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Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome

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Abstract

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.

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Abbreviations

Boc:

tert-butoxycarbonyl

BODIPY:

(4,4-difluoro-5,7-dimethyl-4-bora)-3a,4a-diaza-s-indacene-3-pentanoic acid

CAM:

chloramphenicol amine

CHL:

chloramphenicol

DIC:

N,N′-diisopropylcarbodiimide

DIPEA:

N,N-diisopropylethylamine

DMF:

N,N-dimethylformamide

DMS:

dimethyl sulfate

ERY:

erythromycin

Fmoc:

fluorenylmethoxycarbonyl

LC-MS:

liquid chromatography-mass spectrometry

MALDI TOF MS:

matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry

NPET:

ribosome nascent peptide exit tunnel

Onc112:

oncocin112 (VDKPPYLPRPRPPRrIYNr-NH2)

P :

2-chlorotrityl chloride resin

Pbf:

2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl

Pip:

piperidine

PrAMPs:

proline-rich antimicrobial peptides

PTC:

peptidyl transferase center

Reagent K:

TFA/phenol/H2O/thioanisole/β-mercaptoethanol = 82.5/5/5/5/2.5, v/v

TFA:

trifluoroacetic acid

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Acknowledgements

The authors are grateful to A. A. Bogdanov for initiating and supporting studies on peptide derivatives of ribosomal antibiotics, to A. L. Konevega for providing the ribosomes and BODIPY-Met-tRNA for the work, to M. V. Serebryakova for help with mass spectrometric analysis, and to Y. K. Grishin for help with NMR spectra.

Funding

This work was financially supported by the Russian Foundation for Basic Research [projects nos. 20-04-00873-a (synthesis of analogues, molecular docking, binding to ribosomes) and 19-34-51021 (in vitro translation, chemical probing)]. The study was carried out using equipment purchased at the expense of the Moscow University Development Program.

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    Authors and Affiliations

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

      Z. Z. Khairullina, V. N. Tashlitsky, I. A. Osterman & N. V. Sumbatyan

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

      A. G. Tereshchenkov

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

      S. A. Zavyalova

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

      E. S. Komarova

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

      E. S. Komarova, D. A. Lukianov & I. A. Osterman

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    1. Z. Z. Khairullina
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    Khairullina, Z.Z., Tereshchenkov, A.G., Zavyalova, S.A. et al. Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome. Biochemistry Moscow 85, 1443–1457 (2020). https://doi.org/10.1134/S0006297920110127

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