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Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms for its evasion. bioRxiv 2023:2023.09.27.559749. [PMID: 37808676 PMCID: PMC10557674 DOI: 10.1101/2023.09.27.559749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The ribosome is an essential drug target as many classes of clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent mechanisms of resistance to PTC-acting drugs is C8-methylation of the universally conserved adenine residue 2503 (A2503) of the 23S rRNA by the methyltransferase Cfr. Despite its clinical significance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. In this work, we developed a method to express a functionally-active Cfr-methyltransferase in the thermophilic bacterium Thermus thermophilus and report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-tRNAs. Our structures reveal that an allosteric rearrangement of nucleotide A2062 upon Cfr-methylation of A2503 is likely responsible for the inability of some PTC inhibitors to bind to the ribosome, providing additional insights into the Cfr resistance mechanism. Lastly, by determining the structures of the Cfr-methylated ribosome in complex with the antibiotics iboxamycin and tylosin, we provide the structural bases behind two distinct mechanisms of evading Cfr-mediated resistance.
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Affiliation(s)
- Elena V. Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kelvin J. Y. Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben I. C. Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Egor A. Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Erin E. Killeavy
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Samson M. Balasanyants
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Maxim S. Svetlov
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Steven T. Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Gemma C. Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Andrew G. Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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2
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. Biochemistry (Mosc) 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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3
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Chen CW, Pavlova JA, Lukianov DA, Tereshchenkov AG, Makarov GI, Khairullina ZZ, Tashlitsky VN, Paleskava A, Konevega AL, Bogdanov AA, Osterman IA, Sumbatyan NV, Polikanov YS. Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome. Antibiotics (Basel) 2021; 10:390. [PMID: 33916420 PMCID: PMC8066774 DOI: 10.3390/antibiotics10040390] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Andrey G. Tereshchenkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Gennady I. Makarov
- Laboratory of Multiscale Modeling of Multicomponent Materials, South Ural State University, 454080 Chelyabinsk, Russia;
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- National Research Center (NRC) “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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Svetlov MS, Syroegin EA, Aleksandrova EV, Atkinson GC, Gregory ST, Mankin AS, Polikanov YS. Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Nat Chem Biol 2021; 17:412-20. [PMID: 33462493 DOI: 10.1038/s41589-020-00715-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/22/2020] [Accepted: 11/18/2020] [Indexed: 01/29/2023]
Abstract
Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.
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Baliga C, Brown TJ, Florin T, Colon S, Shah V, Skowron KJ, Kefi A, Szal T, Klepacki D, Moore TW, Vázquez-Laslop N, Mankin AS. Charting the sequence-activity landscape of peptide inhibitors of translation termination. Proc Natl Acad Sci U S A 2021; 118:e2026465118. [PMID: 33674389 DOI: 10.1073/pnas.2026465118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Apidaecin (Api), an unmodified 18-amino-acid-long proline-rich antibacterial peptide produced by bees, has been recently described as a specific inhibitor of translation termination. It invades the nascent peptide exit tunnel of the postrelease ribosome and traps the release factors preventing their recycling. Api binds in the exit tunnel in an extended conformation that matches the placement of a nascent polypeptide and establishes multiple contacts with ribosomal RNA (rRNA) and ribosomal proteins. Which of these interactions are critical for Api's activity is unknown. We addressed this problem by analyzing the activity of all possible single-amino-acid substitutions of the Api variants synthesized in the bacterial cell. By conditionally expressing the engineered api gene, we generated Api directly in the bacterial cytosol, thereby bypassing the need for importing the peptide from the medium. The endogenously expressed Api, as well as its N-terminally truncated mutants, retained the antibacterial properties and the mechanism of action of the native peptide. Taking advantage of the Api expression system and next-generation sequencing, we mapped in one experiment all the single-amino-acid substitutions that preserve or alleviate the on-target activity of the Api mutants. Analysis of the inactivating mutations made it possible to define the pharmacophore of Api involved in critical interactions with the ribosome, transfer RNA (tRNA), and release factors. We also identified the Api segment that tolerates a variety of amino acid substitutions; alterations in this segment could be used to improve the pharmacological properties of the antibacterial peptide.
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Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome. RNA 2020; 26:715-723. [PMID: 32144191 PMCID: PMC7266154 DOI: 10.1261/rna.073817.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/27/2019] [Indexed: 05/05/2023]
Abstract
Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the Thermus thermophilus 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating Escherichia coli 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
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Affiliation(s)
- Evgeny B Pichkur
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Pavel Kasatsky
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Dmitrii I Shiriaev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Yury S Polikanov
- Departments of Biological Sciences and Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Alexander G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- Centre for Integrative Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, Illkirch, 67404, France
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
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7
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Khabibullina NF, Tereshchenkov AG, Komarova ES, Syroegin EA, Shiriaev DI, Paleskava A, Kartsev VG, Bogdanov AA, Konevega AL, Dontsova OA, Sergiev PV, Osterman IA, Polikanov YS. Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob Agents Chemother 2019; 63:e02266-18. [PMID: 30936109 DOI: 10.1128/AAC.02266-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 11/20/2022] Open
Abstract
Although macrolides are known as excellent antibacterials, their medical use has been significantly limited due to the spread of bacterial drug resistance. Therefore, it is necessary to develop new potent macrolides to combat the emergence of drug-resistant pathogens. One of the key steps in rational drug design is the identification of chemical groups that mediate binding of the drug to its target and their subsequent derivatization to strengthen drug-target interactions. In the case of macrolides, a few groups are known to be important for drug binding to the ribosome, such as desosamine. Search for new chemical moieties that improve the interactions of a macrolide with the 70S ribosome might be of crucial importance for the invention of new macrolides. For this purpose, here we studied a classic macrolide, dirithromycin, which has an extended (2-methoxyethoxy)-methyl side chain attached to the C-9/C-11 atoms of the macrolactone ring that can account for strong binding of dirithromycin to the 70S ribosome. By solving the crystal structure of the 70S ribosome in complex with dirithromycin, we found that its side chain interacts with the wall of the nascent peptide exit tunnel in an idiosyncratic fashion: its side chain forms a lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4. To our knowledge, the ability of this side chain to form a contact in the macrolide binding pocket has not been reported previously and potentially can open new avenues for further exploration by medicinal chemists developing next-generation macrolide antibiotics active against resistant pathogens.
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8
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Svetlov MS, Plessa E, Chen CW, Bougas A, Krokidis MG, Dinos GP, Polikanov YS. High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA 2019; 25:600-606. [PMID: 30733327 PMCID: PMC6467010 DOI: 10.1261/rna.069260.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/28/2019] [Indexed: 05/22/2023]
Abstract
The 70S ribosome is a major target for antibacterial drugs. Two of the classical antibiotics, chloramphenicol (CHL) and erythromycin (ERY), competitively bind to adjacent but separate sites on the bacterial ribosome: the catalytic peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), respectively. The previously reported competitive binding of CHL and ERY might be due either to a direct collision of the two drugs on the ribosome or due to a drug-induced allosteric effect. Because of the resolution limitations, the available structures of these antibiotics in complex with bacterial ribosomes do not allow us to discriminate between these two possible mechanisms. In this work, we have obtained two crystal structures of CHL and ERY in complex with the Thermus thermophilus 70S ribosome at a higher resolution (2.65 and 2.89 Å, respectively) allowing unambiguous placement of the drugs in the electron density maps. Our structures provide evidence of the direct collision of CHL and ERY on the ribosome, which rationalizes the observed competition between the two drugs.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Elena Plessa
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Anthony Bougas
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Marios G Krokidis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Yury S Polikanov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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9
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Abstract
The ribosome is a major antibiotic target. Many types of inhibitors can stop cells from growing by binding at functional centers of the ribosome and interfering with its ability to synthesize proteins. These antibiotics were usually viewed as general protein synthesis inhibitors, which indiscriminately stop translation at every codon of every mRNA, preventing the ribosome from making any protein. However, at each step of the translation cycle, the ribosome interacts with multiple ligands (mRNAs, tRNA substrates, translation factors, etc.), and as a result, the properties of the translation complex vary from codon to codon and from gene to gene. Therefore, rather than being indiscriminate inhibitors, many ribosomal antibiotics impact protein synthesis in a context-specific manner. This review presents a snapshot of the growing body of evidence that some, and possibly most, ribosome-targeting antibiotics manifest site specificity of action, which is modulated by the nature of the nascent protein, the mRNA, or the tRNAs.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, Illinois 60607, USA; ,
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, Illinois 60607, USA; ,
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