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Modeling Interactions of Erythromycin Derivatives with Ribosomes

A. V. Shishkina1, T. M. Makarova2, A. G. Tereshchenkov2, G. I. Makarov2, G. A. Korshunova1*, and A. A. Bogdanov1

1Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; E-mail: korsh@genebee.msu.ru

2Lomonosov Moscow State University, Faculty of Chemistry, 119991 Moscow, Russia; fax: +7 (495) 939-3181

* To whom correspondence should be addressed.

Received July 6, 2015; Revision received July 24, 2015
Using a method of static simulation, a series of erythromycin A analogs was designed with aldehyde functions introduced instead of one of the methyl substituents in the 3′-N-position of the antibiotic that was potentially capable of forming a covalent bond with an amino group of one of the nucleotide residues of the 23S rRNA in the ribosomal exit tunnel. Similar interaction is observed for antibiotics of the tylosin series, which bind tightly to the large ribosomal subunit and demonstrate high antibacterial activity. Binding of novel erythromycin derivatives with the bacterial ribosome was investigated with the method of fluorescence polarization. It was found that the erythromycin analog containing a 1-methyl-3-oxopropyl group in the 3′-N-position demonstrates the best binding. Based on the ability to inhibit protein biosynthesis, it is on the same level as erythromycin, and it is significantly better than desmethyl-erythromycin. Molecular dynamic modeling of complexes of the derivatives with ribosomes was conducted to explain the observed effects.
KEY WORDS: ribosomal tunnel, macrolides, erythromycin, modeling

DOI: 10.1134/S0006297915110127