1
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QIN CJ, DING MR, TIAN GZ, ZOU XP, FU JJ, HU J, YIN J. Chemical approaches towards installation of rare functional groups in bacterial surface glycans. Chin J Nat Med 2022; 20:401-420. [DOI: 10.1016/s1875-5364(22)60177-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Indexed: 11/24/2022]
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2
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Popadynec M, Baradaran-Heravi A, Alford B, Cameron SA, Clinch K, Mason JM, Rendle PM, Zubkova OV, Gan Z, Liu H, Rebollo O, Whitfield DM, Yan F, Roberge M, Powell DA. Reducing the Toxicity of Designer Aminoglycosides as Nonsense Mutation Readthrough Agents for Therapeutic Targets. ACS Med Chem Lett 2021; 12:1486-1492. [PMID: 34531957 DOI: 10.1021/acsmedchemlett.1c00349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022] Open
Abstract
A significant proportion of genetic disease cases arise from truncation of proteins caused by premature termination codons. In eukaryotic cells some aminoglycosides cause readthrough of premature termination codons during protein translation. Inducing readthrough of these codons can potentially be of therapeutic value in the treatment of numerous genetic diseases. A significant drawback to the repeated use of aminoglycosides as treatments is the lack of balance between their readthrough efficacy and toxicity. The synthesis and biological testing of designer aminoglycoside compounds is documented herein. We disclose the implementation of a strategy to reduce cellular toxicity and maintain readthrough activity of a library of compounds by modification of the overall cationic charge of the aminoglycoside scaffold through ring I modifications.
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Affiliation(s)
- Michael Popadynec
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Benjamin Alford
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Scott A. Cameron
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jennifer M. Mason
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Phillip M. Rendle
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Olga V. Zubkova
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Zhonghong Gan
- Sussex Research Laboratories, Inc., 100 Sussex Drive, Suite 1120B, Ottawa, Ontario K1A 0R6, Canada
| | - Hui Liu
- Sussex Research Laboratories, Inc., 100 Sussex Drive, Suite 1120B, Ottawa, Ontario K1A 0R6, Canada
| | - Oscar Rebollo
- Sussex Research Laboratories, Inc., 100 Sussex Drive, Suite 1120B, Ottawa, Ontario K1A 0R6, Canada
| | - Dennis M. Whitfield
- Sussex Research Laboratories, Inc., 100 Sussex Drive, Suite 1120B, Ottawa, Ontario K1A 0R6, Canada
| | - Fengyang Yan
- Sussex Research Laboratories, Inc., 100 Sussex Drive, Suite 1120B, Ottawa, Ontario K1A 0R6, Canada
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - David A. Powell
- Inception Sciences Canada, 210-887 Great Northern Way, Vancouver, British Columbia, V5T 4T5, Canada
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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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Sabbavarapu NM, Pieńko T, Zalman BH, Trylska J, Baasov T. Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives. MEDCHEMCOMM 2018; 9:503-508. [PMID: 30108940 DOI: 10.1039/c8md00001h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 01/31/2018] [Indexed: 11/21/2022]
Abstract
New derivatives of aminoglycosides containing 6'-carboxylic acid or 6'-amide on their ring I were designed, synthesized and their ability to readthrough nonsense mutations was examined in vitro, along with the protein translation inhibition in prokaryotic and eukaryotic systems. The observed structure-activity relationships, along with the comparative molecular dynamics simulations within the eukaryotic rRNA decoding site, showed high sensitivity of 6'-position to substitution, indicating that the rational design of potent stop-codon read-through inducers requires consideration of not only the structure and energetics of the drug-RNA interaction but also the dynamics associated with that interaction.
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Affiliation(s)
- Narayana Murthy Sabbavarapu
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
| | - Tomasz Pieńko
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland . ; Tel: +48 22 554 3683.,Department of Drug Chemistry , Faculty of Pharmacy with the Laboratory Medicine Division , Medical University of Warsaw , Banacha 1a , 02-097 Warsaw , Poland
| | - Bat-Hen Zalman
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland . ; Tel: +48 22 554 3683
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
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5
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Sabbavarapu NM, Shavit M, Degani Y, Smolkin B, Belakhov V, Baasov T. Design of Novel Aminoglycoside Derivatives with Enhanced Suppression of Diseases-Causing Nonsense Mutations. ACS Med Chem Lett 2016; 7:418-23. [PMID: 27096052 DOI: 10.1021/acsmedchemlett.6b00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/08/2016] [Indexed: 12/19/2022] Open
Abstract
New pseudotrisaccharide derivatives of aminoglycosides that exploit additional interaction on the shallow groove face of the decoding-site rRNA of eukaryotic ribosome were designed, synthesized and biologically evaluated. Novel lead structures (6 and 7 with an additional 7'-OH), exhibiting enhanced specificity to eukaryotic cytoplasmic ribosome, and superior nonsense mutation suppression activity than those of gentamicin, were discovered. The comparative benefit of new leads was demonstrated in four different nonsense DNA-constructs underling the genetic diseases cystic fibrosis, Usher syndrome, and Hurler syndrome.
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Affiliation(s)
- Narayana Murthy Sabbavarapu
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - Michal Shavit
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - Yarden Degani
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - Boris Smolkin
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - Valery Belakhov
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
| | - Timor Baasov
- The Edith
and Joseph Fischer
Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion−Israel Institute of Technology, Haifa 32000, Israel
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6
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Shalev M, Rozenberg H, Smolkin B, Nasereddin A, Kopelyanskiy D, Belakhov V, Schrepfer T, Schacht J, Jaffe CL, Adir N, Baasov T. Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics. Nucleic Acids Res 2015; 43:8601-13. [PMID: 26264664 PMCID: PMC4787808 DOI: 10.1093/nar/gkv821] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/01/2015] [Indexed: 11/13/2022] Open
Abstract
Leishmaniasis comprises an array of diseases caused by pathogenic species of Leishmania, resulting in a spectrum of mild to life-threatening pathologies. Currently available therapies for leishmaniasis include a limited selection of drugs. This coupled with the rather fast emergence of parasite resistance, presents a dire public health concern. Paromomycin (PAR), a broad-spectrum aminoglycoside antibiotic, has been shown in recent years to be highly efficient in treating visceral leishmaniasis (VL)—the life-threatening form of the disease. While much focus has been given to exploration of PAR activities in bacteria, its mechanism of action in Leishmania has received relatively little scrutiny and has yet to be fully deciphered. In the present study we present an X-ray structure of PAR bound to rRNA model mimicking its leishmanial binding target, the ribosomal A-site. We also evaluate PAR inhibitory actions on leishmanial growth and ribosome function, as well as effects on auditory sensory cells, by comparing several structurally related natural and synthetic aminoglycoside derivatives. The results provide insights into the structural elements important for aminoglycoside inhibitory activities and selectivity for leishmanial cytosolic ribosomes, highlighting a novel synthetic derivative, compound 3, as a prospective therapeutic candidate for the treatment of VL.
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Affiliation(s)
- Moran Shalev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Smolkin
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Abedelmajeed Nasereddin
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dmitry Kopelyanskiy
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Valery Belakhov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thomas Schrepfer
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles L Jaffe
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Timor Baasov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
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7
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Mavridis I, Kythreoti G, Koltsida K, Vourloumis D. Rigid spiroethers targeting the decoding center of the bacterial ribosome. Bioorg Med Chem 2014; 22:1329-41. [PMID: 24457095 DOI: 10.1016/j.bmc.2013.12.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/30/2013] [Accepted: 12/30/2013] [Indexed: 01/21/2023]
Abstract
Continuing our efforts towards understanding the principles governing ribosomal recognition and function, we have synthesized and evaluated a series of diversely functionalized 5,6-, 6,6- and 7,6-spiroethers. These compounds successfully mimic natural aminoglycosides regarding their binding to the decoding center of the bacterial ribosome. Their potential to inhibit prokaryotic protein production in vitro along with their antibacterial potencies have also been examined.
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Affiliation(s)
- Ioannis Mavridis
- Chemical Biology Laboratories, National Center for Scientific Research 'Demokritos', Agia Paraskevi Attikis, GR-15310, Greece
| | - Georgia Kythreoti
- Chemical Biology Laboratories, National Center for Scientific Research 'Demokritos', Agia Paraskevi Attikis, GR-15310, Greece
| | - Konstantina Koltsida
- Chemical Biology Laboratories, National Center for Scientific Research 'Demokritos', Agia Paraskevi Attikis, GR-15310, Greece
| | - Dionisios Vourloumis
- Chemical Biology Laboratories, National Center for Scientific Research 'Demokritos', Agia Paraskevi Attikis, GR-15310, Greece.
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8
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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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9
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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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10
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Jiang FJ, Fu XZ, Wang SW, Huang Y, Zhou W, Wang AM, Wang YL. Synthesis and physiochemical property evaluation of carbamate derivatives of scutellarin methyl ester. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2013.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Kiviniemi A, Virta P, Lönnberg H. Solid-supported synthesis and click conjugation of 4'-C-alkyne functionalized oligodeoxyribonucleotides. Bioconjug Chem 2011; 21:1890-901. [PMID: 20828203 DOI: 10.1021/bc100268w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
4'-C-[N,N-Di(4-pentyn-1-yl)aminomethyl]thymidine and 4'-C-[N-methyl-N-(4-pentyn-1-yl)aminomethyl]thymidine 3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidites (1, 2) were synthesized, and one or two such monomers were incorporated into a 15-mer oligodeoxyribonucleotide. After chain assembly, azido-functionalized ligands, including appropriate derivatives of 1,4-phenylenedimethaneamine, mannose, paromamine, and neomycin, were conjugated to the alkynyl groups by the click chemistry on a solid support. The influence of the 4'-modifications on the melting temperature with DNA and 2'-O-methyl RNA targets was studied. Oligonucleotides containing one to four mannose ligands in the central part of the chain (up to two 4'-C-[N,N-di(4-pentyn-1-yl)aminomethyl]thymidine units) form equally stable duplexes with complementary 2'-OMe RNA as the corresponding unmodified DNA sequence. At high salt content, the mannose conjugation is even stabilizing. On using a DNA target, a modest destabilization occurs. All the amino group bearing conjugates stabilized the duplexes, the DNA·DNA duplexes more than the DNA·2'-O-methyl RNA duplexes.
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, Turku, Finland
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12
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Cottin T, Pyrkotis C, Stathakis CI, Mavridis I, Katsoulis IA, Anastasopoulou P, Kythreoti G, Zografos AL, Nahmias VR, Papakyriakou A, Vourloumis D. Designed Spiro-Bicyclic Analogues Targeting the Ribosomal Decoding Center. Chembiochem 2010; 12:71-87. [DOI: 10.1002/cbic.201000591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Second generation analogs of rigid 6,7-spiro scaffolds targeting the bacterial ribosome. Bioorg Med Chem Lett 2010; 20:7488-92. [DOI: 10.1016/j.bmcl.2010.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 09/30/2010] [Accepted: 10/01/2010] [Indexed: 11/19/2022]
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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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Li Y, Shen J, Sun X, Li W, Liu G, Tang Y. Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. J Chem Inf Model 2010; 50:1134-46. [DOI: 10.1021/ci9004157] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yaozong Li
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jie Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xianqiang Sun
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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16
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Abstract
Bacterial ribosomal RNA is the target of clinically important antibiotics, while biologically important RNAs in viral and eukaryotic genomes present a range of potential drug targets. The physicochemical properties of RNA present difficulties for medicinal chemistry, particularly when oral availability is needed. Peptidic ligands and analysis of their RNA-binding properties are providing insight into RNA recognition. RNA-binding ligands include far more chemical classes than just aminoglycosides. Chemical functionalities from known RNA-binding small molecules are being exploited in fragment- and ligand-based projects. While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA–ligand interaction will be necessary to realize the full potential of this class of targets.
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17
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Katsoulis IA, Pyrkotis C, Papakyriakou A, Kythreoti G, Zografos AL, Mavridis I, Nahmias VR, Anastasopoulou P, Vourloumis D. Unnatural Rigid Scaffolds Targeting the Bacterial Ribosome. Chembiochem 2009; 10:1969-72. [DOI: 10.1002/cbic.200900268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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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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19
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Blount KF, Tor Y. A tale of two targets: differential RNA selectivity of nucleobase-aminoglycoside conjugates. Chembiochem 2007; 7:1612-21. [PMID: 16915600 DOI: 10.1002/cbic.200600109] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Aminoglycoside antibiotics are RNA-binding polyamines that can bind with similar affinities to structurally diverse RNA targets. To design new semisynthetic aminoglycosides with improved target selectivity, it is important to understand the energetic and structural basis by which diverse RNA targets recognize similar ligands. It is also imperative to discover how novel aminoglycosides could be rationally designed to have enhanced selectivity for a given target. Two RNA drug targets, the prokaryotic ribosomal A-site and the HIV-1 TAR, provide an excellent model system in which to dissect the issue of target selectivity, in that they each have distinctive interactions with aminoglycosides. We report herein the design, synthesis, and binding activity of novel nucleobase-aminoglycoside conjugates that were engineered to be more selective for the A-site binding pocket. Contrary to the structural design, the conjugates bind the A-site more weakly than does the parent compound and bind the TAR more tightly than the parent compound. This result implies that the two RNA targets differ in their ability to adapt to structurally diverse ligands and thus have inherently different selectivities. This work emphasizes the importance of considering the inherent selectivity traits of the RNA target when engineering new ligands.
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Affiliation(s)
- Kenneth F Blount
- Department of Molecular, Cellular, and Developmental Biology Yale University 266 Whitney Ave, KBT 516, New Haven, CT 06520, USA
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20
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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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21
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Zhao F, Zhao Q, Blount KF, Han Q, Tor Y, Hermann T. Molecular recognition of RNA by neomycin and a restricted neomycin derivative. Angew Chem Int Ed Engl 2006; 44:5329-34. [PMID: 16037995 DOI: 10.1002/anie.200500903] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fang Zhao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, 92093, USA
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22
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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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23
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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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24
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Rao Y, Venot A, Swayze EE, Griffey RH, Boons GJ. Trisaccharide mimetics of the aminoglycoside antibiotic neomycin. Org Biomol Chem 2006; 4:1328-37. [PMID: 16557321 DOI: 10.1039/b517725a] [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] [Indexed: 11/21/2022]
Abstract
A highly convergent approach for the chemical synthesis of eight structurally related trisaccharides that contain 3 to 5 amino groups has been described. Fourier-transformation ion cyclotron resonance mass spectrometry (FT-ICR MS) has been employed to determine the dissociation constants (Kd) for the binding of the trisaccharides to a prototypical fragment of 16S ribosomal RNA. A compound that contained a 4,6-dideoxy-4-amino-beta-D-glucopyranoside moiety at C-3 displayed binding in the low micromolar range. It was found that small structural changes of the saccharides resulted in large differences in affinity. The described structure-activity relationship is expected to be valuable for the development of novel antibiotics that target rRNA.
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Affiliation(s)
- Yu Rao
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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25
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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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26
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Blount KF, Zhao F, Hermann T, Tor Y. Conformational constraint as a means for understanding RNA-aminoglycoside specificity. J Am Chem Soc 2005; 127:9818-29. [PMID: 15998086 DOI: 10.1021/ja050918w] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lack of high RNA target selectivity displayed by aminoglycoside antibiotics results from both their electrostatically driven binding mode and their conformational adaptability. The inherent flexibility around their glycosidic bonds allows them to easily assume a variety of conformations, permitting them to structurally adapt to diverse RNA targets. This structural promiscuity results in the formation of aminoglycoside complexes with diverse RNA targets in which the antibiotics assume distinct conformations. Such differences suggest that covalently linking individual rings in an aminoglycoside could reduce its available conformations, thereby altering target selectivity. To explore this possibility, conformationally constrained neomycin and paromomycin analogues designed to mimic the A-site bound aminoglycoside structure have been synthesized and their affinities to the TAR and A-site, two therapeutically relevant RNA targets, have been evaluated. As per design, this constraint has minimal deleterious effect on binding to the A-site. Surprisingly, however, preorganizing these neomycin-class antibiotics into a TAR-disfavored structure has no deleterious effect on binding to this HIV-1 RNA sequence. We rationalize these observations by suggesting that the A-site and HIV TAR possess inherently different selectivities toward aminoglycosides. The inherent plasticity of the TAR RNA, coupled to the remaining flexibility within the conformationally constrained analogues, makes this RNA site an accommodating target for such polycationic ligands. In contrast, the deeply encapsulating A-site is a more discriminating RNA target. These observations suggest that future design of novel target selective RNA-based therapeutics will have to consider the inherent "structural" selectivity of the RNA target and not only the selectivity patterns displayed by the low molecular weight ligands.
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Affiliation(s)
- Kenneth F Blount
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA
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27
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Zhang X, Wang X, Liu C. Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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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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29
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Zhao F, Zhao Q, Blount KF, Han Q, Tor Y, Hermann T. Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500903] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Ayida BK, Simonsen KB, Vourloumis D, Hermann T. Synthesis of dehydroalanine fragments as thiostrepton side chain mimetics. Bioorg Med Chem Lett 2005; 15:2457-60. [PMID: 15863296 DOI: 10.1016/j.bmcl.2005.03.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 03/18/2005] [Accepted: 03/21/2005] [Indexed: 11/17/2022]
Abstract
Syntheses of dehydroalanine derivatives via a solid-support route, starting from selenocystein, and via conventional solution phase chemistry are described along with initial biological testing. The target compounds were designed as mimetics of the dehydroalanine side chain of the macrocyclic antibiotic thiostrepton that acts on the bacterial ribosome.
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Affiliation(s)
- Benjamin K Ayida
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA
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31
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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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32
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33
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Vourloumis D, Winters GC, Simonsen KB, Takahashi M, Ayida BK, Shandrick S, Zhao Q, Han Q, Hermann T. Aminoglycoside-Hybrid Ligands Targeting the Ribosomal Decoding Site. Chembiochem 2004; 6:58-65. [PMID: 15568198 DOI: 10.1002/cbic.200400197] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dionisios Vourloumis
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA.
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34
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Barluenga S, Simonsen KB, Littlefield ES, Ayida BK, Vourloumis D, Winters GC, Takahashi M, Shandrick S, Zhao Q, Han Q, Hermann T. Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome. Bioorg Med Chem Lett 2004; 14:713-8. [PMID: 14741274 DOI: 10.1016/j.bmcl.2003.11.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RNA recognition by natural aminoglycoside antibiotics depends on the 2-deoxystreptamine (2-DOS) scaffold which participates in specific hydrogen bonds with the ribosomal decoding-site target. Three-dimensional structure information has been used for the design of azepane-monoglycosides, building blocks for novel antibiotics in which 2-DOS is replaced by a heterocyclic scaffold. Azepane-glycosides showed target binding and translation inhibition in the low micromolar range and inhibited growth of Staphylococcus aureus, including aminoglycoside-resistant strains.
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Affiliation(s)
- Sofia Barluenga
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc, 9050 Camino Santa Fe, San Diego, CA 92121, USA
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35
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McPike MP, Goodisman J, Dabrowiak JC. Specificity of neomycin analogues bound to the packaging region of human immunodeficiency virus type 1 RNA. Bioorg Med Chem 2004; 12:1835-43. [PMID: 15051052 DOI: 10.1016/j.bmc.2004.01.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Revised: 01/28/2004] [Accepted: 01/28/2004] [Indexed: 11/24/2022]
Abstract
The packaging region of HIV-1 RNA contains a number of structural features which are important in the life cycle of the virus, making this segment of RNA a potential target for new types of AIDS-directed drugs. We studied the binding of three neomycin analogues (neo-guanidino, neo-acridine, and neo-neo) to a 171-mer RNA molecule from the packaging region of HIV-1 using quantitative footprinting and circular dichroism. Neo-guanidino produced footprinting patterns and effects on the CD similar to those observed for neomycin and paromomycin, indicating that all three compounds bind to the same regions of the 171-mer. Neo-guanidino binds to SL 1 where it joins the large internal loop, near a bulge in the stem of SL 1, and on SL 2. Neo-acridine, which has an acridine attached to neomycin, and neo-neo, which has two neomycins linked by a flexible tether, bind bivalently, and give very different footprinting and CD results from the other compounds. The neomycin portion of neo-acridine binds to the same sites as neomycin, while the attached acridine group appears to bind to a duplex region in the main stem of the folded 171-mer. Since the footprinting data for this analogue show few enhancements, bivalent binding of neo-acridine appears to stabilize the folded structure of RNA by effectively 'stapling' parts of the structure together. Neo-neo induces significant structural changes in RNA where neomycin binds. This may be related to the inability of both neomycins of neo-neo it find optimal binding sites adjacent to one another without changing RNA structure. The intensity of a strong negative CD band in the spectrum of psi-RNA at 208 nm is sensitive to drug-induced changes in RNA structure. Neo-guanidino and neo-neo (also neomycin and paromomycin), which change RNA structure, cause an increase in intensity while neo-acridine, which induces little distortion to RNA, causes a decrease in intensity. Molecular modeling analysis shows that C-5' of ribose of neo-acridine and neo-neo must be directed away from the binding pocket when these analogues are bivalently bound to RNA. This study showed how variations in the structure of aminoglycosides lead to different binding specificity to part of the packaging region of HIV-1. Such knowledge will be important in design of drugs to target this region.
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Affiliation(s)
- Mark P McPike
- Department of Chemistry, Center for Science and Technology, R 1-014, Syracuse University, Syracuse, New York 13244-4100, USA
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36
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Vourloumis D, Winters GC, Takahashi M, Simonsen KB, Ayida BK, Shandrick S, Zhao Q, Hermann T. Novel acyclic deoxystreptamine mimetics targeting the ribosomal decoding site. Chembiochem 2003; 4:879-85. [PMID: 12964163 DOI: 10.1002/cbic.200300688] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dionisios Vourloumis
- Department of Medicinal Chemistry, Anadys Pharmaceuticals Inc., 9050 Camino Santa Fe, San Diego, CA 92121, USA.
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37
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Simonsen KB, Ayida BK, Vourloumis D, Winters GC, Takahashi M, Shandrick S, Zhao Q, Hermann T. Piperidine glycosides targeting the ribosomal decoding site. Chembiochem 2003; 4:886-90. [PMID: 12964164 DOI: 10.1002/cbic.200300689] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Klaus B Simonsen
- Department of Medicinal Chemistry, Anadys Pharmaceuticals Inc., 9050 Camino Santa Fe, San Diego, CA 92121, USA.
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38
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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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39
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Carlson CB, Vuyisich M, Gooch BD, Beal PA. Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution. CHEMISTRY & BIOLOGY 2003; 10:663-72. [PMID: 12890540 DOI: 10.1016/s1074-5521(03)00147-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5'-CpG-3' sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (K(D) = 20 nM) contains a base-paired 5'-CpG-3' step flanked on the 5' side by a 4 nt internal loop and the 3' side by a bulged U. Several viral 5'- and 3'-UTR RNA sequences that likely form binding sites for this PAC are identified.
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Affiliation(s)
- Coby B Carlson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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40
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Yu L, Oost TK, Schkeryantz JM, Yang J, Janowick D, Fesik SW. Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA. J Am Chem Soc 2003; 125:4444-50. [PMID: 12683814 DOI: 10.1021/ja021354o] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA. Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens. To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E. coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target. From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM. Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides. Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.
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Affiliation(s)
- Liping Yu
- Pharmaceutical Discovery Division, GPRD, Abbott Laboratories, Abbott Park, IL 60064-6098, USA.
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