Unraveling new features of clindamycin interaction with functional ribosomes and dependence of the drug potency on polyamines.

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Kouvela EC, Petropoulos AD, Kalpaxis DL

Unraveling new features of clindamycin interaction with functional ribosomes and dependence of the drug potency on polyamines.

J Biol Chem. 2006 Aug 11;281(32):23103-10. doi: 10.1074/jbc.M603263200. Epub 2006 Jun 7.

PubMed ID

16760473 [ View in PubMed

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Abstract

The effect of spermine on the inhibition of peptide-bond formation by clindamycin, an antibiotic of the Macrolide-Lincosamide-StreptograminsB family, was investigated in a cell-free system derived from Escherichia coli. In this system peptide bond is formed between puromycin, a pseudo-substrate of the A-site, and acetylphenylalanyl-tRNA, bound at the P-site of poly(U)-programmed 70 S ribosomes. Biphasic kinetics revealed that one molecule of clindamycin, after a transient interference with the A-site of ribosomes, is slowly accommodated near the P-site and perturbs the 70 S/acetylphenylalanyl-tRNA complex so that a peptide bond is still formed but with a lower velocity compared with that observed in the absence of the drug. The above mechanism requires a high temperature (25 degrees C as opposed to 5 degrees C). If this is not met, the inhibition is simple competitive. It was found that at 25 degrees C spermine favors the clindamycin binding to ribosomes; the affinity of clindamycin for the A-site becomes 5 times higher, whereas the overall inhibition constant undergoes a 3-fold decrease. Similar results were obtained when ribosomes labeled with N1-azidobenzamidinospermine, a photo-reactive analogue of spermine, were used or when a mixture of spermine and spermidine was added in the reaction mixture instead of spermine alone. Polyamines cannot compensate for the loss of biphasic kinetics at 5 degrees C nor can they stimulate the clindamycin binding to ribosomes. Our kinetic results correlate well with photoaffinity labeling data, suggesting that at 25 degrees C polyamines bound at the vicinity of the drug binding pocket affect the tertiary structure of ribosomes and influence their interaction with clindamycin.

DrugBank Data that Cites this Article

Drugs

Lincomycin

Drug Targets

Drug	Target	Kind	Organism	Pharmacological Action	Actions
Lincomycin	23S ribosomal RNA	Nucleotide	Enteric bacteria and other eubacteria	Yes	Binder	Details