Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome.

Gennady I Makarov,Vadim N Tashlitsky,Dmitrii A Lukianov,Yury S Polikanov,Ilya A Osterman,Andrey L Konevega,Alexey A Bogdanov,Alena Paleskava,Julia A Pavlova,Natalia V Sumbatyan,Zimfira Z Khairullina,Andrey G Tereshchenkov,Chih-Wei Chen

doi:10.3390/antibiotics10040390

Abstract

Chloramphenicol (CHL) is a ribosome-targeting antibiotic that binds to the peptidyl transferase center (PTC) of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving the properties of this inhibitor, we explored ribosome binding and inhibitory properties of a semi-synthetic triphenylphosphonium analog of CHL—CAM-C4-TPP. Our data demonstrate that this compound exhibits a ~5-fold stronger affinity for the bacterial ribosome and higher potency as an in vitro protein synthesis inhibitor compared to CHL. The X-ray crystal structure of the Thermus thermophilus 70S ribosome in complex with CAM-C4-TPP reveals that, while its amphenicol moiety binds at the PTC in a fashion identical to CHL, the C4-TPP tail adopts an extended propeller-like conformation within the ribosome exit tunnel where it establishes multiple hydrophobic Van der Waals interactions with the rRNA. The synthesized compound represents a promising chemical scaffold for further development by medicinal chemists because it simultaneously targets the two key functional centers of the bacterial ribosome—PTC and peptide exit tunnel.

Highlights

The majority of antibiotics suppress pathogenic bacteria, and thereby cure infections, by selectively inhibiting their ribosomes—molecular machines that are responsible for protein biosynthesis
We set out to explore the properties of the triphenylphosphonium (TPP) analog of CHL—chloramphenicol amine (CAM)-C4-TPP
The rationale for such a chemical scaffold came from our initial idea to create a hybrid molecule that would consist of two parts: (i) the amphenicol moiety anchoring it in the canonical CHL binding site within the peptidyl transferase center (PTC) of the bacterial ribosome; and (ii) an additional nascent peptide exit tunnel (NPET)-binding group forming multiple interactions with the walls of NPET, which should be strong enough but non-specific so that interactions with various different nucleotides would be possible, and (iii) the linker connecting the two endpieces

Summary

Introduction

The majority of antibiotics suppress pathogenic bacteria, and thereby cure infections, by selectively inhibiting their ribosomes—molecular machines that are responsible for protein biosynthesis. Recent in vitro (toe-printing) and in vivo (Ribo-seq) studies showed that CHL does not act as a universal inhibitor of peptide bond formation and, instead, exhibits a context-specific mode of action inhibiting peptide bond formation only when the ribosome carries a nascent peptide with either alanine, serine, or threonine in the penultimate position [5]. These data suggest that the ribosome-bound CHL molecule interacts with the ribosomal parts and with the growing polypeptide chain located in the nascent peptide exit tunnel (NPET), through which the newly synthesized proteins exit the ribosome [1]

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