design and development of more active and less toxic antibiotics.
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Affiliation(s)
- Appi Reddy Mandhapati
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (USA)
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7
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Abstract
The first total syntheses of a variety of antibiotics have been accomplished by using carbohydrates as a chiral source. The key target molecules were members of the 'Big Four' classes of antibiotics (macrolides, aminoglycosides, β-lactams and tetracyclines), naphthoquinone antibiotics and their related antibiotics.
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8
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Tatsuta K. Total synthesis and development of bioactive natural products. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2008; 84:87-106. [PMID: 18941289 PMCID: PMC2805509 DOI: 10.2183/pjab.84.87] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 02/26/2008] [Indexed: 05/26/2023]
Abstract
The first total synthesis and development of a variety of bioactive natural products have been accomplished by using carbohydrates as a chiral source. In addition, practically useful intermediates have been created, analogs of natural products have been prepared, their structure-activity relationships studied, and the large-scale preparations of medicinally useful compounds established. The key target molecules have been the "Big Four" antibiotics (macrolides, aminoglycosides, beta-lactams and tetracyclines), pyranonaphthoquinone antibiotics, glycosidase inhibitors, and a side-chain of cephem antibiotics.
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Affiliation(s)
- Kuniaki Tatsuta
- Graduate School of Science and Engineering, Waseda University, Tokyo, Japan.
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9
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Xu M, Zhu Y, Zhu Y, Jin Z, Wu H, Li X, Yang Y, Jiao R, Jiang W, Wu H, Tian W, Bai X, Zhao G. Glycine origin of the methyl substituent on C7'-N of octodiose for the biosynthesis of apramycin. ACTA ACUST UNITED AC 2006; 49:362-9. [PMID: 16989282 DOI: 10.1007/s11427-006-2009-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Apramycin is unique in the aminoglycoside family due to its octodiose moiety. However, either the biosynthesis process or the precursors involved are largely unknown. Addition of glycine, as well as serine or threonine, to the Streptomyces tenebrabrius UD2 fermentation medium substantially increases the production of apramycin with little effect on the growth of mycelia, indicating that glycine and/or serine might be involved in the biosynthesis of apramycin. The 13C-NMR analysis of [2-13C] glycine-fed (25% enrichment) apramycin showed that glycine specifically and efficiently incorporated into the only N-CH3 substituent of apramycin on the C7' of the octodiose moiety. We noticed that the in vivo concentration of S-adenosyl methionine increased in parallel with the addition of glycine, while the addition of methione in the fermentation medium significantly decreased the productivity of apramycin. Therefore, the methyl donor function of glycine is proposed to be involved in the methionine cycle but methionine itself was proposed to inhibit the methylation and methyl transfer processes a previously reported for the case of rapamycin. The 15N NMR spectra of [2-13C,15N]serine labeled apramycin indicated that serine may also act as a limiting precursor contributing to the -NH2 substituents of apramycin.
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Affiliation(s)
- Mingxuan Xu
- Laboratory of Molecular Microbiology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
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10
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Tatsuta K, Akimoto K, Takahashi H, Hamatsu T, Annaka M, Kinoshita M. Total Synthesis of Aminoglycoside Antibiotics, Apramycin and Saccharocin (KA-5685). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1984. [DOI: 10.1246/bcsj.57.529] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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