Journal Article

Structural basis for the inhibition of the eukaryotic ribosome

Holtkamp, Wolf, Yusupova, Gulnara, Garreau de Loubresse, Nicolas, Rodnina, Marina V., Prokhorova, Irina, Yusupov, Marat

2014

Overview

The ribosome is a molecular machine responsible for protein synthesis and a major target for small-molecule inhibitors. Compared to the wealth of structural information available on ribosome-targeting antibiotics in bacteria, our understanding of the binding mode of ribosome inhibitors in eukaryotes is currently limited. Here we used X-ray crystallography to determine 16 high-resolution structures of 80S ribosomes from Saccharomyces cerevisiae in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors. All inhibitors were found associated with messenger RNA and transfer RNA binding sites. In combination with kinetic experiments, the structures suggest a model for the action of cycloheximide and lactimidomycin, which explains why lactimidomycin, the larger compound, specifically targets the first elongation cycle. The study defines common principles of targeting and resistance, provides insights into translation inhibitor mode of action and reveals the structural determinants responsible for species selectivity which could guide future drug development. Whereas previous structural investigation of ribosome inhibitors has been done using the prokaryotic ribosome, this work presents X-ray crystal structures of the yeast ribosome in complex with 16 inhibitors including eukaryotic-specific inhibitors; the inhibitors all bind the mRNA or tRNA binding sites, larger molecules appear to target specifically the first elongation cycle. Mechanisms of eukaryotic ribosome inhibition As the ribosome is a common target of antibiotics, there is a wealth of structural data on the binding of the bacterial ribosome to various inhibitors. Our understanding of inhibitor binding to the larger eukaryotic ribosome is limited. Marat Yusupov and colleagues present the structure of the yeast 80S ribosome bound to 12 eukaryote-specific and 4 broad-spectrum inhibitors. On the basis of structural data and kinetic studies, the authors propose a model for the action of cycloheximide and lactimidomycin that demonstrates that the size of an inhibitor can dictate its accessibility to the ribosome and thus its mechanism of action. This new model suggests general principles for structure-based design of new antibiotics as well as therapeutics against fungal and protozoan infections, cancers and genetic disorders induced by premature stop codons.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/154/349 / 631/337/574/1789 / 631/535/1266 / 631/92/609 / Analysis / Antibiotics / Bacteria / Base Sequence / Binding sites / Binding Sites - drug effects / Crystallography / Crystallography, X-Ray / Cycloheximide - pharmacology / Drug resistance / Drug Resistance - drug effects / Eukaryotes / Eukaryotic Cells - chemistry / Eukaryotic Cells - drug effects / Eukaryotic Cells - enzymology / Health aspects / Humanities and Social Sciences / Inhibitors / Kinetics / Life Sciences / Macrolides - pharmacology / Mode of action / Models, Molecular / Molecular Targeted Therapy / Molecular Weight / multidisciplinary / Peptide Chain Elongation, Translational - drug effects / Peptides / Peptidyl Transferases - chemistry / Peptidyl Transferases - metabolism / Piperidones - pharmacology / Protein synthesis / Protein Synthesis Inhibitors - chemistry / Protein Synthesis Inhibitors - pharmacology / Proteins / Ribonucleoproteins / Ribosome Subunits, Large, Eukaryotic - chemistry / Ribosome Subunits, Large, Eukaryotic - drug effects / Ribosome Subunits, Large, Eukaryotic - metabolism / Ribosomes / Ribosomes - chemistry / Ribosomes - drug effects / Ribosomes - metabolism / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA, Transfer - genetics / RNA, Transfer - metabolism / Saccharomyces cerevisiae - chemistry / Science / Species Specificity / Substrate Specificity / Transfer RNA / Yeast