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Zhang J, Suzuki K, Ohmori K. Total Syntheses of Sparsomycin and Sparoxomycins A 1 and A 2 via Sulfenate-Anion-Mediated Iterative C-S Bond Formation. Org Lett 2023; 25:9036-9040. [PMID: 38090756 DOI: 10.1021/acs.orglett.3c03791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The total synthesis of the pyrimidinylpropenamide antibiotics sparsomycin and sparoxomycins A1 and A2 has been achieved. The synthesis of sparsomycin relies on the iterative nucleophilic attack of sulfenate anions on alkyl halides to construct the dithioacetal monoxide chain with high diastereoselectivity. Subsequently, the reagent-controlled diastereoselective oxidation of the terminal sulfide moiety of sparsomycin directly provides sparoxomycins A1 and A2.
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Affiliation(s)
- Jian Zhang
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Keisuke Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Ken Ohmori
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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A. Cordell G, Daley SK. Sparsomycin – a Review and Re-assessment. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Yin Y, Chen CJ, Yu RN, Shu L, Wang ZJ, Zhang TT, Zhang DY. Novel 1H-pyrazolo[3,4-d]pyrimidin-6-amino derivatives as potent selective Janus kinase 3 (JAK3) inhibitors. Evaluation of their improved effect for the treatment of rheumatoid arthritis. Bioorg Chem 2020; 98:103720. [DOI: 10.1016/j.bioorg.2020.103720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 11/24/2019] [Accepted: 03/02/2020] [Indexed: 01/26/2023]
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Wu Y, Ding X, Yang Y, Li Y, Qi Y, Hu F, Qin M, Liu Y, Sun L, Zhao Y. Optimization of biaryloxazolidinone as promising antibacterial agents against antibiotic-susceptible and antibiotic-resistant gram-positive bacteria. Eur J Med Chem 2020; 185:111781. [DOI: 10.1016/j.ejmech.2019.111781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/01/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022]
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Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic. Sci Rep 2019; 9:5634. [PMID: 30948752 PMCID: PMC6449356 DOI: 10.1038/s41598-019-42155-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/26/2019] [Indexed: 01/05/2023] Open
Abstract
Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with the peptidyl transferase reaction. Cadazolid is the first member of quinoxolidinone antibiotics, which are characterized by combining the pharmacophores of oxazolidinones and fluoroquinolones, and it is evaluated for treatment of Clostridium difficile gastrointestinal infections that frequently occur in hospitalized patients. In vitro protein synthesis inhibition by cadazolid was shown in Escherichia coli and Staphylococcus aureus, including an isolate resistant against linezolid, the prototypical oxazolidinone antibiotic. To better understand the mechanism of inhibition, we determined a 3.0 Å cryo-electron microscopy structure of cadazolid bound to the E. coli ribosome in complex with mRNA and initiator tRNA. Here we show that cadazolid binds with its oxazolidinone moiety in a binding pocket in close vicinity of the PTC as observed previously for linezolid, and that it extends its unique fluoroquinolone moiety towards the A-site of the PTC. In this position, the drug inhibits protein synthesis by interfering with the binding of tRNA to the A-site, suggesting that its chemical features also can enable the inhibition of linezolid-resistant strains.
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Rui Z, Huang W, Xu F, Han M, Liu X, Lin S, Zhang W. Sparsomycin Biosynthesis Highlights Unusual Module Architecture and Processing Mechanism in Non-ribosomal Peptide Synthetase. ACS Chem Biol 2015; 10:1765-9. [PMID: 26046698 DOI: 10.1021/acschembio.5b00284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sparsomycin is a model protein synthesis inhibitor that blocks peptide bond formation by binding to the large ribosome subunit. It is a unique dipeptidyl alcohol, consisting of a uracil acrylic acid moiety and a monooxo-dithioacetal group. To elucidate the biosynthetic logic of sparsomycin, a biosynthetic gene cluster for sparsomycin was identified from the producer Streptomyces sparsogenes by genome mining, targeted gene mutations, and heterologous expression. Both the genetic and enzymatic studies revealed a minimum set of non-ribosomal peptide synthetases needed for generating the dipeptidyl alcohol scaffold of sparsomycin, featuring unusual mechanisms in dipeptidyl assembly and off-loading.
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Affiliation(s)
- Zhe Rui
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
| | - Wei Huang
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
| | - Fei Xu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Mo Han
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinyu Liu
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wenjun Zhang
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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Abstract
The ribosome is one of the main antibiotic targets in the bacterial cell. Crystal structures of naturally produced antibiotics and their semi-synthetic derivatives bound to ribosomal particles have provided unparalleled insight into their mechanisms of action, and they are also facilitating the design of more effective antibiotics for targeting multidrug-resistant bacteria. In this Review, I discuss the recent structural insights into the mechanism of action of ribosome-targeting antibiotics and the molecular mechanisms of bacterial resistance, in addition to the approaches that are being pursued for the production of improved drugs that inhibit bacterial protein synthesis.
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Ermolenko DN, Cornish PV, Ha T, Noller HF. Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. RNA (NEW YORK, N.Y.) 2013; 19:158-66. [PMID: 23249745 PMCID: PMC3543091 DOI: 10.1261/rna.035964.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the absence of elongation factor EF-G, ribosomes undergo spontaneous, thermally driven fluctuation between the pre-translocation (classical) and intermediate (hybrid) states of translocation. These fluctuations do not result in productive mRNA translocation. Extending previous findings that the antibiotic sparsomycin induces translocation, we identify additional peptidyl transferase inhibitors that trigger productive mRNA translocation. We find that antibiotics that bind the peptidyl transferase A site induce mRNA translocation, whereas those that do not occupy the A site fail to induce translocation. Using single-molecule FRET, we show that translocation-inducing antibiotics do not accelerate intersubunit rotation, but act solely by converting the intrinsic, thermally driven dynamics of the ribosome into translocation. Our results support the idea that the ribosome is a Brownian ratchet machine, whose intrinsic dynamics can be rectified into unidirectional translocation by ligand binding.
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MESH Headings
- Anti-Bacterial Agents/metabolism
- Anti-Bacterial Agents/pharmacology
- Chloramphenicol/metabolism
- Chloramphenicol/pharmacology
- Clindamycin/metabolism
- Clindamycin/pharmacology
- Enzyme Inhibitors/metabolism
- Enzyme Inhibitors/pharmacology
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/drug effects
- Escherichia coli Proteins/metabolism
- Fluorescence Resonance Energy Transfer
- Lincomycin/metabolism
- Lincomycin/pharmacology
- Peptide Elongation Factor G/drug effects
- Peptide Elongation Factor G/metabolism
- Peptidyl Transferases/drug effects
- Peptidyl Transferases/metabolism
- Protein Biosynthesis/drug effects
- RNA Transport/drug effects
- RNA, Bacterial/drug effects
- RNA, Bacterial/metabolism
- RNA, Messenger/drug effects
- RNA, Messenger/metabolism
- RNA, Transfer/drug effects
- RNA, Transfer/metabolism
- Ribosome Subunits, Large, Bacterial/drug effects
- Ribosome Subunits, Large, Bacterial/metabolism
- Sparsomycin/metabolism
- Sparsomycin/pharmacology
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Affiliation(s)
- Dmitri N Ermolenko
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.
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Gao S, Zhang R, Yu Z, Xi Z. Antofine Analogues Can Inhibit Tobacco Mosaic Virus Assembly through Small-Molecule-RNA Interactions. Chembiochem 2012; 13:1622-7. [DOI: 10.1002/cbic.201200313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Indexed: 11/10/2022]
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