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Umuhire Juru A, Hargrove AE. Frameworks for targeting RNA with small molecules. J Biol Chem 2021; 296:100191. [PMID: 33334887 PMCID: PMC7948454 DOI: 10.1074/jbc.rev120.015203] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022] Open
Abstract
Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including proteins, DNA, other RNAs, and metabolites. Through these interactions, RNAs mediate cellular processes such as the regulation of gene transcription and the enhancement or inhibition of protein activity. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, and RNA molecules have been increasingly recognized as potential targets for drug development efforts, which in the past had focused primarily on proteins. Although both small molecule-based and oligonucleotide-based therapies have been pursued in efforts to target RNA, small-molecule modalities are often favored owing to several advantages including greater oral bioavailability. In this review, we discuss three general frameworks (sets of premises and hypotheses) that, in our view, have so far dominated the discovery of small-molecule ligands for RNA. We highlight the unique merits of each framework as well as the pitfalls associated with exclusive focus of ligand discovery efforts within only one framework. Finally, we propose that RNA ligand discovery can benefit from using progress made within these three frameworks to move toward a paradigm that formulates RNA-targeting questions at the level of RNA structural subclasses.
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Affiliation(s)
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina, USA.
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2
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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3
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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4
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Abstract
Aminoglycoside antibiotics are protein synthesis inhibitors applied to treat infections caused mainly by aerobic Gram-negative bacteria. Due to their adverse side effects they are last resort antibiotics typically used to combat pathogens resistant to other drugs. Aminoglycosides target ribosomes. We describe the interactions of aminoglycoside antibiotics containing a 2-deoxystreptamine (2-DOS) ring with 16S rRNA. We review the computational studies, with a focus on molecular dynamics (MD) simulations performed on RNA models mimicking the 2-DOS aminoglycoside binding site in the small ribosomal subunit. We also briefly discuss thermodynamics of interactions of these aminoglycosides with their 16S RNA target.
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5
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Yadav S, Deka SR, Jha D, Gautam HK, Sharma AK. Amphiphilic azobenzene-neomycin conjugate self-assembles into nanostructures and transports plasmid DNA efficiently into the mammalian cells. Colloids Surf B Biointerfaces 2016; 148:481-486. [DOI: 10.1016/j.colsurfb.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/17/2016] [Accepted: 09/05/2016] [Indexed: 11/08/2022]
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6
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Synthesis of triazole-functionalized 2-DOS analogues and their evaluation as A-site binders. Bioorg Med Chem Lett 2014; 24:1122-6. [DOI: 10.1016/j.bmcl.2013.12.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/30/2013] [Accepted: 12/31/2013] [Indexed: 11/19/2022]
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7
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Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Böttger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun 2014; 5:3112. [PMID: 24473108 PMCID: PMC3942853 DOI: 10.1038/ncomms4112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023] Open
Abstract
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
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Affiliation(s)
- Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
- These authors contributed equally to this work
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
- These authors contributed equally to this work
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Ng Chyan Leong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- These authors contributed equally to this work
| | - Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashmi Patak
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Srinivas Reddy Dubbaka
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Swapna Vaddi
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - Pia Thommes
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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Ennifar E, Aslam MW, Strasser P, Hoffmann G, Dumas P, van Delft FL. Structure-guided discovery of a novel aminoglycoside conjugate targeting HIV-1 RNA viral genome. ACS Chem Biol 2013; 8:2509-17. [PMID: 24015986 DOI: 10.1021/cb400498n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The dimerization initiation site (DIS) of the HIV-1 genomic RNA is a conserved stem-loop that promotes viral genome dimerization by forming a loop-loop complex. The DIS constitutes a potentially interesting target because it is crucial for several key steps of the viral replication. In this work we describe the synthesis of a rationally designed aminoglycoside conjugate that binds the HIV-1 DIS viral RNA with high specificity, as shown by an extensive in vitro binding characterization. We propose a three-dimensional model of the drug-RNA interaction that perfectly fits with binding data. Our results show the feasibility of targeting the HIV DIS viral RNA dimer and open the way to the rationale design of a new class of antiviral drugs. In addition, due to similarities between the HIV-1 DIS RNA and the bacterial aminoacyl decoding site (A site) RNA, we show that this novel aminoglycoside conjugate also binds the bacterial A site with a similar affinity as natural aminoglycoside antibiotics.
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Affiliation(s)
- Eric Ennifar
- Architecture et Réactivité
de l’ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France
| | - Muhammad Waqar Aslam
- Institute for Molecules and Materials, Radboud University Nijmegen, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Perrine Strasser
- Architecture et Réactivité
de l’ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France
| | - Guillaume Hoffmann
- Architecture et Réactivité
de l’ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Dumas
- Architecture et Réactivité
de l’ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France
| | - Floris L. van Delft
- Institute for Molecules and Materials, Radboud University Nijmegen, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Zimmermann L, Bussière A, Ouberai M, Baussanne I, Jolivalt C, Mingeot-Leclercq MP, Décout JL. Tuning the Antibacterial Activity of Amphiphilic Neamine Derivatives and Comparison to Paromamine Homologues. J Med Chem 2013; 56:7691-705. [DOI: 10.1021/jm401148j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Louis Zimmermann
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Antoine Bussière
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Myriam Ouberai
- Unité de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, Avenue E. Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Isabelle Baussanne
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Claude Jolivalt
- Ecole Nationale de Chimie de Paris/CNRS, UMR
7573, 11 rue Pierre et Marie Curie, F-75231 Paris cedex 05, France
| | - Marie-Paule Mingeot-Leclercq
- Unité de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, Avenue E. Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Jean-Luc Décout
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
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10
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Trylska J, Thoduka SG, Dąbrowska Z. Using sequence-specific oligonucleotides to inhibit bacterial rRNA. ACS Chem Biol 2013; 8:1101-9. [PMID: 23631412 DOI: 10.1021/cb400163t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of antibiotics used in the clinic target bacterial protein synthesis. However, the widespread emergence of bacterial resistance to existing drugs creates a need to discover or develop new therapeutic agents. Ribosomal RNA (rRNA) has been a target for numerous antibiotics that bind to functional rRNA regions such as the peptidyl transferase center, polypeptide exit tunnel, and tRNA binding sites. Even though the atomic resolution structures of many ribosome-antibiotic complexes have been solved, improving the ribosome-acting drugs is difficult because the large rRNA has a complicated 3D architecture and is surrounded by numerous proteins. Computational approaches, such as structure-based design, often fail when applied to rRNA binders because electrostatics dominate the interactions and the effect of ions and bridging waters is difficult to account for in the scoring functions. Improving the classical anti-ribosomal agents has not proven particularly successful and has not kept pace with acquired resistance. So one needs to look for other ways to combat the ribosomes, finding either new rRNA targets or totally different compounds. There have been some efforts to design translation inhibitors that act on the basis of the sequence-specific hybridization properties of nucleic acid bases. Indeed oligonucleotides hybridizing with functional regions of rRNA have been shown to inhibit translation. Also, some peptides have been shown to be reasonable inhibitors. In this review we describe these nonconventional approaches to screening for ribosome inhibition and function of particular rRNA regions. We discuss inhibitors against rRNA that may be designed according to nucleotide sequence and higher order structure.
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Affiliation(s)
- Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Sapna G. Thoduka
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Zofia Dąbrowska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
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11
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Schitter G, Wrodnigg TM. Update on carbohydrate-containing antibacterial agents. Expert Opin Drug Discov 2013; 4:315-56. [PMID: 23489128 DOI: 10.1517/17460440902778725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Since the first known use of antibiotics > 2,500 years ago, a research field with immense importance for the welfare of mankind has been developed. After a decrease in interest in this topic by the end of the 20th century the occurrence of (poly-)resistant strains of bacteria induced a revival of antibiotics research. Health systems have been seeking viable and reliable solutions to this dangerous and expansive threat. OBJECTIVE This review will focus on carbohydrate-containing antibiotics and will give an outline of recently published novel isolated, semisynthetic as well as synthetic structures, their mechanism of action, if known, and the strategies for the design of compounds with potential by improved antibacterial properties. METHODS The literature between 2000 and 2008 was screened with main focus on recent examples of novel structures and strategies for the lead finding of exclusively antibacterial agents. RESULTS/CONCLUSION With the explanation of the role of the carbohydrate moieties in the respective antibacterial agents together with better synthetic strategies in carbohydrate chemistry as well as improvements in assay development for high throughput screening methods, carbohydrate-containing antibiotics can be used for the finding of potential drug leads that contribute to the fight against infections and diseases caused by (resistant) bacterial pathogens.
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Affiliation(s)
- Georg Schitter
- Technical University Graz, Institute of Organic Chemistry, Univ.-Doz. TMW, Dip.-Ing. GS, Glycogroup, A-8010 Graz, Austria +43 316 873 8744 ; +43 316 873 8740 ;
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12
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Jackowski O, Bussière A, Vanhaverbeke C, Baussanne I, Peyrin E, Mingeot-Leclercq MP, Décout JL. Major increases of the reactivity and selectivity in aminoglycoside O-alkylation due to the presence of fluoride ions. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.10.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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13
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Chemical and structural biology of nucleic acids and protein-nucleic acid complexes for novel drug discovery. Sci China Chem 2011. [DOI: 10.1007/s11426-010-4174-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Matt T, Akbergenov R, Shcherbakov D, Böttger EC. The Ribosomal A-site: Decoding, Drug Target, and Disease. Isr J Chem 2010. [DOI: 10.1002/ijch.201000003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Houghton JL, Green KD, Chen W, Garneau-Tsodikova S. The future of aminoglycosides: the end or renaissance? Chembiochem 2010; 11:880-902. [PMID: 20397253 DOI: 10.1002/cbic.200900779] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 11/05/2022]
Abstract
Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.
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Affiliation(s)
- Jacob L Houghton
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
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16
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Dibrov SM, Parsons J, Hermann T. A model for the study of ligand binding to the ribosomal RNA helix h44. Nucleic Acids Res 2010; 38:4458-65. [PMID: 20215440 PMCID: PMC2910043 DOI: 10.1093/nar/gkq159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand–RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region.
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Affiliation(s)
- Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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17
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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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18
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19
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Setny P, Trylska J. Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring. J Chem Inf Model 2009; 49:390-400. [PMID: 19434840 DOI: 10.1021/ci800361a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the existing methods were developed for protein ligands. Here, we present an approach that allows for evading the problems related to still poorly developed RNA docking and scoring algorithms. It is aimed at identification of new molecular scaffolds potentially binding to the A site. The considered molecules are based on the neamine core, which is common for all aminoglycosides and provides specificity toward the binding site, linked with diverse molecular fragments via its O5 or O6 oxygen atom. Suitable fragments are selected with the use of 3D searches of molecular fragments library against two distinct pharmacophores designed on the basis of available structural data for aminoglycoside-RNA complexes. The compounds resulting from fragments assembly with neamine are then scored with a 3D-QSAR model developed using the biological data for known aminoglycoside derivatives. Twenty-one new potential ligands are obtained, four of which have predicted activities comparable to less potent aminoglycoside antibiotics.
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Affiliation(s)
- Piotr Setny
- Interdisciplinary Centre for Mathematical and Computational Modelling and Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
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20
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Cavdar H, Saracoglu N. Synthesis of New β-Hydroxy Nitrate Esters as Potential Glycomimetics or Vasodilators. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800481] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Kondo J, Hainrichson M, Nudelman I, Shallom-Shezifi D, Barbieri CM, Pilch DS, Westhof E, Baasov T. Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites. Chembiochem 2008; 8:1700-9. [PMID: 17705310 DOI: 10.1002/cbic.200700271] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and is a significant clinical problem. The use of this disadvantage of aminoglycoside antibiotics for the possible treatment of human genetic diseases is extremely challenging. Here, we have used a combination of biochemical and structural analysis to compare and contrast the molecular mechanisms of action and the structure-activity relationships of a new synthetic aminoglycoside, NB33, and a structurally similar natural aminoglycoside apramycin. The data presented herein demonstrate the general molecular principles that determine the decreased selectivity of apramycin for the prokaryotic decoding site, and the increased selectivity of NB33 for the eukaryotic decoding site. These results are therefore extremely beneficial for further research on both the design of new aminoglycoside-based antibiotics with diminished deleterious effects on humans, as well as the design of new aminoglycoside-based structures that selectively target the eukaryotic ribosome.
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Affiliation(s)
- Jiro Kondo
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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22
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Bauder C. A convenient synthesis of orthogonally protected 2-deoxystreptamine (2-DOS) as an aminocyclitol scaffold for the development of novel aminoglycoside antibiotic derivatives against bacterial resistance. Org Biomol Chem 2008; 6:2952-60. [DOI: 10.1039/b804784g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Zhou J, Wang G, Zhang LH, Ye XS. Modifications of aminoglycoside antibiotics targeting RNA. Med Res Rev 2007; 27:279-316. [PMID: 16892199 DOI: 10.1002/med.20085] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The increased awareness of the central role of RNA has led to realization that RNA, as structural and functional information accumulation, is also drug target to small molecular therapy. Aminoglycosides are a group of well-known antibiotics, which function through binding to specific sites in prokaryotic ribosomal RNA (rRNA) and affecting the fidelity of protein synthesis. Unfortunately, their clinical practice has been curtailed by toxicity and rapid increasing number of resistant strains. Therefore, it is highly desirable to design new modified aminoglycosides that will overcome the undesirable properties of natural occurring aminoglycosides. On the other hand, aminoglycosides as potential antiviral (HIV) agents were also reported. Herein, we survey the current efforts to develop new aminoglycoside derivatives with modification and reconstruction on each sugar ring and review the latest advances in structure-activity relationships (SAR).
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Affiliation(s)
- Jian Zhou
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100083, China
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24
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Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex. Angew Chem Int Ed Engl 2006; 44:2694-2700. [PMID: 15849690 DOI: 10.1002/anie.200500028] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qing Han
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Qiang Zhao
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Sarah Fish
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
| | - Klaus B Simonsen
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., USA
- Current address: H. Lundbeck A/S, Copenhagen Valby, Denmark
| | | | | | - Daniel Wall
- Department of Microbiology, Anadys Pharmaceuticals, Inc., USA
| | - Thomas Hermann
- Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: (+1) 858-527-1539
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25
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Moitessier N, Westhof E, Hanessian S. Docking of aminoglycosides to hydrated and flexible RNA. J Med Chem 2006; 49:1023-33. [PMID: 16451068 DOI: 10.1021/jm0508437] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although much effort has been devoted to the development of programs suited for the docking of ligands to proteins, much less progress has been achieved in the nucleic acid field. We have developed a unique approach for docking aminoglycosides to RNA considering the flexibility of these macromolecules using conformational ensembles and accounting for the role of the first hydration shell. This concept, successfully implemented in AutoDock, relies on the computation of the intermolecular interaction energy that accounts for the presence of dynamically bound water molecules to the RNA. As an application, a set of 11 aminoglycosides was docked with an average root-mean-square deviation (RMSD) of 1.41 A to be compared with an average RMSD of 3.25 A when the original AutoDock protocol was used.
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Affiliation(s)
- Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 2K6, Canada.
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26
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Zhou Y, Gregor VE, Sun Z, Ayida BK, Winters GC, Murphy D, Simonsen KB, Vourloumis D, Fish S, Froelich JM, Wall D, Hermann T. Structure-guided discovery of novel aminoglycoside mimetics as antibacterial translation inhibitors. Antimicrob Agents Chemother 2006; 49:4942-9. [PMID: 16304156 PMCID: PMC1315978 DOI: 10.1128/aac.49.12.4942-4949.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the structure-guided discovery, synthesis, and initial characterization of 3,5-diamino-piperidinyl triazines (DAPT), a novel translation inhibitor class that targets bacterial rRNA and exhibits broad-spectrum antibacterial activity. DAPT compounds were designed as structural mimetics of aminoglycoside antibiotics which bind to the bacterial ribosomal decoding site and thereby interfere with translational fidelity. We found that DAPT compounds bind to oligonucleotide models of decoding-site RNA, inhibit translation in vitro, and induce translation misincorporation in vivo, in agreement with a mechanism of action at the ribosomal decoding site. The novel DAPT antibacterials inhibit growth of gram-positive and gram-negative bacteria, including the respiratory pathogen Pseudomonas aeruginosa, and display low toxicity to human cell lines. In a mouse protection model, an advanced DAPT compound demonstrated efficacy against an Escherichia coli infection at a 50% protective dose of 2.4 mg/kg of body weight by single-dose intravenous administration.
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Affiliation(s)
- Yuefen Zhou
- Anadys Pharmaceuticals, San Diego, California, USA
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27
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Chênevert R, Jacques F. Enzymatic desymmetrization of 2,5-dideoxystreptamine precursors. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Franceschi F, Duffy EM. Structure-based drug design meets the ribosome. Biochem Pharmacol 2006; 71:1016-25. [PMID: 16443192 DOI: 10.1016/j.bcp.2005.12.026] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 12/08/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
The high-resolution structures of the bacterial ribosomal subunits and those of their complexes with antibiotics have advanced significantly our understanding of small-molecule interactions with RNA. The wealth of RNA structural data generated by these structures has allowed computational chemists to employ a drug discovery paradigm focused on RNA-based targets. The structures also show how target-based resistance affects antibiotics acting at the level of the ribosome. Not only are the sites pinpointed where different classes of antibiotics inhibit protein synthesis, but their orientations, relative dispositions, and unique mechanisms of action are also revealed at the atomic level. Both the 30S and the 50S ribosomal subunits have been shown to be "targets of targets", offering several adjacent, functionally relevant binding pockets for antibiotics. It is the detailed knowledge of these validated locations, or ribofunctional loci, plus the mapping of the resistance hot-spots that allow the rational design of next-generation antibacterials. When the structural information is combined with a data-driven computational toolkit able to describe and predict molecular properties appropriate for bacterial cell penetration and drug-likeness, a structure-based drug design approach for novel antibacterials shows great promise.
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Affiliation(s)
- François Franceschi
- Rib-X Pharmaceuticals, Inc., 300 George Street, Suite 301, New Haven, CT 06511, USA.
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29
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Hoda JC, Krause R, Bertrand S, Bertrand D. Unexpected sensitivity of the human α7 neuronal nicotinic acetylcholine receptor to aminoglycosides. Neuroreport 2006; 17:65-70. [PMID: 16361952 DOI: 10.1097/01.wnr.0000192736.85287.2f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The wide use of antibiotics and the development of resistance is a major health concern and, despite their relatively severe side effects, aminoglycoside antibiotics are still used in clinics. Effects of seven aminoglycosides were investigated at the human homomeric alpha7 and heteromeric alpha4beta2 neuronal nicotinic acetylcholine receptors. All aminoglycosides tested inhibited the acetylcholine-evoked responses with more pronounced effects at alpha7 than at alpha4beta2. Neomycin displayed higher blockade with a half inhibition in the nanomolar range at low calcium concentration and in the micromolar range in physiological calcium concentration but still exerted blockade below the concentration used in the clinic. These data suggest that some of their side effects may be attributable to their interactions with neuronal nicotinic acetylcholine receptors.
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Affiliation(s)
- Jean-Charles Hoda
- Department of Neuroscience, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Kaiser M, Sainlos M, Lehn JM, Bombard S, Teulade-Fichou MP. Aminoglycoside-Quinacridine Conjugates: Towards Recognition of the P6.1 Element of Telomerase RNA. Chembiochem 2006; 7:321-9. [PMID: 16408312 DOI: 10.1002/cbic.200500354] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A modular synthesis has been developed which allows easy and rapid attachment of one or two aminoglycoside units to a quinacridine intercalator, thereby leading to monomeric and dimeric conjugates. Melting temperature (Tm) experiments show that the tobramycin dimeric conjugate TD1 exhibits strong binding to the P6.1 element of human telomerase RNA. By contrast, tobramycin alone is much less efficient and the monomeric compound TM1 elicits a poor binding ability. Monitoring of the interaction by an electrophoretic mobility shift assay shows a 1:1 stoichiometry for the binding of the dimeric compound to the hairpin structure and confirms the lower affinity for a control duplex. Protection experiments with RNase T1 indicate interaction of the drug both in the stem and in the loop of the hairpin. Taken together, the data suggest a binding of TD1 inside the hairpin at the stem-loop junction. The same trends are observed with paromomycin and kanamycin analogues but with a lower affinity.
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Affiliation(s)
- Markus Kaiser
- Laboratoire de Chimie des Interactions Moléculaires, CNRS UPR 285, Collège de France
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31
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Sutcliffe JA. Improving on nature: antibiotics that target the ribosome. Curr Opin Microbiol 2005; 8:534-42. [PMID: 16111914 DOI: 10.1016/j.mib.2005.08.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 08/08/2005] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance, along with the resolution of antibiotic-ribosomal subunit complexes at the atomic level, has provided new insights into modifications of clinically relevant antimicrobials that target the ribosome. Modifications to the aminoglycoside or negamycin scaffolds have been reported in the past, but few derivatives appear to be greatly improved compared to their parent compound. Computational and/or traditional screening efforts have yielded novel compounds that bind to the decoding site of the small (30S) ribosomal subunit; naphthyridones appear to bind only in the presence of poly(U) and tRNA(Phe), whereas quinolines bind in a similar manner to aminoglycosides. Streptogramin B analogs were designed that have an amide replacement of the labile ester bond. The resultant molecules were not substrates for the inactivating lyase, but were no longer inhibitors of translation. The synthesis of 16-membered macrolides that are modified at the C6 position with peptidyl moieties as well as conjugates of chloramphenicol to either nucleotide groups or pyrene have been described, but no antibacterial activity has been reported. X-ray crystal structures are now available that can be used to improve on natural or synthetic antibiotics that bind to either the 30S or the 50S ribosomal subunit.
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32
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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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33
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Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin-RNA Complex. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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