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Tran TPA, Poulet S, Pernak M, Rayar A, Azoulay S, Di Giorgio A, Duca M. Development of 2-deoxystreptamine-nucleobase conjugates for the inhibition of oncogenic miRNA production. RSC Med Chem 2022; 13:311-319. [PMID: 35434630 PMCID: PMC8942232 DOI: 10.1039/d1md00345c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 01/21/2024] Open
Abstract
The discovery of new original scaffolds for selective RNA targeting is one of the main challenges of current medicinal chemistry since therapeutically relevant RNAs represent potential targets for a number of pathologies. Recent efforts have been devoted to the search for RNA ligands targeting the biogenesis of oncogenic miRNAs whose overexpression has been directly linked to the development of various cancers. In this work, we developed a new series of RNA ligands for the targeting of oncogenic miRNA biogenesis based on the 2-deoxystreptamine scaffold. The latter is part of the aminoglycoside neomycin and is known to play an essential role in the RNA interaction of this class of RNA binders. 2-deoxystreptamine was thus conjugated to natural and artificial nucleobases to obtain new binders of the oncogenic miR-372 precursor (pre-miR-372). We identified some conjugates exhibiting a similar biological activity to previously synthesized neomycin analogs and studied their mode of binding with the target pre-miR-372.
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Affiliation(s)
| | - Sylvain Poulet
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
| | - Mélanie Pernak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
| | - Anita Rayar
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
| | - Stéphane Azoulay
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice (ICN) Nice France
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2
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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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Hayashi M. Progress of Chiral Schiff Bases withC1Symmetry in Metal-Catalyzed Asymmetric Reactions. CHEM REC 2016; 16:2708-2735. [DOI: 10.1002/tcr.201600091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Masahiko Hayashi
- Department of Chemistry Graduate School of Science; Kobe University; Nada Kobe 657-8501 Japan
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5
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Crawford DW, Blakeley BD, Chen PH, Sherpa C, Le Grice SF, Laird-Offringa IA, McNaughton BR. An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chem Biol 2016; 11:2206-15. [PMID: 27253715 DOI: 10.1021/acschembio.6b00145] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potent and selective recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA recognition motif as a scaffold for tailoring new RNA hairpin recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5'-untranslated region, inhibits the interaction between TAR RNA and an HIV trans-activator of transcription (Tat)-derived peptide, and suppresses Tat/TAR-dependent transcription. Proteins described in this work are among the tightest TAR RNA-binding reagents-small molecule, nucleic acid, or protein-reported to date and thus have potential utility as therapeutics and basic research tools. Moreover, our findings demonstrate how a naturally occurring RNA recognition motif can be dramatically resurfaced through mutation, leading to potent and selective recognition-and modulation-of disease-relevant RNA.
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Affiliation(s)
| | | | - Po-Han Chen
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
| | - Chringma Sherpa
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stuart F.J. Le Grice
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ite A. Laird-Offringa
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
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6
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Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine. PLoS One 2015; 10:e0137674. [PMID: 26353054 PMCID: PMC4564172 DOI: 10.1371/journal.pone.0137674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022] Open
Abstract
Modified nucleobase analogues can serve as powerful tools for changing physicochemical and biological properties of DNA or RNA. Guanosine derivatives containing bulky substituents at 8 position are known to adopt syn conformation of N-glycoside bond. On the contrary, in RNA the anti conformation is predominant in Watson-Crick base pairing. In this paper two 8-substituted guanosine derivatives, 8-methoxyguanosine and 8-benzyloxyguanosine, were synthesized and incorporated into oligoribonucleotides to investigate their influence on the thermodynamic stability of RNA duplexes. The methoxy and benzyloxy substituents are electron-donating groups, decreasing the rate of depurination in the monomers, as confirmed by N-glycoside bond stability assessments. Thermodynamic stability studies indicated that substitution of guanosine by 8-methoxy- or 8-benzyloxyguanosine significantly decreased the thermodynamic stability of RNA duplexes. Moreover, the presence of 8-substituted guanosine derivatives decreased mismatch discrimination. Circular dichroism spectra of modified RNA duplexes exhibited patterns typical for A-RNA geometry.
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Blakeley BD, McNaughton BR. Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA. ACS Chem Biol 2014; 9:1320-9. [PMID: 24635165 DOI: 10.1021/cb500138h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A multitude of RNA hairpins are directly implicated in human disease. Many of these RNAs are potentially valuable targets for drug discovery and basic research. However, very little is known about the molecular requirements for achieving sequence-selective recognition of a particular RNA sequence and structure. Although a relatively modest number of synthetic small to medium-sized RNA-binding molecules have been reported, rapid identification of sequence-selective RNA-binding molecules remains a daunting challenge. RNA recognition motif (RRM) domains may represent unique privileged scaffolds for the generation of synthetic proteins that selectively recognize structured disease-relevant RNAs, including RNA hairpins. As a demonstration of this potential, we mutated putative RNA-binding regions within the U1A RRM and a variant thereof and screened these synthetic proteins for affinity to HIV-1 trans-activation response (TAR) element hairpin RNA. Some of these U1A-derived proteins bind TAR with single-digit micromolar dissociation constants, and they do so preferentially over the native protein's original target RNA (U1hpII) and a DNA TAR variant. Binding affinity is not appreciably diminished by addition of 10 molar equivalents of cellular tRNAs from Escherichia coli. Taken together, our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research.
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Affiliation(s)
- Brett D. Blakeley
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brian R. McNaughton
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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Moumné R, Catala M, Larue V, Micouin L, Tisné C. Fragment-based design of small RNA binders: Promising developments and contribution of NMR. Biochimie 2012; 94:1607-19. [DOI: 10.1016/j.biochi.2012.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/01/2012] [Indexed: 02/06/2023]
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9
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Warui DM, Baranger AM. Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex. J Med Chem 2012; 55:4132-41. [PMID: 22480197 DOI: 10.1021/jm2007694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.
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Affiliation(s)
- Douglas M Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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10
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Conjugate of neamine and 2-deoxystreptamine mimic connected by an amide bond. Bioorg Med Chem Lett 2011; 21:4713-5. [DOI: 10.1016/j.bmcl.2011.06.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/16/2011] [Accepted: 06/17/2011] [Indexed: 11/24/2022]
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11
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Kumar S, Xue L, Arya DP. Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes. J Am Chem Soc 2011; 133:7361-75. [PMID: 21524066 PMCID: PMC3641821 DOI: 10.1021/ja108118v] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ∼10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634
| | | | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634
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12
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Davis AR, Kirkpatrick CC, Znosko BM. Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res 2010; 39:1081-94. [PMID: 20876693 PMCID: PMC3035445 DOI: 10.1093/nar/gkq793] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence–structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.
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Affiliation(s)
- Amber R Davis
- Department of Chemistry, Saint Louis University, St Louis, MO 63103, USA
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13
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Palde PB, Ofori LO, Gareiss PC, Lerea J, Miller BL. Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence. J Med Chem 2010; 53:6018-27. [PMID: 20672840 DOI: 10.1021/jm100231t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.
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Affiliation(s)
- Prakash B Palde
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
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Kurumbang NP, Park JW, Yoon YJ, Liou K, Sohng JK. Heterologous production of ribostamycin derivatives in engineered Escherichia coli. Res Microbiol 2010; 161:526-33. [PMID: 20561584 DOI: 10.1016/j.resmic.2010.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/25/2010] [Accepted: 04/29/2010] [Indexed: 11/18/2022]
Abstract
Aminoglycosides are a class of important antibiotic compounds used for various therapeutic indications. In recent times, their efficacy has been curtailed due to the rapid development of bacterial resistance. There is a need to develop novel derivatives with an improved spectrum of activity and higher sensitivity against pathogenic bacteria. Although efforts have been focused on the development of newer therapeutic agents by chemical synthesis, to our knowledge, there has been no attempt to harness the potential of microorganisms for this purpose. Escherichia coli affords a widely studied cellular system that could be utilized not only for understanding but also for attempting to engineer the biosynthetic pathway of secondary metabolites. The primary metabolic pathway of E. coli can be engineered to divert the precursor pool required for the biosynthesis of secondary metabolites. Utilizing this approach previously, we engineered E. coli host and generated E. coli M1. Here, we produced a ribostamycin derivative in the engineered host by heterologous expression of the recombinants constructed from the genes encoding the biosynthetic pathway in aminoglycoside-producing strains. The products obtained from the transformants were isolated, analyzed and verified to be ribostamycin derivatives. The study further demonstrated the importance of E. coli as surrogate antibiotic producer and also offered future possibility for the production of other aminoglycoside derivatives through genetic engineering and expression in a heterologous background.
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Affiliation(s)
- Nagendra Prasad Kurumbang
- Institute of Biomolecule Reconstruction, Department of Pharmaceutical Engineering, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea
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Alzeer J, Luedtke NW. pH-Mediated Fluorescence and G-Quadruplex Binding of Amido Phthalocyanines. Biochemistry 2010; 49:4339-48. [DOI: 10.1021/bi9020583] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jawad Alzeer
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Switzerland 8057
| | - Nathan W. Luedtke
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Switzerland 8057
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16
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Meyer ST, Hergenrother PJ. Small molecule ligands for bulged RNA secondary structures. Org Lett 2010; 11:4052-5. [PMID: 19678613 DOI: 10.1021/ol901478x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.
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Affiliation(s)
- S Todd Meyer
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61801, USA
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17
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Warui DM, Baranger AM. Identification of Specific Small Molecule Ligands for Stem Loop 3 Ribonucleic Acid of the Packaging Signal Ψ of Human Immunodeficiency Virus-1. J Med Chem 2009; 52:5462-73. [DOI: 10.1021/jm900599v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Douglas M. Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Anne M. Baranger
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
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18
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Tan Q, Hayashi M. Asymmetric desymmetrization of 4,5-epoxycyclohex-1-ene by enantioselective allylic oxidation. Org Lett 2009; 11:3314-7. [PMID: 19580258 DOI: 10.1021/ol901284v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Asymmetric desymmetrization of allylic oxidation of 4,5-epoxycyclohex-1-ene (1) took place in the presence of 2.5 mol % of Cu(CH(3)CN)(4)PF(6) and 3 mol % of chiral N,N-bidentate ligand (S)-2 to afford (3S,4S,5S)-3-benzoyloxy-4,5-epoxycyclohex-1-ene (3) in 84% ee, which was increased up to >99% ee after recrystallization of 3-4'-nitrobenzoyloxy derivative 6. Optically pure 6 proved to be a key intermediate for enantioselective synthesis of O-protected 2-deoxystreptamine (2-DOS) precursor 12.
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Affiliation(s)
- Qitao Tan
- Department of Frontier Research and Technology, Headquarters for Innovative Cooperation and Development, Kobe University, Nada, Kobe 657-8501, Japan
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19
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Klemm CM, Berthelmann A, Neubacher S, Arenz C. Short and Efficient Synthesis of Alkyne-Modified Amino Glycoside Building Blocks. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Chittapragada M, Roberts S, Ham YW. Aminoglycosides: molecular insights on the recognition of RNA and aminoglycoside mimics. PERSPECTIVES IN MEDICINAL CHEMISTRY 2009; 3:21-37. [PMID: 19812740 PMCID: PMC2754922 DOI: 10.4137/pmc.s2381] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
RNA is increasingly recognized for its significant functions in biological systems and has recently become an important molecular target for therapeutics development. Aminoglycosides, a large class of clinically significant antibiotics, exert their biological functions by binding to prokaryotic ribosomal RNA (rRNA) and interfering with protein translation, resulting in bacterial cell death. They are also known to bind to viral mRNAs such as HIV-1 RRE and TAR. Consequently, aminoglycosides are accepted as the single most important model in understanding the principles that govern small molecule-RNA recognition, which is essential for the development of novel antibacterial, antiviral or even anti-oncogenic agents. This review outlines the chemical structures and mechanisms of molecular recognition and antibacterial activity of aminoglycosides and various aminoglycoside mimics that have recently been devised to improve biological efficacy, binding affinity and selectivity, or to circumvent bacterial resistance.
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Affiliation(s)
- Maruthi Chittapragada
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, U.S.A
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Pang LJ, Wang D, Zhou J, Zhang LH, Ye XS. Synthesis of neamine-derived pseudodisaccharides by stereo- and regio-selective functional group transformations. Org Biomol Chem 2009; 7:4252-66. [DOI: 10.1039/b907518f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Cline LL, Waters ML. Design of a β-hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA. Org Biomol Chem 2009; 7:4622-30. [DOI: 10.1039/b913024a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Kren V, Rezanka T. Sweet antibiotics - the role of glycosidic residues in antibiotic and antitumor activity and their randomization. FEMS Microbiol Rev 2008; 32:858-89. [PMID: 18647177 DOI: 10.1111/j.1574-6976.2008.00124.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A large number of antibiotics are glycosides. In numerous cases the glycosidic residues are crucial to their activity; sometimes, glycosylation only improves their pharmacokinetic parameters. Recent developments in molecular glycobiology have improved our understanding of aglycone vs. glycoside activities and made it possible to develop new, more active or more effective glycodrugs based on these findings - a very illustrative recent example is vancomycin. The majority of attention has been devoted to glycosidic antibiotics including their past, present, and probably future position in antimicrobial therapy. The role of the glycosidic residue in the biological activity of glycosidic antibiotics, and the attendant targeting and antibiotic selectivity mediated by glycone and aglycone in antibiotics some antitumor agents is discussed here in detail. Chemical and enzymatic modifications of aglycones in antibiotics, including their synthesis, are demonstrated on various examples, with particular emphasis on the role of specific and mutant glycosyltransferases and glycorandomization in the preparation of these compounds. The last section of this review describes and explains the interactions of the glycone moiety of the antibiotics with DNA and especially the design and structure-activity relationship of glycosidic antibiotics, including their classification based on their aglycone and glycosidic moiety. The new enzymatic methodology 'glycorandomization' enabled the preparation of glycoside libraries and opened up new ways to prepare optimized or entirely novel glycoside antibiotics.
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Affiliation(s)
- Vladimír Kren
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Affiliation(s)
- Jason R Thomas
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61822, USA
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25
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Chung F, Tisné C, Lecourt T, Dardel F, Micouin L. NMR-guided fragment-based approach for the design of tRNA(Lys3) ligands. Angew Chem Int Ed Engl 2007; 46:4489-91. [PMID: 17486554 DOI: 10.1002/anie.200605201] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Florence Chung
- Chimie Thérapeutique, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
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26
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Jöge T, Jesberger M, Bröker P, Kirschning A. Synthetic access to spacer-linked 3,6-diamino-2,3,6-trideoxy-α-d-glucopyranosides—potential aminoglycoside mimics for the inhibition of the HIV-1 TAR-RNA/Tat-peptide complex. Carbohydr Res 2007; 342:1704-14. [PMID: 17562328 DOI: 10.1016/j.carres.2007.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 05/01/2007] [Accepted: 05/11/2007] [Indexed: 11/25/2022]
Abstract
The synthesis of spacer-linked neoaminoglycoside 5 is described. Key steps of the synthesis are the introduction of nitrogen functionalities at C-3 and C-6 and the olefin cross metathesis of allyl glycoside 16. Although it is known that Grubbs catalysts tolerate nitrogen functionalities, difficulties were encountered in the cross metathesis reaction. Factors that govern this dimerization are the steric and electronic demands of the catalyst and the substrate. Preliminary biological evaluation of homodimer 5, by studying the inhibition of HIV-1 TAR-RNA/Tat-peptide complex using a method based on fluorescence titration, revealed an inhibitory effect of 5.
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Affiliation(s)
- Thomas Jöge
- Institut für Organische Chemie Leibniz, Universität Hannover and Zentrum für Biomolekulare Wirkstoffe (BMWZ), Schneiderberg 1B, D-30167 Hannover, Germany
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27
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Cai L, Li Q, Ren B, Yang ZJ, Zhang LR, Zhang LH. Synthesis of aminodisaccharide–nucleoside conjugates for RNA binding. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Chung F, Tisné C, Lecourt T, Dardel F, Micouin L. NMR-Guided Fragment-Based Approach for the Design of tRNALys3 Ligands. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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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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30
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van den Broek SBAMW, Gruijters BWT, Rutjes FPJT, van Delft FL, Blaauw RH. A Short and Scalable Route to OrthogonallyO-Protected 2-Deoxystreptamine. J Org Chem 2007; 72:3577-80. [PMID: 17385914 DOI: 10.1021/jo062369y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A seven-step synthesis of orthogonally O-protected 2-deoxy-streptamine has been developed from readily available neomycin, with an overall yield of 28%. Key chemical transformations include a chemoselective glycosidic bond hydrolysis and two regioselective protective group manipulations involving acetylation and deacetylation. The synthetic route is amenable to scale-up for the production of multigram quantities of enantiopure and orthogonally O-protected 2-deoxystreptamine, a versatile scaffold for the generation of libraries of RNA-targeting ligands.
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31
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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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32
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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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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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Onouchi H, Hasegawa T, Kashiwagi D, Ishiguro H, Maeda K, Yashima E. Chirality sensing of various biomolecules with helical poly(phenylacetylene)s bearing acidic functional groups in water. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pola.21621] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Riguet E, Désiré J, Boden O, Ludwig V, Göbel M, Bailly C, Décout JL. Neamine dimers targeting the HIV-1 TAR RNA. Bioorg Med Chem Lett 2005; 15:4651-5. [PMID: 16153833 DOI: 10.1016/j.bmcl.2005.07.082] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 07/28/2005] [Accepted: 07/29/2005] [Indexed: 11/18/2022]
Abstract
Natural aminoglycoside antibiotics, such as neomycin, target bacterial ribosomal RNA. Neomycin also binds strongly to HIV TAR and RRE RNA through the predominant interactions of its neamine core. In the search for antiviral agents targeting multiple binding sites for aminoglycosides in RNA, we report here the synthesis of new neamine dimers and a trimer in which the neamine cores are connected by different linking chains attached at the 4'- and/or 5-positions. Inhibition of TAR-Tat complexation by these oligomers was studied via fluorimetric binding assays performed under two ionic strengths. All dimers strongly inhibit TAR-Tat association, with IC50 values 17-85 times better than the value obtained with neomycin. These results demonstrate that modifying neamine at the 4'- or the 5-position is a promising strategy in the search for antiviral agents.
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Affiliation(s)
- Emmanuel Riguet
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS/Université Joseph Fourier-Grenoble I, ICMG FR 2607, 5 Avenue de Verdun, BP 138 F-38243 Meylan, France
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36
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Busscher GF, Rutjes FPJT, van Delft FL. 2-Deoxystreptamine: central scaffold of aminoglycoside antibiotics. Chem Rev 2005; 105:775-91. [PMID: 15755076 DOI: 10.1021/cr0404085] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guuske F Busscher
- IMM Organic Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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37
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Denap JCB, Thomas JR, Musk DJ, Hergenrother PJ. Combating drug-resistant bacteria: small molecule mimics of plasmid incompatibility as antiplasmid compounds. J Am Chem Soc 2005; 126:15402-4. [PMID: 15563166 DOI: 10.1021/ja044207u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major mechanism for bacterial resistance to antibiotics is through the acquisition of a plasmid coding for resistance-mediating proteins. Described herein is a strategy to eliminate these plasmids from bacteria, thus resensitizing the bacteria to antibiotics. This approach involves mimicking a natural mechanism for plasmid elimination, known as plasmid incompatibility. The compound apramycin was identified as a tight binder to SLI RNA (Kd = 93 nM), the in vivo target of the plasmid incompatibility determinate RNA I, and footprinting/mutagenesis studies indicate apramycin binds SLI in the important regulatory region that dictates plasmid replication control and incompatibility. In vivo studies demonstrate that this compound causes significant plasmid loss and resensitizes bacteria to conventional antibiotics. The demonstration that a small molecule can mimic incompatibility, cause plasmid elimination, and resensitize bacteria to antibiotics opens up new targets for antibacterial research.
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Affiliation(s)
- Johna C B Denap
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL 61801, USA
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