Capreomycin and hygromycin B modulate the catalytic activity of the delta ribozyme in a manner that depends on the protonation and complexation with Cu2+ ions of these antibiotics

Szafraniec, Milena; Stokowa-Sołtys, Kamila; Nagaj, Justyna; Kasprowicz, Aleksandra; Wrzesiński, Jan; Jeżowska‐Bojczuk, Małgorzata; Ciesiołka, Jerzy

doi:10.1039/c2dt30794d

Cited by 7 publications

(13 citation statements)

References 37 publications

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“…At higher anti- biotic concentrations, 0.8 and 1 mM, the cleavage reaction was inhibited. 24 The impact of the Cu(II)-viomycin complex on the delta ribozyme was similar to that observed with Cu(II)-capreomycin. A slight inhibition of ribozyme catalysis occurred in the presence of a 0.05 mM Cu(II)-viomycin complex (Fig.…”

Section: Plasmid Dna Damage By Cu-viomycin Complexessupporting

confidence: 63%

“…The established dependence differs from that determined previously for another peptide antibioticcapreomycin. 24 In that case the cleavage reaction was stimulated at the antibiotic concentration in the range of 0.2 to 0.75 mM with the highest stimulation occurring at 0.4 mM capreomycin. At higher anti- biotic concentrations, 0.8 and 1 mM, the cleavage reaction was inhibited.…”

Section: Plasmid Dna Damage By Cu-viomycin Complexesmentioning

confidence: 94%

“…13). Most importantly, the Cu(II)capreomycin complex at pH 5.5 and 6.5 inhibits the ribozyme cleavage almost completely, 24 while the Cu(II)-viomycin complex has no impact on the reaction under these conditions. Besides, at pH 7.5, viomycin stimulates catalysis twofold better than capreomycin.…”

Section: Ph Dependence Of Ribozyme Cleavage Rate Upon Addition Of Viomentioning

confidence: 94%

“…15 The results were extremely useful for explaining the impact of capreomycin and its complex on the catalytic activity of the delta ribozyme and for evaluating the possible mechanisms of modulation of ribozyme activity. 24 In this report we describe the results of comprehensive studies of viomycin, which is structurally related to capreomycin. We attempted to determine copper(II) coordination properties of this drug, its DNA degradation abilities, and the impact on delta ribozyme cleavage activity.…”

Section: Introductionmentioning

confidence: 99%

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Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

et al. 2016

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Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis. In this paper we provide the characteristics of its acid base properties, coordination preferences towards the Cu(ii) ions, as well as the reactivity of the resulting complexes against plasmid DNA and HDV ribozyme. Careful coordination studies throughout the wide pH range allow for the characterisation of all the Cu(ii)-viomycin complex species. The assignment of proton chemical shifts was achieved by NMR experiments, while the DTF level of theory was applied to support molecular structures of the studied complexes. The experiments with the plasmid DNA reveal that at the physiological levels of hydrogen peroxide the Cu(ii)-viomycin complex is more aggressive against DNA than uncomplexed metal ions. Moreover, the degradation of DNA by viomycin can be carried out without the presence of transition metal ions. In the studies of antigenomic delta ribozyme catalytic activity, viomycin and its complex are shown to modulate the ribozyme functioning. The molecular modelling approach allows the indication of two different locations of viomycin binding sites to the ribozyme.

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Section: Plasmid Dna Damage By Cu-viomycin Complexessupporting

confidence: 63%

Section: Plasmid Dna Damage By Cu-viomycin Complexesmentioning

confidence: 94%

Section: Ph Dependence Of Ribozyme Cleavage Rate Upon Addition Of Viomentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

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Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

et al. 2016

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“…Previously, several factors have been suggested that affect the delta ribozyme cleavage reaction by antibiotics, such as the displacement of the catalytic Mg 2+ , an impact on the catalytic cleavage reaction trajectory, and the protonation state of antibiotics or their complexation with Cu 2+ ions . In this study, we showed that some antibiotics and their Cu 2+ complexes inhibiting the delta ribozyme could bind to its different regions or bind in different ways.…”

Section: Discussionmentioning

confidence: 61%

Mapping the interactions of selected antibiotics and their Cu²⁺ complexes with the antigenomic delta ribozyme

et al. 2013

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The interactions of selected antibiotics with the trans-acting antigenomic delta ribozyme were mapped. Ribozyme with two oligonucleotide substrates was used, one uncleavable with deoxycytidine at the cleavage site, mimicking the initial state of ribozyme, and the other with an all-RNA substrate mimicking, after cleavage, the product state. Mapping was performed with a set of RNA structural probing methods: Pb 2+ -induced cleavage, nuclease digestion, and the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) approach. The experimental results combined with molecular modeling revealed different binding sites for neomycin B, amikacin and actinomycin D inside the ribozyme structure. Neomycin B, an aminoglycoside antibiotic, which strongly inhibited the catalytic properties of delta ribozyme, was bound to the pocket formed by the P1 stem, the P1.1 pseudoknot, and the J4/2 junction. Amikacin showed less effective binding to the ribozyme catalytic core, resulting in weak inhibition. Complexes of these aminoglycosides with Cu 2+ ions were bound to the same ribozyme regions, but more effectively, showing lower K d values. On the other hand, the Cu 2+ complex of the cyclopeptide antibiotic actinonomycin D was preferentially intercalated into the P2 and the P4 doublestranded region, and was three times more potent in ribozyme inhibition than the free antibiotic. In addition, some differences in SHAPE reactivities between the ribozyme forms containing all-RNA and deoxycytidine-modified substrates in the J4/2 region were detected, pointing to different ribozyme conformations before and after the cleavage event.

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Peptides having antimicrobial activity and their complexes with transition metal ions

Jeżowska‐Bojczuk

Stokowa-Sołtys

2018

European Journal of Medicinal Chemistry

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Capreomycin and hygromycin B modulate the catalytic activity of the delta ribozyme in a manner that depends on the protonation and complexation with Cu2+ ions of these antibiotics

Cited by 7 publications

References 37 publications

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

Mapping the interactions of selected antibiotics and their Cu²⁺ complexes with the antigenomic delta ribozyme

Peptides having antimicrobial activity and their complexes with transition metal ions

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Capreomycin and hygromycin B modulate the catalytic activity of the delta ribozyme in a manner that depends on the protonation and complexation with Cu2+ ions of these antibiotics

Cited by 7 publications

References 37 publications

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

Mapping the interactions of selected antibiotics and their Cu2+ complexes with the antigenomic delta ribozyme

Peptides having antimicrobial activity and their complexes with transition metal ions

Contact Info

Product

Resources

About

Mapping the interactions of selected antibiotics and their Cu²⁺ complexes with the antigenomic delta ribozyme