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Antimicrobial Agents and Chemotherapy Apr 2006Aminoglycoside antibiotics that bind to the aminoacyl-tRNA site (A site) of the ribosome are composed of a common neamine core in which a glycopyranosyl ring is attached...
Aminoglycoside antibiotics that bind to the aminoacyl-tRNA site (A site) of the ribosome are composed of a common neamine core in which a glycopyranosyl ring is attached to position 4 of a 2-deoxystreptamine moiety. The core is further substituted by one (ribostamycin), two (neomycin and paromomycin), or three (lividomycin A) additional sugars attached to position 5 of the 2-deoxystreptamine. To study the role of rings III, IV, and V in aminoglycoside binding, we used isogenic Mycobacterium smegmatis DeltarrnB mutants carrying homogeneous populations of mutant ribosomes with alterations in the 16S rRNA A site. MICs were determined to investigate drug-ribosome interactions, and the results were compared with that of the previously published crystal structure of paromomycin bound to the ribosomal A site. Our analysis demonstrates that the stacking interaction between ring I and G1491 is largely sequence independent, that rings III and IV each increase the strength of drug binding to the ribosome, that ring IV of the 6'-NH3+ aminoglycosides compensates for loss of interactions between ring II and U1495 and between ring III and G1491, that the aminoglycosides rely on pseudo-base pairing between ring I and A1408 for binding independently of the number of sugar rings attached to the neamine core, that addition of ring V to the 6'-OH 4,5-aminoglycoside paromomycin does not alter the mode of binding, and that alteration of the U1406.U1495 wobble base pair to the Watson-Crick interaction pair 1406C-1495G yields ribosomal drug susceptibilities to 4,5-aminoglycosides comparable to those seen with the wild-type A site.
Topics: Anti-Bacterial Agents; Binding Sites; Mutagenesis, Site-Directed; Neomycin; RNA, Ribosomal, 16S; Ribosomes; Structure-Activity Relationship
PubMed: 16569869
DOI: 10.1128/AAC.50.4.1489-1496.2006 -
Journal of Bacteriology Aug 1983We examined the aminoglycoside inactivation enzymes in Pseudomonas aeruginosa strains, seven clinical isolates and seven laboratory strains without plasmids. All strains...
We examined the aminoglycoside inactivation enzymes in Pseudomonas aeruginosa strains, seven clinical isolates and seven laboratory strains without plasmids. All strains were found to possess the enzyme aminoglycoside 3'-phosphotransferase II [APH(3')-II]. We isolated an APH(3')-II-deficient mutant from a PAO strain by mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine. By plasmid (FP5 or R68.45)-mediated conjugation, we determined the locus of the gene specifying the APH(3')-II between trp-6 and pro-82 on the PAO chromosome and designated this gene aphA. It was concluded that the intrinsic resistance of P. aeruginosa to kanamycins, neomycins, paromomycins, ribostamycin, and butirosins was due to this newly determined gene.
Topics: Chromosome Mapping; Chromosomes, Bacterial; Conjugation, Genetic; Genes, Bacterial; Kanamycin Kinase; Mutation; Phosphotransferases; Pseudomonas aeruginosa; Transduction, Genetic
PubMed: 6307974
DOI: 10.1128/jb.155.2.643-649.1983 -
Pathogens (Basel, Switzerland) Aug 2019Chikungunya virus (CHIKV) infection is one of the major public health concerns, leading thousands of cases every year in rural as well as urban regions of several...
Chikungunya virus (CHIKV) infection is one of the major public health concerns, leading thousands of cases every year in rural as well as urban regions of several countries worldwide, few to mention are India, Philippines, Indonesia, and also in American countries. The structural and non-structural proteins of CHIKV are structurally and functionally similar to other alphaviruses such as Sindbis virus, Venezuelan Equine Encephalitis virus. The precursor protein of non-structural proteins is cleaved by proteolytic activity of non-structural protein (nsp2). This multifunctional nsp2 carry out nucleoside-triphosphatase (NTPase) and RNA helicase activity at its N-terminal and protease activity at C-terminal that makes it primarily a drug target to inhibit CHIKV replication. Until the current date, no suitable treatment for chikungunya infection is available. The introduction of a new drug into the market is a lengthy process, therefore, drug repurposing is now familiar approach that cut off the time and cost of drug discovery. In this study, we have implemented this approach with Food and Drug Administration (FDA) approved drugs and known cysteine protease inhibitors against CHIKV nsp2 protease using structure-based drug discovery. Our extensive docking and molecular dynamics simulations studies leads to two best interacting compounds, Ribostamycin sulfate and E-64, with utmost stable complexes at active site of nsp2 protease. Therefore, these compounds could be suitable for inhibiting CHIKV protease activity, and ultimately the viral replication.
PubMed: 31443266
DOI: 10.3390/pathogens8030128 -
Journal of Applied Microbiology 2005To investigate the in vitro antifungal and antioomycete activities of some aminoglycosides against true fungi and Phytophthora and Pythium species and to evaluate the...
AIMS
To investigate the in vitro antifungal and antioomycete activities of some aminoglycosides against true fungi and Phytophthora and Pythium species and to evaluate the potential of the antibiotics against Phytophthora late blight on plants.
METHODS AND RESULTS
Antifungal and antioomycete activities of aminoglycoside antibiotics (neomycin, paromomycin, ribostamycin and streptomycin) and a paromomycin-producing strain (Streptomyces sp. AMG-P1) against Phytophthora and Pythium species and 10 common fungi were measured in potato dextrose broth (PDB) and on seedlings in pots. Paromomycin was the most active against Phytophthora and Pythium species with a minimal inhibitory concentration of 1-10 microg ml(-1) in PDB, but displayed low to moderate activities towards other common fungi at the same concentration. Paromomycin also showed potent in vivo activity against red pepper and tomato late blight diseases with 80 and 99% control value, respectively, at 100 microg ml(-1). In addition, culture broth of Streptomyces sp. AMG-P1 as a paromomycin producer exhibited high in vivo activity against late blight at 500 microg freeze-dried weight per millilitre.
CONCLUSIONS
Among tested aminoglycoside antibiotics, paromomycin was the most active against oomycetes both in vitro and in vivo.
SIGNIFICANCE AND IMPACT OF THE STUDY
Data from this study show that aminoglycoside antibiotics have in vitro and in vivo activities against oomycetes, suggesting that Streptomyces sp. AMG-P1 may be used as a biocontrol agent against oomycete diseases.
Topics: Antifungal Agents; Capsicum; Culture Media; Fungi; Solanum lycopersicum; Neomycin; Paromomycin; Phytophthora; Plant Diseases; Pythium; Ribostamycin; Streptomycin
PubMed: 16162234
DOI: 10.1111/j.1365-2672.2005.02684.x -
Biochemistry Jan 2008Aminoglycosides are antibacterial compounds that act by binding to the A site of the small 30S bacterial ribosomal subunit and inhibiting protein translation. Clinical...
Aminoglycosides are antibacterial compounds that act by binding to the A site of the small 30S bacterial ribosomal subunit and inhibiting protein translation. Clinical resistance to aminoglycosides is generally the result of the expression of enzymes that covalently modify the antibiotic, including phosphorylation, adenylylation, and acetylation. Bisubstrate analogs for the aminoglycoside N-acetyltransferases are nanomolar inhibitors of Enterococcus faecium AAC(6')-Ii. However, in the case of the Salmonella enterica aac(6')-Iy-encoded aminoglycoside N-acetyltransferase, we demonstrate that a series of bisubstrate analogs are only micromolar inhibitors. In contrast to studies with AAC(6')-Ii, the inhibition constants toward AAC(6')-Iy are essentially independent of both the identity of the aminoglycoside component of the bisubstrate and the number of carbon atoms that are used to link the CoA and aminoglycoside components. The patterns of inhibition suggest that the CoA portion of the bisubstrate analog can bind to the enzyme-aminoglycoside substrate complex and that the aminoglycoside portion can bind to the enzyme-CoA product complex. However, at the high concentrations of bisubstrate analog used in crystallization experiments, we could crystallize and solve the three-dimensional structure of the enzyme-bisubstrate complex. The structure reveals that both the CoA and aminoglycoside portions bind in essentially the same positions as those previously observed for the enzyme-CoA-ribostamycin complex, with only a modest adjustment to accommodate the "linker". These results are compared to previous studies of the interaction of similar bisubstrate analogs with other aminoglycoside N-acetyltransferases.
Topics: Acetyltransferases; Binding Sites; Crystallography, X-Ray; Enzyme Inhibitors; Kinetics; Protein Structure, Secondary; Salmonella enterica; Substrate Specificity
PubMed: 18095712
DOI: 10.1021/bi701957c -
The Journal of Biological Chemistry Jul 2000Binding of human immunodeficiency virus type 1 (HIV-1) transactivator (Tat) protein to Tat-responsive RNA (TAR) is essential for viral replication and is considered a...
Binding of human immunodeficiency virus type 1 (HIV-1) transactivator (Tat) protein to Tat-responsive RNA (TAR) is essential for viral replication and is considered a promising starting point for the design of anti-HIV drugs. NMR spectroscopy indicated that the aminoglycosides neomycin B and ribostamycin bind to TAR and that neomycin is able to inhibit Tat binding to TAR. The solution structure of the neomycin-bound TAR has been determined by NMR spectroscopy. Chemical shift mapping and intermolecular nuclear Overhauser effects define the binding region of the aminoglycosides on TAR and give strong evidence for minor groove binding. Based on 15 nuclear Overhauser effect-derived intermolecular distance restraints, a model structure of the TAR-neomycin complex was calculated. Neomycin is bound in a binding pocket formed by the minor groove of the lower stem and the uridine-rich bulge of TAR, which adopts a conformation different from those known. The neamine core of the aminoglycoside (rings I and II) is covered with the bulge, explaining the inhibition of Tat by an allosteric mechanism. Neomycin reduces the volume of the major groove in which Tat is bound and thus impedes essential protein-RNA contacts.
Topics: ATPases Associated with Diverse Cellular Activities; Anti-Bacterial Agents; Carbohydrate Sequence; DNA-Binding Proteins; Framycetin; HIV Long Terminal Repeat; HIV-1; Humans; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Proteasome Endopeptidase Complex; Protein Binding; RNA, Viral; Ribostamycin
PubMed: 10747964
DOI: 10.1074/jbc.M000920200 -
Antimicrobial Agents and Chemotherapy Dec 2007We have isolated a multiple-aminoglycoside-resistant Escherichia coli strain, strain ARS3, and have been the first to identify a novel plasmid-mediated 16S rRNA...
We have isolated a multiple-aminoglycoside-resistant Escherichia coli strain, strain ARS3, and have been the first to identify a novel plasmid-mediated 16S rRNA methyltransferase, NpmA. This new enzyme shared a relatively low level of identity (30%) to the chromosomally encoded 16S rRNA methyltransferase (KamA) of Streptomyces tenjimariensis, an actinomycete aminoglycoside producer. The introduction of a recombinant plasmid carrying npmA could confer on E. coli consistent resistance to both 4,6-disubstituted 2-deoxystreptamines, such as amikacin and gentamicin, and 4,5-disubstituted 2-deoxystreptamines, including neomycin and ribostamycin. The histidine-tagged NpmA elucidated methyltransferase activity against 30S ribosomal subunits but not against 50S subunits and the naked 16S rRNA molecule in vitro. We further confirmed that NpmA is an adenine N-1 methyltransferase specific for the A1408 position at the A site of 16S rRNA. Drug footprinting data indicated that binding of aminoglycosides to the target site was apparently interrupted by methylation at the A1408 position. These observations demonstrate that NpmA is a novel plasmid-mediated 16S rRNA methyltransferase that provides a panaminoglycoside-resistant nature through interference with the binding of aminoglycosides toward the A site of 16S rRNA through N-1 methylation at position A1408.
Topics: Amino Acid Sequence; Aminoglycosides; Anti-Bacterial Agents; Chromatography, High Pressure Liquid; Drug Resistance, Bacterial; Escherichia coli; Escherichia coli Proteins; Methyltransferases; Microbial Sensitivity Tests; Models, Molecular; Molecular Sequence Data; Plasmids; Protein Binding; RNA, Ribosomal, 16S; Ribosome Subunits, Small; Sequence Homology, Amino Acid
PubMed: 17875999
DOI: 10.1128/AAC.00926-07 -
The Journal of Antibiotics Jun 1989Feeding experiments with D-[6,6-2H2]-, D-(6R)-[6-2H1]- and D-(6S)-[6-2H1]glucose in the fermentation of Streptomyces ribosidificus, followed by field desorption MS and...
Feeding experiments with D-[6,6-2H2]-, D-(6R)-[6-2H1]- and D-(6S)-[6-2H1]glucose in the fermentation of Streptomyces ribosidificus, followed by field desorption MS and 2H NMR analyses of the resulting labeled ribostamycin samples, clearly demonstrated that 1) both hydrogens of the C-6 hydroxymethyl group of D-glucose are stereospecifically incorporated into the C-2 position of 2-deoxystreptamine and 2) the pro S hydrogen of the C-6 position of D-glucose is stereospecifically removed during the elaboration of neosamine C in the biosynthesis of ribostamycin. A plausible mechanism of formation of the deoxy-scyllo-inosose, an early precursor to 2-deoxystreptamine, is suggested to be analogous to the dehydroquinate synthesis in the shikimate pathway and the conversion of the C-6 hydroxymethyl group of D-glucose into the aminomethyl group of neosamine C is likely to involve a dehydrogenation step to a formyl group.
Topics: Anti-Bacterial Agents; Chemical Phenomena; Chemistry; Fermentation; Glucosamine; Hexosamines; Isomerism; Magnetic Resonance Spectroscopy; Molecular Structure; Streptomyces
PubMed: 2737952
DOI: 10.7164/antibiotics.42.926 -
Molecules and Cells Jan 2009Amino acid homology analysis predicted that rbmD, a putative glycosyltransferase from Streptomyces ribosidificus ATCC 21294, has the highest homology with neoD in...
Amino acid homology analysis predicted that rbmD, a putative glycosyltransferase from Streptomyces ribosidificus ATCC 21294, has the highest homology with neoD in neomycin biosynthesis. S. fradiae BS1, in which the production of neomycin was abolished, was generated by disruption of the neoD gene in the neomycin producer S. fradiae. The restoration of neomycin by self complementation suggested that there was no polar effect in the mutant. In addition, S. fradiae BS6 was created with complementation by rbmD in S. fradiae BS1, and secondary metabolite analysis by ESI/MS, LC/MS and MS/MS showed the restoration of neomycin production in S. fradiae BS6. These gene inactivation and complementation studies suggested that, like neoD, rbmD functions as a 2-N-acetlyglucosaminyltransferase and demonstrated the potential for the generation of novel aminoglycoside antibiotics using glycosyltransferases in vivo.
Topics: Anti-Bacterial Agents; Genes, Bacterial; Genetic Complementation Test; Genetic Engineering; Glycosyltransferases; Microbial Sensitivity Tests; Multigene Family; Mutation; Neomycin; Ribostamycin; Sequence Analysis, DNA; Spectrometry, Mass, Electrospray Ionization; Streptomyces
PubMed: 19214437
DOI: 10.1007/s10059-009-0008-0 -
Nucleic Acids Research 2005The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and...
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.
The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson-Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.
Topics: Adenine; Aminoglycosides; Anti-Bacterial Agents; Anticodon; Base Sequence; Binding Sites; Codon; Crystallography, X-Ray; Framycetin; Gentamicins; Kanamycin; Models, Molecular; Oligoribonucleotides; Paromomycin; RNA, Ribosomal, 16S; Ribosomes; Ribostamycin
PubMed: 16214802
DOI: 10.1093/nar/gki862