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Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome

Z. Z. Khairullina1#, A. G. Tereshchenkov2#, S. A. Zavyalova3, E. S. Komarova4,5, D. A. Lukianov5, V. N. Tashlitsky1, I. A. Osterman1,5, and N. V. Sumbatyan1,a*

1Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia

2Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia

3Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia

4Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia

5Skolkovo Institute of Science and Technology, 143025 Moscow, Russia

#These authors contributed equally to this work.

* To whom correspondence should be addressed.

Received July 13, 2020; Revised September 7, 2020; Accepted September 9, 2020
Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.
KEY WORDS: ribosome, chloramphenicol, peptide derivatives, molecular docking, antimicrobial peptides, nascent peptide exit tunnel

DOI: 10.1134/S0006297920110127