Interaction of the antibiotics clindamycin and lincomycin with<i>Escherichia coli</i>23S ribosomal RNA

Douthwaite, Stephen

doi:10.1093/nar/20.18.4717

Cited by 74 publications

(54 citation statements)

References 21 publications

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“…3B, lane 2). Furthermore, the translocation efficiency of A-site antibiotics appears to correlate loosely with their affinity for the ribosome, decreasing from sparsomycin (K d < 1 µM) (Lazaro et al 1987) to chloramphenicol (K d ∼ 2-6 µM) (Contreras and Vazquez 1977) and the lincosamides (K d ∼ 4-6 µM) (Contreras and Vazquez 1977;Douthwaite 1992) to linezolid (K d ∼ 20 µM) (Lin et al 1997) and puromycin (K d ∼ 3-4 mM) (Wohlgemuth et al 2006). Recently, it has been demonstrated that while neither linezolid nor the pseudouridine moiety of sparsomycin, which binds to the A and P sites of large subunit, respectively, can stimulate mRNA translocation by themselves, a linezolid-pseudouridine conjugate can induce translocation in a fraction of ribosomes (Li et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

Ermolenko

Cornish

et al. 2012

RNA

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In the absence of elongation factor EF-G, ribosomes undergo spontaneous, thermally driven fluctuation between the pretranslocation (classical) and intermediate (hybrid) states of translocation. These fluctuations do not result in productive mRNA translocation. Extending previous findings that the antibiotic sparsomycin induces translocation, we identify additional peptidyl transferase inhibitors that trigger productive mRNA translocation. We find that antibiotics that bind the peptidyl transferase A site induce mRNA translocation, whereas those that do not occupy the A site fail to induce translocation. Using single-molecule FRET, we show that translocation-inducing antibiotics do not accelerate intersubunit rotation, but act solely by converting the intrinsic, thermally driven dynamics of the ribosome into translocation. Our results support the idea that the ribosome is a Brownian ratchet machine, whose intrinsic dynamics can be rectified into unidirectional translocation by ligand binding.

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Section: Discussionmentioning

confidence: 99%

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

Ermolenko

Cornish

et al. 2012

RNA

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“…Clindamycin, an antibiotic agent belonging to the Lincosamides family, is another example of a PTC-binding drug (46). In D50S, it connects between the PTC and the ribosome exit tunnel ( Figure 5), thus reducing the level of ribosomal flexibility in this area (17).…”

Section: Figurementioning

confidence: 99%

ANTIBIOTICS TARGETING RIBOSOMES: Resistance, Selectivity, Synergism, and Cellular Regulation

Yonath

2005

Annu. Rev. Biochem.

206

145

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Key Words ribosomal crystallography, peptide-bond formation, antibiotic synergism, nascent protein exit tunnel ■ Abstract Antibiotics target ribosomes at distinct locations within functionally relevant sites. They exert their inhibitory action by diverse modes, including competing with substrate binding, interfering with ribosomal dynamics, minimizing ribosomal mobility, facilitating miscoding, hampering the progression of the mRNA chain, and blocking the nascent protein exit tunnel. Although the ribosomes are highly conserved organelles, they possess subtle sequence and/or conformational variations. These enable drug selectivity, thus facilitating clinical usage. The structural implications of these differences were deciphered by comparisons of high-resolution structures of complexes of antibiotics with ribosomal particles from eubacteria resembling pathogens and from an archaeon that shares properties with eukaryotes. The various antibiotic-binding modes detected in these structures demonstrate that members of antibiotic families possessing common chemical elements with minute differences might bind to ribosomal pockets in significantly different modes, governed by their chemical properties.

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“…Resistance to lincosamides, macrolides, and chloramphenicol in bacteria and chloroplasts is commonly associated with mutations affecting the peptidyl transferase loop of 23S rRNA (5,7,10,11). Although sequence analysis of T. gondii ribosomal genes suggests that both cytoplasmic and mitochondrial ribosomes are resistant to clindamycin and macrolides, the putative ribosomal genes from the 35-kb element are likely to be sensitive to these drugs (1).…”

Section: Fig 10mentioning

confidence: 99%

In vitro assays elucidate peculiar kinetics of clindamycin action against Toxoplasma gondii

Fichera

Bhopale

Roos

1995

Antimicrob Agents Chemother

181

129

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In order to characterize the delayed effect of clindamycin and macrolide antibiotics against Toxoplasma gondii tachyzoites (E. R. Pfefferkorn and S. E. Borotz, Antimicrob. Agents Chemother. 38:31-37, 1994), we have carefully examined the replication of parasites as a function of time after drug addition. Intracellular tachyzoites treated with up to 20 M clindamycin (>1,000 times the 50% inhibitory concentration) exhibit doubling times indistinguishable from those of controls (ϳ7 h). Drug-treated parasites emerge from infected cells and establish parasitophorous vacuoles inside new host cells as efficiently as untreated controls, but replication within the second vacuole is dramatically slowed. Growth inhibition in the second vacuole does not require continued presence of drug, but it is dependent solely on the concentration and duration of drug treatment in the first (previous) vacuole. The susceptibility of intracellular parasites to nanomolar concentrations of clindamycin contrasts with that of extracellular tachyzoites, which are completely resistant to treatment, even through several cycles of subsequent intracellular replication. This peculiar phenotype, in which drug effects are observed only in the second infectious cycle, also characterizes azithromycin and chloramphenicol treatment, but not treatment with cycloheximide, tetracycline, or anisomycin. These findings provide new insights into the mode of clindamycin and macrolide action against T. gondii, although the relevant target for their action remains unknown.The protozoan parasite Toxoplasma gondii is a ubiquitous human pathogen long recognized as a source of congenital neurological abnormalities (19). In recent years, this parasite has also acquired considerable notoriety as an opportunistic infection associated with AIDS (16). The ability of T. gondii parasites to persist as latent cysts in the tissues of infected patients mandates chronic treatment for infected AIDS patients, to guard against recrudescence. Unfortunately, the traditional therapeutic regimen of pyrimethamine plus sulfonamides (18) is not always suitable for prolonged treatment, because of the emergence of sulfa hypersensitivity and other adverse side effects (12,14,27).Clindamycin (a lincosamide) and several macrolide antibiotics have proven effective for the treatment of AIDS-toxoplasmosis, usually in combination with pyrimethamine (6, 13, 15). These compounds are known to block protein synthesis in bacteria by interacting with the peptidyl transferase domain of 23S rRNA (5), but their target in T. gondii and related parasites remains unclear (1). Early difficulties in establishing a functional in vitro system to study clindamycin and macrolide action against T. gondii (4, 9, 17) can now be explained by the long lag period between drug administration and effect (20,21). Nanomolar drug concentrations block parasite replication, but only 2 to 3 days after treatment-a remarkable delay, considering that the tachyzoite undergoes ϳ8 generations in this time.In order to more precisely e...

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Interaction of the antibiotics clindamycin and lincomycin withEscherichia coli23S ribosomal RNA

Cited by 74 publications

References 21 publications

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

ANTIBIOTICS TARGETING RIBOSOMES: Resistance, Selectivity, Synergism, and Cellular Regulation

In vitro assays elucidate peculiar kinetics of clindamycin action against Toxoplasma gondii

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