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Biochemistry Oct 2011Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In... (Comparative Study)
Comparative Study
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
Topics: Aminoglycosides; Animals; Binding, Competitive; Cattle; DNA; DNA, A-Form; DNA, B-Form; Fluoresceins; Neomycin; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes; Nucleic Acids; Paromomycin; Polynucleotides; Ribostamycin; Thermodynamics
PubMed: 21863895
DOI: 10.1021/bi201077h -
The Journal of Antibiotics Dec 1972
Topics: Amino Sugars; Anti-Bacterial Agents; Chromatography, Gel; Chromatography, Ion Exchange; Drug Resistance, Microbial; Escherichia coli; Kanamycin; Neomycin; Phosphorylase Kinase; Spectrum Analysis
PubMed: 4568694
DOI: 10.7164/antibiotics.25.748 -
Bioorganic & Medicinal Chemistry Oct 2013RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class...
RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class of small molecules to target RNA. However, the RNA motifs outside of the bacterial rRNA A-site that are likely to be bound by these compounds in biological systems is largely unknown. If such information were known, it could allow for aminoglycosides to be exploited to target other RNAs and, in addition, could provide invaluable insights into potential bystander targets of these clinically used drugs. We utilized two-dimensional combinatorial screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a 3×3 nucleotide internal loop library and in a 6-nucleotide hairpin library that bind with high affinity and selectivity to six aminoglycoside derivatives. The selected RNA motifs were then analyzed using structure-activity relationships through sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif-aminoglycoside interactions in terms of affinity and selectivity. The interactions selected by 2DCS generally have nanomolar affinities, which is higher affinity than the binding of aminoglycosides to a mimic of their therapeutic target, the bacterial rRNA A-site.
Topics: Aminoglycosides; Base Sequence; Carbohydrate Sequence; Drug Design; High-Throughput Screening Assays; Humans; Molecular Sequence Data; Nucleic Acid Conformation; RNA; Small Molecule Libraries; Structure-Activity Relationship
PubMed: 23719281
DOI: 10.1016/j.bmc.2013.04.072 -
The Journal of Antibiotics Apr 1976
Topics: Anti-Bacterial Agents; Butirosin Sulfate; Cyclohexanols; Gentamicins; Kanamycin; Neomycin; Paromomycin; Ribostamycin; Sisomicin; Spectinomycin; Streptomycin
PubMed: 58858
DOI: 10.7164/antibiotics.29.319 -
The Journal of Antibiotics Dec 1972
Topics: Amino Sugars; Anti-Bacterial Agents; Chemical Phenomena; Chemistry; Kanamycin; Pseudomonas aeruginosa; Spectrum Analysis
PubMed: 4631344
DOI: 10.7164/antibiotics.25.746 -
The Journal of Antibiotics Feb 1984The three protected sisamine derivatives 2i, 2j and 3, with a free 5-hydroxyl group, have been synthesized. Glycosylation at the 5 position with various pentofuranose...
The three protected sisamine derivatives 2i, 2j and 3, with a free 5-hydroxyl group, have been synthesized. Glycosylation at the 5 position with various pentofuranose derivatives yielded after deprotection of the 6a approximately i ribostamycin related aminoglycoside. These pseudotrisaccharides showed only low antibacterial activities with respect to the parent compounds.
Topics: Anti-Bacterial Agents; Oligosaccharides; Ribostamycin; Trisaccharides
PubMed: 6706851
DOI: 10.7164/antibiotics.37.150 -
The Journal of Antibiotics Sep 1977A mutant of a neomycin-producting Streptomyces fradiae was found which synthesizes ribostamycin instead of neomycin. After a reverse mutation new colonies were obtained...
A mutant of a neomycin-producting Streptomyces fradiae was found which synthesizes ribostamycin instead of neomycin. After a reverse mutation new colonies were obtained producting neomycin again. Ribostamycin might thus be considered as an intermediate in the biosynthesis of neomycin.
Topics: Anti-Bacterial Agents; Bacteria; Fermentation; Mutation; Neomycin; Ribostamycin; Streptomyces
PubMed: 924894
DOI: 10.7164/antibiotics.30.720 -
Antimicrobial Agents and Chemotherapy Jun 1974A new aminoglycoside antibiotic was isolated from the fermentation broths of two strains of Bacillus species. The antibiotic is active against gram-positive and some...
A new aminoglycoside antibiotic was isolated from the fermentation broths of two strains of Bacillus species. The antibiotic is active against gram-positive and some gram-negative bacteria, and its antimicrobial spectrum is similar to that of ribostamycin. The chemical structure was determined to be 5-beta-d-xylofuranosylneamine, which is identical to the deacylated product obtained from butirosin A.
Topics: Acylation; Aminoglycosides; Anti-Bacterial Agents; Bacillus; Butirosin Sulfate; Fermentation; Framycetin; Hydrolysis
PubMed: 15825408
DOI: 10.1128/AAC.5.6.578 -
Antimicrobial Agents and Chemotherapy Sep 2001Aminoglycosides bind to rRNA in the small subunit of the bacterial ribosome. Mutations in the decoding region of 16S rRNA confer resistance to specific subsets of...
Aminoglycosides bind to rRNA in the small subunit of the bacterial ribosome. Mutations in the decoding region of 16S rRNA confer resistance to specific subsets of aminoglycoside antibiotics. The two major classes of 2-deoxystreptamine aminoglycosides are the 4,5- and the 4,6-disubstituted antibiotics. Antibiotics of the 4,5-disubstituted class include neomycin, paromomycin, and ribostamycin. Gentamicins and kanamycins belong to the 4,6-disubstituted class of aminoglycosides. Structural studies indicated the potential importance of position 1406 (Escherichia coli numbering) in the binding of ring III of the 4,6-disubstituted class of aminoglycosides to 16S rRNA. We have introduced a U1406-to-A mutation in a plasmid-encoded copy of E. coli 16S rRNA which has been expressed either in a mixture with wild-type ribosomes or in a strain in which all rRNA is transcribed from the plasmid-encoded rrn operon. High-level resistance to many of the 4,6-disubstituted aminoglycosides is observed only when all the rRNA contains the U1406-to-A mutation. In contrast to the partial dominance of resistance observed with other mutations in the decoding region, there is a dominance of sensitivity with the 1406A mutation. Chemical footprinting experiments indicate that resistance arises from a reduced affinity of the antibiotic for the rRNA target. These results demonstrate that although position 1406 is an important determinant in the binding and action of the 4,6-disubstituted aminoglycosides, other rRNA mutations that perturb the binding of ring I of both classes of 2-deoxystreptamine aminoglycosides confer higher levels of resistance as well as a partial dominance of resistance.
Topics: Adenosine; Aminoglycosides; Anti-Bacterial Agents; Binding Sites; Drug Resistance, Microbial; Escherichia coli; Heterozygote; Homozygote; Microbial Sensitivity Tests; Nucleic Acid Conformation; Point Mutation; RNA, Ribosomal, 16S; Ribosomes; Uridine
PubMed: 11502507
DOI: 10.1128/AAC.45.9.2414-2419.2001 -
The Journal of Biological Chemistry Oct 1999The aminoglycoside phosphotransferases (APHs) are widely distributed among pathogenic bacteria and are employed to covalently modify, and thereby detoxify, the...
The aminoglycoside phosphotransferases (APHs) are widely distributed among pathogenic bacteria and are employed to covalently modify, and thereby detoxify, the clinically relevant aminoglycoside antibiotics. The crystal structure for one of these aminoglycoside kinases, APH(3')-IIIa, has been determined in complex with ADP and analysis of the electrostatic surface potential indicates that there is a large anionic depression present adjacent to the terminal phosphate group of the nucleotide. This region also includes a conserved COOH-terminal alpha-helix that contains the COOH-terminal residue Phe(264). We report here mutagenesis and computer modeling studies aimed at examining the mode of aminoglycoside binding to APH(3')-IIIa. Specifically, seven site mutants were studied, five from the COOH-terminal helix (Asp(261), Glu(262), and Phe(264)), and two additional residues that line the wall of the anionic depression (Tyr(55) and Arg(211)). Using a molecular modeling approach, six ternary complexes of APH(3')-IIIa.ATP with the antibiotics, kanamycin, amikacin, butirosin, and ribostamycin were independently constructed and these agree well with the mutagenesis data. The results obtained show that the COOH-terminal carboxylate of Phe(264) is critical for proper function of the enzyme. Furthermore, these studies demonstrate that there exists multiple binding modes for the aminoglycosides, which provides a molecular basis for the broad substrate- and regiospecificity observed for this enzyme.
Topics: Amino Acid Sequence; Aminoglycosides; Anti-Bacterial Agents; Binding Sites; Carbohydrate Sequence; Conserved Sequence; Escherichia coli; Kanamycin Kinase; Microbial Sensitivity Tests; Models, Molecular; Molecular Conformation; Molecular Sequence Data; Molecular Structure; Mutagenesis, Site-Directed; Nuclear Magnetic Resonance, Biomolecular; Phenylalanine; Polymerase Chain Reaction; Protein Structure, Secondary; Recombinant Proteins; Sequence Deletion; Static Electricity
PubMed: 10521458
DOI: 10.1074/jbc.274.43.30697