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Park J, Kim LH, Lee JM, Choi S, Son YJ, Hwang HJ, Shin SJ. In vitro and intracellular activities of novel thiopeptide derivatives against macrolide-susceptible and macrolide-resistant Mycobacterium avium complex. Microbiol Spectr 2023; 11:e0182523. [PMID: 37594284 PMCID: PMC10580953 DOI: 10.1128/spectrum.01825-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/29/2023] [Indexed: 08/19/2023] Open
Abstract
Unsatisfactory outcomes following long-term multidrug treatment in patients with Mycobacterium avium complex (MAC) pulmonary disease have urged us to develop novel antibiotics. Thiopeptides, a class of peptide antibiotics derived from natural products, have potential as drug candidates that target bacterial ribosomes, but drug development has been hampered due to their extremely poor solubility. Here, we evaluated three new compounds (AJ-037, AJ-039, and AJ-206) derived from the thiopeptide micrococcin P2 with enhanced aqueous solubility; the derivatives were generated based on structure-activity relationship analysis. We conducted in vitro drug susceptibility and intracellular antimycobacterial activity testing of the three thiopeptide derivatives against various MAC strains, including macrolide-resistant MAC clinical isolates. These compounds showed low MICs against MAC, similar to that of clarithromycin (CLR). In particular, two compounds, AJ-037 and AJ-206, had intracellular antimycobacterial activities, along with synergistic effects with CLR, and inhibited the growth of MAC inside macrophages. Moreover, these two compounds showed in vitro and intracellular anti-MAC activities against macrolide-resistant MAC strains without showing cross-resistance with CLR. Taken together, the results of the current study suggest that AJ-037 and AJ-206 can be promising anti-MAC agents for the treatment of MAC infection, including for macrolide-resistant MAC strains. IMPORTANCE Novel antibiotics for the treatment of MAC infection are urgently needed because the treatment outcomes using the standard regimen for Mycobacterium avium complex (MAC) pulmonary disease remain unsatisfactory. Here, we evaluated three novel thiopeptide derivatives (AJ-037, AJ-039, and AJ-206) derived from the thiopeptide micrococcin P2, and they were confirmed to be effective against macrolide-susceptible and macrolide-resistant MAC. Our thiopeptide derivatives have enhanced aqueous solubility through structural modifications of poorly soluble thiopeptides. The thiopeptide derivatives showed minimal inhibitory concentrations against MAC that were comparable to clarithromycin (CLR). Notably, two compounds, AJ-037 and AJ-206, exhibited intracellular antimycobacterial activities and acted synergistically with CLR to hinder the growth of MAC within macrophages. Additionally, these compounds demonstrated in vitro and intracellular anti-MAC activities against macrolide-resistant MAC strains without showing any cross-resistance with CLR. We believe that AJ-037 and AJ-206 can be promising anti-MAC agents for the treatment of MAC infections, including macrolide-resistant MAC strains.
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Affiliation(s)
- Jiyun Park
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Lee-Han Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Ju Mi Lee
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Sangwon Choi
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | | | | | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Project for Graduate School of Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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3
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Bailly C. The bacterial thiopeptide thiostrepton. An update of its mode of action, pharmacological properties and applications. Eur J Pharmacol 2022; 914:174661. [PMID: 34863996 DOI: 10.1016/j.ejphar.2021.174661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
The bacterial thiopeptide thiostrepton (TS) is used as a veterinary medicine to treat bacterial infections. TS is a protein translation inhibitor, essentially active against Gram-positive bacteria and some Gram-negative bacteria. In procaryotes, TS abrogates binding of GTPase elongation factors to the 70S ribosome, by altering the structure of rRNA-L11 protein complexes. TS exerts also antimalarial effects by disrupting protein synthesis in the apicoplast genome of Plasmodium falciparum. Interestingly, the drug targets both the infectious pathogen (bacteria or parasite) and host cell, by inducing endoplasmic reticulum stress-mediated autophagy which contributes to enhance the host cell defense. In addition, TS has been characterized as a potent chemical inhibitor of the oncogenic transcription factor FoxM1, frequently overexpressed in cancers or other diseases. The capacity of TS to crosslink FoxM1, and a few other proteins such as peroxiredoxin 3 (PRX3) and the 19S proteasome, contributes to the anticancer effects of the thiopeptide. The anticancer activities of TS evidenced using diverse tumor cell lines, in vivo models and drug combinations are reviewed here, together with the implicated targets and mechanisms. The difficulty to formulate TS is a drag on the pharmaceutical development of the natural product. However, the design of hemisynthetic analogues and the use of micellar drug delivery systems should facilitate a broader utilization of the compound in human and veterinary medicines. This review shed light on the many pharmacological properties of TS, with the objective to promote its use as a pharmacological tool and medicinal product.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, Lille, Wasquehal, 59290, France.
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4
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Welty R, Rau M, Pabit S, Dunstan MS, Conn GL, Pollack L, Hall KB. Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain. J Mol Biol 2019; 432:991-1007. [PMID: 31874150 DOI: 10.1016/j.jmb.2019.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/14/2023]
Abstract
The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg2+-dependent folded states, which we suggest lie along the folding pathway of the RNA. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael Rau
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, Clark Hall, Ithaca, NY, 14853, USA
| | - Mark S Dunstan
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta GA, 30322, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Clark Hall, Ithaca, NY, 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA.
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5
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Natural thiopeptides as a privileged scaffold for drug discovery and therapeutic development. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02361-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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6
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Liu J, Lin Z, Li Y, Zheng Q, Chen D, Liu W. Insights into the thioamidation of thiopeptins to enhance the understanding of the biosynthetic logic of thioamide-containing thiopeptides. Org Biomol Chem 2019; 17:3727-3731. [DOI: 10.1039/c9ob00402e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In vivo experiments show that the thioamide moiety of thiopeptins is generated by a TfuA–YcaO pair, before the maturation of the bicyclic scaffold.
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Affiliation(s)
- Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Yuqing Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Dandan Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
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7
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Wang J, Lin Z, Bai X, Tao J, Liu W. Optimal design of thiostrepton-derived thiopeptide antibiotics and their potential application against oral pathogens. Org Chem Front 2019. [DOI: 10.1039/c9qo00219g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new fluorinated thiostrepton-type thiopeptide antibiotic was designed and biosynthesized by using a biological approach with synthetic advantages. Related bioassays indicated that thiostrepton and its derivatives hold potential in oral pathogen treatment.
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Affiliation(s)
- Jian Wang
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
| | - Xuebing Bai
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Jiang Tao
- Department of General Dentistry
- Ninth People's Hospital
- Shanghai Jiao Tong University School of Medicine
- Shanghai Key Laboratory of Stomatology
- Shanghai 200011
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence on Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Shanghai 200032
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8
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Welty R, Pabit SA, Katz AM, Calvey GD, Pollack L, Hall KB. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA (NEW YORK, N.Y.) 2018; 24:1828-1838. [PMID: 30254137 PMCID: PMC6239185 DOI: 10.1261/rna.068361.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 05/22/2023]
Abstract
Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg2+, Ca2+, or Sr2+ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg2+ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg2+ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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9
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Nikulin AD. Structural Aspects of Ribosomal RNA Recognition by Ribosomal Proteins. BIOCHEMISTRY (MOSCOW) 2018; 83:S111-S133. [DOI: 10.1134/s0006297918140109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Mitroshin IV, Garber MB, Gabdulkhakov AG. Investigation of Structure of the Ribosomal L12/P Stalk. BIOCHEMISTRY (MOSCOW) 2017; 81:1589-1601. [PMID: 28260486 DOI: 10.1134/s0006297916130022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review contains recent data on the structure of the functionally important ribosomal domain, L12/P stalk, of the large ribosomal subunit. It is the most mobile site of the ribosome; it has been found in ribosomes of all living cells, and it is involved in the interaction between ribosomes and translation factors. The difference between the structures of the ribosomal proteins forming this protuberance (despite their general resemblance) determines the specificity of interaction between eukaryotic and prokaryotic ribosomes and the respective protein factors of translation. In this review, works on the structures of ribosomal proteins forming the L12/P-stalk in bacteria, archaea, and eukaryotes and data on structural aspects of interactions between these proteins and rRNA are described in detail.
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Affiliation(s)
- I V Mitroshin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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11
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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12
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Larik FA, Saeed A, Muqadar U, El-Seedi H, Faisal M, Channar PA, Mehfooz H. The role of Lawesson's reagent in the total synthesis of macrocyclic natural products. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2016.1259236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Fayaz Ali Larik
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Urooj Muqadar
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hesham El-Seedi
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Muhammad Faisal
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Haroon Mehfooz
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
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13
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Mitroshin I, Garber M, Gabdulkhakov A. Crystallographic analysis of archaeal ribosomal protein L11. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1083-7. [PMID: 26249704 DOI: 10.1107/s2053230x15011395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/12/2015] [Indexed: 11/10/2022]
Abstract
Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11-rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. Here, the crystallization and X-ray analysis of the ribosomal protein L11 from Methanococcus jannaschii are reported. Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space group I222 and were suitable for structural studies. Native and single-wavelength anomalous dispersion data sets have been collected and determination of the structure is in progress.
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Affiliation(s)
- Ivan Mitroshin
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Maria Garber
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
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14
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Abstract
Thiostrepton, a powerful antibiotic belonging to the thiopeptide class, was synthesized in the laboratory for the first time in 2004 through an arduous campaign involving novel strategies and tactics, scenic detours, and unexpected roadblocks. In this Review the author narrates the long journey to success, not so dissimilar to Odysseus' return voyage to Ithaca, full of adventure, knowledge, and wisdom.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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15
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16
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Walter JD, Hunter M, Cobb M, Traeger G, Spiegel PC. Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4. Nucleic Acids Res 2011; 40:360-70. [PMID: 21908407 PMCID: PMC3245911 DOI: 10.1093/nar/gkr623] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Thiostrepton, a macrocyclic thiopeptide antibiotic, inhibits prokaryotic translation by interfering with the function of elongation factor G (EF-G). Here, we have used 70S ribosome binding and GTP hydrolysis assays to study the effects of thiostrepton on EF-G and a newly described translation factor, elongation factor 4 (EF4). In the presence of thiostrepton, ribosome-dependent GTP hydrolysis is inhibited for both EF-G and EF4, with IC(50) values equivalent to the 70S ribosome concentration (0.15 µM). Further studies indicate the mode of thiostrepton inhibition is to abrogate the stable binding of EF-G and EF4 to the 70S ribosome. In support of this model, an EF-G truncation variant that does not possess domains IV and V was shown to possess ribosome-dependent GTP hydrolysis activity that was not affected by the presence of thiostrepton (>100 µM). Lastly, chemical footprinting was employed to examine the nature of ribosome interaction and tRNA movements associated with EF4. In the presence of non-hydrolyzable GTP, EF4 showed chemical protections similar to EF-G and stabilized a ratcheted state of the 70S ribosome. These data support the model that thiostrepton inhibits stable GTPase binding to 70S ribosomal complexes, and a model for the first step of EF4-catalyzed reverse-translocation is presented.
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Affiliation(s)
- Justin D Walter
- Department of Chemistry, Western Washington University, 516 High Street, MS 9150, Bellingham, WA 98225-9150, USA
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17
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Ciufolini MA, Lefranc D. Micrococcin P1: Structure, biology and synthesis. Nat Prod Rep 2010; 27:330-42. [DOI: 10.1039/b919071f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Abstract
Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, LMU, Munich, Germany.
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19
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Starosta AL, Qin H, Mikolajka A, Leung GYC, Schwinghammer K, Chen DYK, Cooperman BS, Wilson DN. Identification of distinct thiopeptide-antibiotic precursor lead compounds using translation machinery assays. CHEMISTRY & BIOLOGY 2009; 16:1087-96. [PMID: 19875082 PMCID: PMC3117328 DOI: 10.1016/j.chembiol.2009.09.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 09/06/2009] [Accepted: 09/10/2009] [Indexed: 11/20/2022]
Abstract
Most thiopeptide antibiotics target the translational machinery: thiostrepton (ThS) and nosiheptide (NoS) target the ribosome and inhibit translation factor function, whereas GE2270A/T binds to the elongation factor EF-Tu and prevents ternary complex formation. We have used several in vitro translational machinery assays to screen a library of thiopeptide antibiotic precursor compounds and identified four families of precursor compounds that are either themselves inhibitory or are able to relieve the inhibitory effects of ThS, NoS, or GE2270T. Some of these precursors represent distinct compounds with respect to their ability to bind to ribosomes. The results not only provide insight into the mechanism of action of thiopeptide compounds but also demonstrate the potential of such assays for identifying lead compounds that might be missed using conventional inhibitory screening protocols.
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Affiliation(s)
- Agata L. Starosta
- Gene Center and Department of Chemistry and Biochemistry
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, LMU, Feodor Lynen Str. 25, 81377, Munich, Germany
| | - Haiou Qin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Aleksandra Mikolajka
- Gene Center and Department of Chemistry and Biochemistry
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, LMU, Feodor Lynen Str. 25, 81377, Munich, Germany
| | - Gulice Y. C. Leung
- Chemical Synthesis Laboratory@Biopolis, Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, The Helios Block, #03–08 Singapore 138667
| | - Kathrin Schwinghammer
- Gene Center and Department of Chemistry and Biochemistry
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, LMU, Feodor Lynen Str. 25, 81377, Munich, Germany
| | - David Y.-K. Chen
- Chemical Synthesis Laboratory@Biopolis, Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, The Helios Block, #03–08 Singapore 138667
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Daniel N. Wilson
- Gene Center and Department of Chemistry and Biochemistry
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, LMU, Feodor Lynen Str. 25, 81377, Munich, Germany
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20
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Schoof S, Baumann S, Ellinger B, Arndt HD. A fluorescent probe for the 70 S-ribosomal GTPase-associated center. Chembiochem 2009; 10:242-5. [PMID: 19072817 DOI: 10.1002/cbic.200800642] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sebastian Schoof
- Technische Universität Dortmund, Fakultät Chemie, Otto-Hahn-Str. 6, 44221 Dortmund, Germany
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21
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Nicolaou K, Chen J, Edmonds D, Estrada A. Fortschritte in der Chemie und Biologie natürlicher Antibiotika. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200801695] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Nicolaou KC, Chen JS, Edmonds DJ, Estrada AA. Recent advances in the chemistry and biology of naturally occurring antibiotics. Angew Chem Int Ed Engl 2009; 48:660-719. [PMID: 19130444 PMCID: PMC2730216 DOI: 10.1002/anie.200801695] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ever since the world-shaping discovery of penicillin, nature's molecular diversity has been extensively screened for new medications and lead compounds in drug discovery. The search for agents intended to combat infectious diseases has been of particular interest and has enjoyed a high degree of success. Indeed, the history of antibiotics is marked with impressive discoveries and drug-development stories, the overwhelming majority of which have their origin in natural products. Chemistry, and in particular chemical synthesis, has played a major role in bringing naturally occurring antibiotics and their derivatives to the clinic, and no doubt these disciplines will continue to be key enabling technologies. In this review article, we highlight a number of recent discoveries and advances in the chemistry, biology, and medicine of naturally occurring antibiotics, with particular emphasis on total synthesis, analogue design, and biological evaluation of molecules with novel mechanisms of action.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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23
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Baumann S, Schoof S, Harkal SD, Arndt HD. Mapping the binding site of thiopeptide antibiotics by proximity-induced covalent capture. J Am Chem Soc 2008; 130:5664-6. [PMID: 18380436 DOI: 10.1021/ja710608w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proximity-induced covalent capture (PICC) has been established for the investigation of ligand binding to composite protein/oligonucleotide target complexes. The RNA-induced attachment of the thiopeptides Thiostrepton and Nosiheptide to engineered Cys mutants of the ribosomal protein L11 was highly position selective and allowed mapping of their binding site at amino acid resolution.
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Affiliation(s)
- Sascha Baumann
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany
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24
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Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P. Translational Regulation via L11: Molecular Switches on the Ribosome Turned On and Off by Thiostrepton and Micrococcin. Mol Cell 2008; 30:26-38. [DOI: 10.1016/j.molcel.2008.01.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 12/21/2007] [Accepted: 01/09/2008] [Indexed: 11/17/2022]
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25
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Iben JR, Draper DE. Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11. Biochemistry 2008; 47:2721-31. [PMID: 18247578 DOI: 10.1021/bi701838y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large ribosomal subunit proteins L10 and L12 form a pentameric protein complex, L10(L12) 4, that is intimately involved in the ribosome elongation cycle. Its contacts with rRNA or other ribosomal proteins have been only partially resolved by crystallography. In Escherichia coli, L10 and L12 are encoded from a single operon for which L10(L12) 4 is a translational repressor that recognizes a secondary structure in the mRNA leader. In this study, L10(L12) 4 was expressed from the moderate thermophile Bacillus stearothermophilus to quantitatively compare strategies for binding of the complex to mRNA and ribosome targets. The minimal mRNA recognition structure is widely distributed among bacteria and has the potential to form a kink-turn structure similar to one identified in the rRNA as part of the L10(L12) 4 binding site. Mutations in equivalent positions between the two sequences have similar effects on L10(L12) 4-RNA binding affinity and identify the kink-turn motif and a loop AA sequence as important recognition elements. In contrast to the larger rRNA structure, the mRNA apparently positions the kink-turn motif and loop for protein recognition without the benefit of Mg (2+)-dependent tertiary structure. The mRNA and rRNA fragments bind L10(L12) 4 with similar affinity ( approximately 10 (8) M (-1)), but fluorescence binding studies show that a nearby protein in the ribosome, L11, enhances L10(L12) 4 binding approximately 100-fold. Thus, mRNA and ribosome targets use similar RNA features, held in different structural contexts, to recognize L10(L12) 4, and the ribosome ensures the saturation of its L10(L12) 4 binding site by means of an additional protein-protein interaction.
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Affiliation(s)
- James R Iben
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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26
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Abstract
Total synthesis campaigns toward complex heterocyclic natural products are a prime source of inspiration for the design and execution of complex cascade sequences, powerful reactions, and efficient synthetic strategies. We highlight selected examples of such innovations in the course of our total syntheses of diazonamide A, azaspiracid-1, thiostrepton, 2,2'-epi-cytoskyrin A and rugulosin, abyssomycin C, platensimycin, and uncialamycin.
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Affiliation(s)
- K. C. Nicolaou
- 1Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA and the Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jason S. Chen
- 1Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA and the Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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27
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García-Marcos A, Morreale A, Guarinos E, Briones E, Remacha M, Ortiz AR, Ballesta JPG. In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton. Nucleic Acids Res 2007; 35:7109-17. [PMID: 17940088 PMCID: PMC2175356 DOI: 10.1093/nar/gkm773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic ribosomal stalk protein L12 and its bacterial orthologue L11 play a central role on ribosomal conformational changes during translocation. Deletion of the two genes encoding L12 in Saccharomyces cerevisiae resulted in a very slow-growth phenotype. Gene RPL12B, but not the RPL12A, cloned in centromeric plasmids fully restored control protein level and the growth rate when expressed in a L12-deprived strain. The same strain has been transformed to express Escherichia coli protein EcL11 under the control of yeast RPL12B promoter. The bacterial protein has been found in similar amounts in washed ribosomes from the transformed yeast strain and from control E. coli cells, however, EcL11 was unable to restore the defective acidic protein stalk composition caused by the absence of ScL12 in the yeast ribosome. Protein EcL11 induced a 10% increase in L12-defective cell growth rate, although the in vitro polymerizing capacity of the EcL11-containing ribosomes is restored in a higher proportion, and, moreover, the particles became partially sensitive to the prokaryotic specific antibiotic thiostrepton. Molecular dynamic simulations using modelled complexes support the correct assembly of bacterial L11 into the yeast ribosome and confirm its direct implication of its CTD in the binding of thiostrepton to ribosomes.
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Affiliation(s)
- Alberto García-Marcos
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and Consejo Superior de investigaciones Científicas, Cantoblanco, Madrid 28049, Spain
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28
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Hofstadler SA, Sannes‐Lowery KA. Interrogation of Noncovalent Complexes by ESI‐MS: A Powerful Platform for High Throughput Drug Discovery. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9783527610907.ch10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Jonker HRA, Ilin S, Grimm SK, Wöhnert J, Schwalbe H. L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Nucleic Acids Res 2006; 35:441-54. [PMID: 17169991 PMCID: PMC1802607 DOI: 10.1093/nar/gkl1066] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11ctd). In addition, the N-terminal domain of L11 (L11ntd) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11ntd, placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11ntd in elongation factor binding.
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Affiliation(s)
- Hendrik R. A. Jonker
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Serge Ilin
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - S. Kaspar Grimm
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- University of Texas Health Science Center SA, Department of Biochemistry7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jens Wöhnert
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- University of Texas Health Science Center SA, Department of Biochemistry7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Harald Schwalbe
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- To whom correspondence should be addressed. Tel: +69 7982 9737; Fax: +69 7982 9515;
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30
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Jenvert RM, Schiavone LH. The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor. J Mol Biol 2006; 365:764-72. [PMID: 17095013 DOI: 10.1016/j.jmb.2006.10.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 10/09/2006] [Accepted: 10/19/2006] [Indexed: 11/18/2022]
Abstract
The stringent response is activated by the binding of stringent factor to stalled ribosomes that have an unacylated tRNA in the ribosomal aminoacyl-site. Ribosomes lacking ribosomal protein L11 are deficient in stimulating stringent factor. L11 consists of a dynamic N-terminal domain (amino acid residues 1-72) connected to an RNA-binding C-terminal domain (amino acid residues 76-142) by a flexible linker (amino acid residues 73-75). In vivo data show that mutation of proline 22 in the N-terminal domain is important for initiation of the stringent response. Here, six different L11 point and deletion-mutants have been constructed to determine which regions of L11 are necessary for the activation of stringent factor. The different mutants were reconstituted with programmed 70 S(DeltaL11) ribosomes and tested for their ability to stimulate stringent factor in a sensitive in vitro pppGpp synthesis assay. It was found that a single-site mutation at proline 74 in the linker region between the two domains did not affect the stimulatory activity of the reconstituted ribosomes, whereas the single-site mutation at proline 22 reduced the activity of SF to 33% compared to ribosomes reconstituted with wild-type L11. Removal of the entire linker between the N and C-terminal domains or removal of the entire proline-rich helix beginning at proline 22 in L11 resulted in an L11 protein, which was unable to stimulate stringent factor in the ribosome-dependent assay. Surprisingly, the N-terminal domain of L11 on its own activated stringent factor in a ribosome-dependent manner without restoring the L11 footprint in 23 S rRNA in the 50 S subunit. This suggests that the N-terminal domain can activate stringent factor in trans. It is also shown that this activation is dependent on unacylated tRNA.
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31
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Naidu BN, Sorenson ME, Matiskella JD, Li W, Sausker JB, Zhang Y, Connolly TP, Lam KS, Bronson JJ, Pucci MJ, Yang H, Ueda Y. Synthesis and antibacterial activity of nocathiacin I analogues. Bioorg Med Chem Lett 2006; 16:3545-9. [PMID: 16621551 DOI: 10.1016/j.bmcl.2006.03.079] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 03/23/2006] [Accepted: 03/24/2006] [Indexed: 11/16/2022]
Abstract
Stereoselective reduction of dehydroalanine double bond in nocathiacin I afforded the primary amide 2. Enzymatic hydrolysis of the amide 2 provided the carboxylic acid 3, which upon coupling with a variety of amines furnished amides 4-32. Some of these semi-synthetic derivatives have retained very good antibacterial activity and have improved aqueous solubility.
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Affiliation(s)
- B Narasimhulu Naidu
- The Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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32
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Maeder C, Conn GL, Draper DE. Optimization of a ribosomal structural domain by natural selection. Biochemistry 2006; 45:6635-43. [PMID: 16716074 PMCID: PMC2698295 DOI: 10.1021/bi052544p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A conserved, independently folding domain in the large ribosomal subunit consists of 58 nt of rRNA and a single protein, L11. The tertiary structure of an rRNA fragment carrying the Escherichia coli sequence is marginally stable in vitro but can be substantially stabilized by mutations found in other organisms. To distinguish between possible reasons why natural selection has not evolved a more stable rRNA structure in E. coli, mutations affecting the rRNA tertiary structure were assessed for their in vitro effects on rRNA stability and L11 affinity (in the context of an rRNA fragment) or in vivo effects on cell growth rate and L11 content of ribosomes. The rRNA fragment stabilities ranged from -4 to +9 kcal/mol relative to the wild-type sequence. Variants in the range of -4 to +5 kcal/mol had almost no observable effect in vivo, while more destabilizing mutations (>7 kcal/mol) were not tolerated. The data suggest that the in vivo stability of the complex is roughly -6 kcal/mol and that any single tertiary interaction is dispensable for function as long as a minimum stability of the complex is maintained. On the basis of these data, it seems that the evolution of this domain has not been constrained by inherent structural or functional limits on stability. The estimated stability corresponds to only a few ribosomes per bacterial cell dissociated from L11 at any time; thus the selective advantage for any further increase in stability may be so small as to be outweighed by other competing selective pressures.
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Affiliation(s)
- Corina Maeder
- Program in Molecular and Computational Biophysics Johns Hopkins University Baltimore, MD 21218
- Department of Chemistry Johns Hopkins University Baltimore, MD 21218
| | - Graeme L. Conn
- Department of Chemistry Johns Hopkins University Baltimore, MD 21218
| | - David E. Draper
- Program in Molecular and Computational Biophysics Johns Hopkins University Baltimore, MD 21218
- Department of Chemistry Johns Hopkins University Baltimore, MD 21218
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33
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Sato H, Ito K, Nakamura Y. Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity. Mol Microbiol 2006; 60:108-20. [PMID: 16556224 DOI: 10.1111/j.1365-2958.2006.05094.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacterial release factors (RFs) 1 and 2 catalyse translation termination at UAG/UAA and UGA/UAA stop codons respectively. It has been shown that limiting the amount of ribosomal protein L11 affects translation termination at UAG and UGA differently. To understand the functional interplay between L11 and RF1/RF2, we isolated 21 distinct mutations in L11 as suppressors of either temperature-sensitive (ts) RF1/RF2 strains or read-through mutants of lacZ nonsense (UAG or UGA) strains. 10 of 21 mutants restored ts lethal growth of RF1 and/or RF2 strains. All the selected L11 mutants, including the RF1ts- and RF2ts-specific suppressors, had the same effect, either enhancing or reducing, on UAG and UGA termination efficiency in vivo. The specific properties of the selected L11 mutations remained unchanged in an RF3 deletion strain. Moreover, ribosomes absent of L11 had equally reduced activity for both RF1- and RF2-mediated peptide release in vitro. These results suggest that, unlike the previous notion, L11 has a common, cooperative role with RF1 and RF2. These L11 mutations were located on the surface of two domains of L11, and interpreted to affect the interaction between L11 and rRNA or the RFs thereby leading to the altered translation termination.
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Affiliation(s)
- Hanae Sato
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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34
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Nicolaou KC, Zak M, Rahimipour S, Estrada AA, Lee SH, O'Brate A, Giannakakou P, Ghadiri MR. Discovery of a biologically active thiostrepton fragment. J Am Chem Soc 2006; 127:15042-4. [PMID: 16248640 DOI: 10.1021/ja0552803] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Design, synthesis, and biological evaluation of several domains of the thiopeptide antibiotic thiostrepton led to the discovery of a biologically active fragment. The biological properties of this novel small organic molecule include antibiotic activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VREF) bacterial strains, as well as cytotoxic action against a number of cancer cell lines.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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35
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Ilin S, Hoskins A, Ohlenschläger O, Jonker HRA, Schwalbe H, Wöhnert J. Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima. Chembiochem 2006; 6:1611-8. [PMID: 16094695 DOI: 10.1002/cbic.200500091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
L11, a protein of the large ribosomal subunit, binds to a highly conserved domain of 23S rRNA and mediates ribosomal GTPase activity. Its C-terminal domain is the main determinant for rRNA binding, whereas its N-terminal domain plays only a limited role in RNA binding. The N-terminal domain is thought to be involved in interactions with elongation and release factors as well as with the antibiotics thiostrepton and micrococcin. This report presents the NMR solution structure of the full-length L11 protein from the thermophilic eubacterium Thermotoga maritima in its free form. The structure is based on a large number of orientational restraints derived from residual dipolar couplings in addition to conventional NOE-based restraints. The solution structure of L11 demonstrates that, in contrast to many other multidomain RNA-binding proteins, the relative orientation of the two domains is well defined. This is shown both by heteronuclear 15N-relaxation and residual dipolar-coupling data. Comparison of this NMR structure with the X-ray structure of RNA-bound L11, reveals that binding not only induces a rigidification of a flexible loop in the C-terminal domain, but also a sizeable reorientation of the N-terminal domain. The domain orientation in free L11 shows limited similarity to that of ribosome-bound L11 in complex with elongation factor, EF-G.
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Affiliation(s)
- Sergey Ilin
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe Universität, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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36
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Nicolaou KC, Safina BS, Zak M, Lee SH, Nevalainen M, Bella M, Estrada AA, Funke C, Zécri FJ, Bulat S. Total synthesis of thiostrepton. Retrosynthetic analysis and construction of key building blocks. J Am Chem Soc 2006; 127:11159-75. [PMID: 16076224 DOI: 10.1021/ja0529337] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first phase of the total synthesis of thiostrepton (1), a highly complex thiopeptide antibiotic, is described. After a brief introduction to the target molecule and its structural motifs, it is shown that retrosynthetic analysis of thiostrepton reveals compounds 23, 24, 26, 28, and 29 as potential key building blocks for the projected total synthesis. Concise and stereoselective constructions of all these intermediates are then described. The synthesis of the dehydropiperidine core 28 was based on a biosynthetically inspired aza-Diels-Alder dimerization of an appropriate azadiene system, an approach that was initially plagued with several problems which were, however, resolved satisfactorily by systematic investigations. The quinaldic acid fragment 24 and the thiazoline-thiazole segment 26 were synthesized by a series of reactions that included asymmetric and other stereoselective processes. The dehydroalanine tail precursor 23 and the alanine equivalent 29 were also prepared from the appropriate amino acids. Finally, a method was developed for the direct coupling of the labile dehydropiperidine key building block 28 to the more advanced and stable peptide intermediate 27 through capture with the highly reactive alanine equivalent 67 under conditions that avoided the initially encountered destructive ring contraction process.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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37
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Bausch SL, Poliakova E, Draper DE. Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA. J Biol Chem 2005; 280:29956-63. [PMID: 15972821 DOI: 10.1074/jbc.m504182200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal protein L11 has two domains: the C-terminal domain (L11-C76) binds rRNA, whereas the N-terminal domain (L11-NTD) may variously interact with elongation factor G, the antibiotic thiostrepton, and rRNA. To begin to quantitate these interactions, L11 from Bacillus stearothermophilus has been overexpressed and its properties compared with those of L11-C76 alone in a fluorescence assay for protein-rRNA binding. The assay relies on 2'-amino-butyryl-pyrene-uridine incorporated in a 58-nucleotide rRNA fragment, which gives approximately 15-fold enhancement when L11 or L11-C76 is bound. Although the pyrene tag weakens protein binding, unbiased protein-RNA association constants were obtained in competition experiments with untagged RNA. It was found that (i) intact B. stearothermophilus L11 binds rRNA with K approximately 1.2 x 10(9) m(-1) in buffers with 0.2 m KCl, about 100-fold tighter than Escherichia coli L11; (ii) the N-terminal domain makes a small, salt-dependent contribution to the overall L11-RNA binding affinity (approximately 8-fold enhancement at 0.2 m KCl), (iii) L11 stimulates thiostrepton binding by 2.3 +/- 0.6 x 10(3)-fold, predicting an overall thiostrepton affinity for the ribosome of approximately 10(9) m(-1), and (iv) the yeast homolog of L11 shows no stimulation of thiostrepton binding. The latter observation resolves the question of why eukaryotes are insensitive to the antibiotic. These measurements also show that it is plausible for thiostrepton to compete directly with EF-G.GDP for binding to the L11-RNA complex, and provide a quantitative basis for further studies of L11 function and thiostrepton mechanism.
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Affiliation(s)
- Sarae L Bausch
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21210, USA
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38
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Hermann T. Drugs targeting the ribosome. Curr Opin Struct Biol 2005; 15:355-66. [PMID: 15919197 DOI: 10.1016/j.sbi.2005.05.001] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 01/31/2005] [Accepted: 05/04/2005] [Indexed: 11/30/2022]
Abstract
Several classes of clinically important antibiotics target the bacterial ribosome, where they interfere with microbial protein synthesis. Structural studies of the interaction of antibiotics with the ribosome have revealed that these small molecules recognize predominantly the rRNA components. Over the past two years, three-dimensional structures of ribosome-antibiotic complexes have been determined, providing a detailed picture of the binding sites and mechanism of action of antibacterials, including 'blockbuster' drugs such as the macrolides. Structure-based approaches have come to fruition that comprise the design and crystal structure analysis of novel semi-synthetic antibiotics that target the ribosome decoding site.
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Affiliation(s)
- Thomas Hermann
- Department of Structural Chemistry, Anadys Pharmaceuticals Inc, 3115 Merryfield Row, San Diego, CA 92121, USA.
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39
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Affiliation(s)
- Mark C Bagley
- School of Chemistry, Main Building, Cardiff University, Park Place, Cardiff, CF10 3AT, Wales, United Kingdom.
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40
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Naidu BN, Sorenson ME, Bronson JJ, Pucci MJ, Clark JM, Ueda Y. Synthesis, in vitro, and in vivo antibacterial activity of nocathiacin I thiol-Michael adducts. Bioorg Med Chem Lett 2005; 15:2069-72. [DOI: 10.1016/j.bmcl.2005.02.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 02/15/2005] [Accepted: 02/16/2005] [Indexed: 10/25/2022]
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41
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Naidu BN, Sorenson ME, Zhang Y, Kim OK, Matiskella JD, Wichtowski JA, Connolly TP, Li W, Lam KS, Bronson JJ, Pucci MJ, Clark JM, Ueda Y. Nocathiacin I analogues: synthesis, in vitro and in vivo biological activity of novel semi-synthetic thiazolyl peptide antibiotics. Bioorg Med Chem Lett 2005; 14:5573-7. [PMID: 15482927 DOI: 10.1016/j.bmcl.2004.08.058] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 08/20/2004] [Accepted: 08/26/2004] [Indexed: 11/28/2022]
Abstract
Several nocathiacin I analogues (4-35) were synthesized and evaluated for their antibacterial activity. Most of these semi-synthetic analogues retained very good in vitro and in vivo antibacterial activity of 1.
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Affiliation(s)
- B Narasimhulu Naidu
- The Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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42
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Dresios J, Chan YL, Wool IG. A determination of the identity elements in yeast 18 S ribosomal RNA for the recognition of ribosomal protein YS11: the role of the kink-turn motif in helix 11. J Mol Biol 2005; 345:681-93. [PMID: 15588818 DOI: 10.1016/j.jmb.2004.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 10/08/2004] [Accepted: 10/11/2004] [Indexed: 11/16/2022]
Abstract
A description of the site of interaction of YS11, the yeast homolog of eubacterial S17, with 18 S rRNA was obtained by assessing the binding of the ribosomal protein, in a filter retention assay, to oligoribonucleotides that reproduce regions of 18 S rRNA. YS11 binds predominantly to domain I; the Kd value is 113 nM. The dimensions of the YS11 binding site were refined, guided by chemical protection data and by the atomic structure of the Thermus thermophilus 30 S subunit, which has the S17 recognition site in 16 S rRNA. An oligoribonucleotide that mimics helix 11, a phylogenetically conserved region in domain I, binds YS11 with a Kd value of 230 nM; a second oligoribonucleotide that contains only the kink-turn motif in helix 11 binds YS11 with a Kd value of 528 nM. Thus, helix 11 has most of the nucleotides required for the recognition of YS11. To identify those nucleotides a set of 27 transversion mutations in H11 was constructed and their contribution to the binding of YS11 determined. Mutations of nine nucleotides (U313, C314, A316, G337, C338, G347, U348, U350, and C351) increased the Kd value for YS11 binding by at least eightfold; G325U and U349A mutations increased the Kd value fivefold. Eight of the 11 mutations are in the kink-turn in H11, confirming the critical importance of the motif for YS11 recognition. The other three nucleotides are in the lower stem and the terminal loop of H11, which makes a lesser, but still important, contribution to YS11 binding. The identity elements for YS11 recognition are: A316, G325, G337, G347, U348, U349, U350, and C351. The effect of the other nucleotides that decrease binding is probably indirect, presumably they affect the conformation of the binding site but do not have contacts to YS11 amino acid residues. The eight identity element nucleotides are in regions of H11 that deviate from A-form geometry and the contacts are predominantly, if not exclusively, to backbone phosphate and sugar oxygen atoms, indicating that YS11 recognizes the shape of the rRNA binding site rather than reading the sequence of nucleotides.
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Affiliation(s)
- John Dresios
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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43
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Bagley MC, Chapaneri K, Dale JW, Xiong X, Bower J. One-Pot Multistep Bohlmann−Rahtz Heteroannulation Reactions: Synthesis of Dimethyl Sulfomycinamate. J Org Chem 2005; 70:1389-99. [PMID: 15704975 DOI: 10.1021/jo048106q] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] The synthesis of dimethyl sulfomycinamate, the acidic methanolysis product of the sulfomycin family of thiopeptide antibiotics, from methyl 2-oxo-4-(trimethylsilyl)but-3-ynoate is achieved in a 2,3,6-trisubstituted pyridine synthesis that proceeds with total regiocontrol in 13 steps by the Bohlmann-Rahtz heteroannulation of a 1-(oxazol-4-yl)enamine or in 12 steps and 9% yield by three-component cyclocondensation with N-[3-oxo-3-(oxazol-4-yl)propanoyl]serine and ammonia in ethanol.
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Affiliation(s)
- Mark C Bagley
- School of Chemistry, Main Building, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom.
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44
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45
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Pucci MJ, Bronson JJ, Barrett JF, DenBleyker KL, Discotto LF, Fung-Tomc JC, Ueda Y. Antimicrobial evaluation of nocathiacins, a thiazole peptide class of antibiotics. Antimicrob Agents Chemother 2004; 48:3697-701. [PMID: 15388422 PMCID: PMC521901 DOI: 10.1128/aac.48.10.3697-3701.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocathiacins are cyclic thiazolyl peptides with inhibitory activity against gram-positive bacteria. BMS-249524 (nocathiacin I), identified from screening a library of compounds against a multiply antibiotic-resistant Enterococcus faecium strain, was used as a lead chemotype to obtain additional structurally related compounds. The MIC assay results of BMS-249524 and two more water-soluble derivatives, BMS-411886 and BMS-461996, revealed potent in vitro activities against a variety of gram-positive pathogens including methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, vancomycin intermediate-resistant S. aureus, vancomycin-resistant enterococci, Mycobacterium tuberculosis and Mycobacterium avium. Analysis of killing kinetics revealed that these compounds are bactericidal for S. aureus with at least a 3-log(10) reduction of bacterial growth within 6 h of exposure to four times the MICs. Nocathiacin-resistant mutants were characterized by DNA sequence analyses. The mutations mapped to the rplK gene encoding the L11 ribosomal protein in the 50S subunit in a region previously shown to be involved in the binding of related thiazolyl peptide antibiotics. These compounds demonstrated potential for further development as a new class of antibacterial agents with activity against key antibiotic-resistant gram-positive bacterial pathogens.
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Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, 300 George St., New Haven, CT 06511, USA.
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46
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Bowen WS, Van Dyke N, Murgola EJ, Lodmell JS, Hill WE. Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain. J Biol Chem 2004; 280:2934-43. [PMID: 15492007 DOI: 10.1074/jbc.m407008200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal protein L11 and the L11 binding region of ribosomal RNA constitute an important domain involved in active functions of the ribosome during translation. We studied the effects of L11 knock-out and truncation mutations on the structure of the rRNA in this region and on its interactions with a translation elongation factor and the antibiotic thiostrepton. The results indicated that the structure of the L11-binding rRNA becomes conformationally flexible when ribosomes lack the entire L11 protein, but not when the C-terminal domain is present on ribosomes. Probing wild type and mutant ribosomes in the presence of the antibiotic thiostrepton and elongation factor-G (EF-G) rigorously localized the binding cleft of thiostrepton and suggested a role for the rRNA in the L11-binding domain in modulating factor binding. Our results also provide evidence that the structure of the rRNA stabilized by the C-terminal domain of L11 is necessary to stabilize EF-G binding in the post-translocation state, and thiostrepton may modulate this structure in a manner that interferes with the ribosome-EF-G interaction. The implications for recent models of thiostrepton activity and factor interactions are discussed.
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Affiliation(s)
- William S Bowen
- Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA
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47
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Naidu BN, Sorenson ME, Hudyma T, Zheng X, Zhang Y, Bronson JJ, Pucci MJ, Clark JM, Ueda Y. Synthesis and antibacterial activity of O-substituted nocathiacin I derivatives. Bioorg Med Chem Lett 2004; 14:3743-6. [PMID: 15203154 DOI: 10.1016/j.bmcl.2004.04.102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 04/29/2004] [Accepted: 04/30/2004] [Indexed: 11/16/2022]
Abstract
The synthesis and antibacterial activity of a series of new nocathiacin I derivatives (1-12) containing polar water solubilizing groups is described. Most of these compounds exhibited potent antibacterial activity and have improved water solubility. In addition, compounds 5, 7-9 also exhibited potent in vivo activity.
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Affiliation(s)
- B Narasimhulu Naidu
- The Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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48
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Triantafillidou D, Persidou E, Lazarou D, Andrikopoulos P, Leontiadou F, Choli-Papadopoulou T. Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution. Biol Chem 2004; 385:31-9. [PMID: 14977044 DOI: 10.1515/bc.2004.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Thermus thermophilus L11 protein has previously been reported to be resistant against tryptic and chymotryptic proteolysis under native conditions. With a single amino acid substitution, namely Trp101Arg, conformational changes were induced that resulted in the exhibition of specific amino acids that served as targets for tryptic and chymotryptic action and rendered the protein highly unstable even during purification. This unexpected process was evidenced by the isolation with size exclusion gel chromatography of the well-structured chymotryptic N-terminal domain in a high amount and its characterization both by Edman degradation and QTOF-EMS spectroscopy. On the other hand, the substitution of Val38Cys, which did not contribute to structural changes, indicates a very possible implication of this amino acid in the protein methylation process. The data reported in this work illustrate the distinctive amino acid dynamics in a thermophilic protein, which, while serving the function common to its counterparts from mesophilic organisms, has had to adapt to the extreme environmental conditions typical of thermophilic organisms.
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Affiliation(s)
- Dimitra Triantafillidou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki, GR-54006 Thessaloniki, Greece
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49
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Abstract
Functional RNAs such as ribosomal RNA and structured domains of mRNA are targets for small molecule ligands that can act as modulators of the RNA biological activity. Natural ligands for RNA display a bewildering structural and chemical complexity that has yet to be matched by synthetic RNA binders. Comparison of natural and artificial ligands for RNA may help to direct future approaches to design and synthesize potent novel scaffolds for specific recognition of RNA targets.
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Affiliation(s)
- Thomas Hermann
- Department of Computational Chemistry & Structure, Anadys Parmaceuticals, Inc., 9050 Camino Santa Fe, San Diego, CA 92121, USA.
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50
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Bower J, Drysdale M, Hebdon R, Jordan A, Lentzen G, Matassova N, Murchie A, Powles J, Roughley S. Structure-based design of agents targeting the bacterial ribosome. Bioorg Med Chem Lett 2003; 13:2455-8. [PMID: 12852942 DOI: 10.1016/s0960-894x(03)00495-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rational structure-based drug design has been applied to the antibiotic thiostrepton, in an attempt to overcome some of its' limitations. The identification of a proposed binding fragment allowed construction of a number of key fragments, which were derivatised to generate a library of potential antibiotics. These were then evaluated to determine their ability to bind to the L11 binding domain of the prokaryotic ribosome and inhibit bacterial protein translation.
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Affiliation(s)
- Justin Bower
- Department of Medicinal Chemistry, RiboTargets Ltd., Granta Park, Abington, Cambridge CB1 6GB, UK
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