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Ekemezie CL, Melnikov SV. Hibernating ribosomes as drug targets? Front Microbiol 2024; 15:1436579. [PMID: 39135874 PMCID: PMC11317432 DOI: 10.3389/fmicb.2024.1436579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/24/2024] [Indexed: 08/15/2024] Open
Abstract
When ribosome-targeting antibiotics attack actively growing bacteria, they occupy ribosomal active centers, causing the ribosomes to stall or make errors that either halt cellular growth or cause bacterial death. However, emerging research indicates that bacterial ribosomes spend a considerable amount of time in an inactive state known as ribosome hibernation, in which they dissociate from their substrates and bind to specialized proteins called ribosome hibernation factors. Since 60% of microbial biomass exists in a dormant state at any given time, these hibernation factors are likely the most common partners of ribosomes in bacterial cells. Furthermore, some hibernation factors occupy ribosomal drug-binding sites - leading to the question of how ribosome hibernation influences antibiotic efficacy, and vice versa. In this review, we summarize the current state of knowledge on physical and functional interactions between hibernation factors and ribosome-targeting antibiotics and explore the possibility of using antibiotics to target not only active but also hibernating ribosomes. Because ribosome hibernation empowers bacteria to withstand harsh conditions such as starvation, stress, and host immunity, this line of research holds promise for medicine, agriculture, and biotechnology: by learning to regulate ribosome hibernation, we could enhance our capacity to manage the survival of microorganisms in dormancy.
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Affiliation(s)
- Chinenye L. Ekemezie
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sergey V. Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Medical School of Newcastle University, Newcastle upon Tyne, United Kingdom
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2
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Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria. Nat Commun 2023; 14:918. [PMID: 36806263 PMCID: PMC9938272 DOI: 10.1038/s41467-023-36528-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
Thermorubin (THB) is a long-known broad-spectrum ribosome-targeting antibiotic, but the molecular mechanism of its action was unclear. Here, our precise fast-kinetics assays in a reconstituted Escherichia coli translation system and 1.96 Å resolution cryo-EM structure of THB-bound 70S ribosome with mRNA and initiator tRNA, independently suggest that THB binding at the intersubunit bridge B2a near decoding center of the ribosome interferes with the binding of A-site substrates aminoacyl-tRNAs and class-I release factors, thereby inhibiting elongation and termination steps of bacterial translation. Furthermore, THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. Our results show that THB does not inhibit translation initiation as proposed earlier and provide a complete mechanism of how THB perturbs bacterial protein synthesis. This in-depth characterization will hopefully spur efforts toward the design of THB analogs with improved solubility and effectivity against multidrug-resistant bacteria.
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3
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Paranjpe M, Marina V, Grachev A, Maviza T, Tolicheva O, Paleskava A, Osterman I, Sergiev P, Konevega A, Polikanov Y, Gagnon M. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin. Nucleic Acids Res 2023; 51:449-462. [PMID: 36546783 PMCID: PMC9841432 DOI: 10.1093/nar/gkac1189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.
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Affiliation(s)
- Madhura N Paranjpe
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Valeria I Marina
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Aleksandr A Grachev
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Tinashe P Maviza
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Olga A Tolicheva
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Alena Paleskava
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Ilya A Osterman
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey L Konevega
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, 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
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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4
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Ibrahim I, Ayariga JA, Xu J, Adebanjo A, Robertson BK, Samuel-Foo M, Ajayi OS. CBD resistant Salmonella strains are susceptible to epsilon 34 phage tailspike protein. Front Med (Lausanne) 2023; 10:1075698. [PMID: 36960333 PMCID: PMC10028193 DOI: 10.3389/fmed.2023.1075698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
The rise of antimicrobial resistance is a global public health crisis that threatens the effective control and prevention of infections. Due to the emergence of pandrug-resistant bacteria, most antibiotics have lost their efficacy. Bacteriophages or their components are known to target bacterial cell walls, cell membranes, and lipopolysaccharides (LPS) and hydrolyze them. Bacteriophages being the natural predators of pathogenic bacteria, are inevitably categorized as "human friends", thus fulfilling the adage that "the enemy of my enemy is my friend". Leveraging on their lethal capabilities against pathogenic bacteria, researchers are searching for more ways to overcome the current antibiotic resistance challenge. In this study, we expressed and purified epsilon 34 phage tailspike protein (E34 TSP) from the E34 TSP gene, then assessed the ability of this bacteriophage protein in the killing of two CBD-resistant strains of Salmonella spp. We also assessed the ability of the tailspike protein to cause bacteria membrane disruption, and dehydrogenase depletion. We observed that the combined treatment of CBD-resistant strains of Salmonella with CBD and E34 TSP showed poor killing ability whereas the monotreatment with E34 TSP showed considerably higher killing efficiency. This study demonstrates that the inhibition of the bacteria by E34 TSP was due in part to membrane disruption, and dehydrogenase inactivation by the protein. The results of this work provides an interesting background to highlight the crucial role phage protein such as E34 TSP could play in pathogenic bacterial control.
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Affiliation(s)
- Iddrisu Ibrahim
- The Microbiology Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
| | - Joseph Atia Ayariga
- The Industrial Hemp Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
- *Correspondence: Joseph Atia Ayariga,
| | - Junhuan Xu
- The Industrial Hemp Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
| | - Ayomide Adebanjo
- The Industrial Hemp Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
| | - Boakai K. Robertson
- The Microbiology Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
| | - Michelle Samuel-Foo
- The Industrial Hemp Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
| | - Olufemi S. Ajayi
- The Industrial Hemp Program, College of Science, Technology, Engineering, and Mathematics (C-STEM), Alabama State University, Montgomery, AL, United States
- Olufemi S. Ajayi,
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5
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McCord JP, Kohanov ZA, Lowell AN. Thermorubin Biosynthesis Initiated by a Salicylate Synthase Suggests an Unusual Conversion of Phenols to Pyrones. ACS Chem Biol 2022; 17:3169-3177. [PMID: 36255735 DOI: 10.1021/acschembio.2c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Thermorubin is a tetracyclic naphthoisocoumarin natural product that demands investigation due to its novel mechanism of bacterial protein synthesis inhibition and its unusual structural features. In this work, we describe the identification of the biosynthetic cluster responsible for thermorubin from the sequenced Laceyella sacchari producer species and its confirmation via heterologous production in Escherichia coli. Based on an in-depth annotation of the cluster, we propose a biosynthetic pathway that accounts for the formation of the unique, nonterminal pyrone. Additionally, the expression and use of salicylate synthase TheO enabled testing of the stability properties of this extremophile-derived enzyme. TheO displayed rapid kinetics and a remarkably robust secondary structure, converting chorismate to salicylate with a KM of 109 ± 12 μM, kcat of 9.17 ± 0.36 min-1, and catalytic efficiency (kcat/KM) of 84 ± 9 nM-1 min-1, and retained significant activity up to 50 °C. These studies serve as the basis for continued biosynthetic investigations and bioinspired synthetic approaches.
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Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
| | - Zachary A Kohanov
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
| | - Andrew N Lowell
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
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6
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Khisamutdinov EF, Sweeney BA, Leontis NB. Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs. Nucleic Acids Res 2021; 49:9574-9593. [PMID: 34403481 PMCID: PMC8450098 DOI: 10.1093/nar/gkab703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/29/2021] [Indexed: 02/01/2023] Open
Abstract
Sequence variation in a widespread, recurrent, structured RNA 3D motif, the Sarcin/Ricin (S/R), was studied to address three related questions: First, how do the stabilities of structured RNA 3D motifs, composed of non-Watson–Crick (non-WC) basepairs, compare to WC-paired helices of similar length and sequence? Second, what are the effects on the stabilities of such motifs of isosteric and non-isosteric base substitutions in the non-WC pairs? And third, is there selection for particular base combinations in non-WC basepairs, depending on the temperature regime to which an organism adapts? A survey of large and small subunit rRNAs from organisms adapted to different temperatures revealed the presence of systematic sequence variations at many non-WC paired sites of S/R motifs. UV melting analysis and enzymatic digestion assays of oligonucleotides containing the motif suggest that more stable motifs tend to be more rigid. We further found that the base substitutions at non-Watson–Crick pairing sites can significantly affect the thermodynamic stabilities of S/R motifs and these effects are highly context specific indicating the importance of base-stacking and base-phosphate interactions on motif stability. This study highlights the significance of non-canonical base pairs and their contributions to modulating the stability and flexibility of RNA molecules.
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Affiliation(s)
- Emil F Khisamutdinov
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403, USA.,Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Blake A Sweeney
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Neocles B Leontis
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403, USA
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7
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Belardinelli R, Sharma H, Peske F, Rodnina MV. Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation. RNA (NEW YORK, N.Y.) 2021; 27:981-990. [PMID: 34117118 PMCID: PMC8370747 DOI: 10.1261/rna.078758.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 05/02/2023]
Abstract
Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc, and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB, and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.
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Affiliation(s)
- Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Heena Sharma
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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8
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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9
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Nicholson D, Edwards TA, O'Neill AJ, Ranson NA. Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Structure 2020; 28:1087-1100.e3. [PMID: 32857965 PMCID: PMC7546915 DOI: 10.1016/j.str.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/06/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022]
Abstract
Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii. Cryo-EM structures of the ribosome from the pathogenic bacteria A. baumannii Unique structural features compared with other bacterial ribosomes The site and mode of binding of amikacin and tigecycline to this ribosome A putative alternative tigecycline-binding site at the 50S central protuberance
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Affiliation(s)
- David Nicholson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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10
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Inhibitory Effects of the Bioactive Thermorubin Isolated from the Fungus Thermoactinomyces Antibioticus on Melanogenesis. COSMETICS 2020. [DOI: 10.3390/cosmetics7030061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Skin hyperpigmentation disorders arise due to aberrant regulation of melanin synthesis and export. Current treatments include natural compounds like kojic acid and hydroquinone, which suffer from limitations due to adverse reactions. Thermorubin (TR) is a secondary metabolite derived from the fungus Thermoactinomyces antibioticus and has previously demonstrated to possess anti-inflammatory properties by inhibition of matrix metalloproteinases (MMPs), as well as antimicrobial activity. In the current study, we explored whether TR might be a used as a candidate for the treatment of skin hyperpigmentation disorders by studying its effects on melanin synthesis and melanin export in B16F10 mouse melanoma cells and primary human melanocytes derived from darkly-pigmented (DP) skin. Non-toxic doses of TR were first identified in B16F10 mouse melanoma cells. These doses were subsequently tested for their effects on both extracellular and intracellular melanin levels under conditions of basal and hormone-stimulated melanogenesis. Our results demonstrated that TR at 25 µM inhibited total melanin levels with selective inhibition of extracellular melanin in B16F10 cells under both basal and hormone-stimulated conditions. The mechanisms of inhibition did not include tyrosinase inhibition, either in cellular lysates or cell-free system. However, TR potently inhibited activity of α-glucosidase enzyme in vitro and exhibited antioxidant activity. Furthermore, our results with primary human melanocytes from DP skin showed that TR at 10 µM significantly suppressed dendricity along with an increase in accumulation of intracellular melanin. These findings point to a mechanism of action of TR as an exclusive inhibitor of melanosome export. Taken together, our preliminary results demonstrate that TR might offer a novel ingredient as a skin depigmenting agent for inclusion in cosmetic formulations. Further studies delineating molecular mechanisms of hypopigmentation of TR and testing in human skin tissue-equivalents are warranted.
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11
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Wang HH, Lee HM, Raja V, Hou W, Iacono VJ, Scaduto J, Johnson F, Golub LM, Gu Y. Enhanced efficacy of chemically modified curcumin in experimental periodontitis: systemic implications. J Exp Pharmacol 2019; 11:1-14. [PMID: 30774454 PMCID: PMC6350653 DOI: 10.2147/jep.s171119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Introduction Dental microbial biofilm initiates gingival inflammation, and its suppression is the current dominant strategy for treating periodontitis. However, the host response to the biofilm is largely responsible for the connective tissue breakdown including alveolar bone loss, which is mediated by proinflammatory cytokines and matrix metalloproteinases (MMPs). Methods The current study compared the efficacy of a novel host-modulation compound, a chemically modified curcumin (CMC 2.24), to that of its parent compound (natural curcumin), in both lipopolysaccharide (LPS) (a bacterial endotoxin)-induced cell culture and in vivo models of periodontitis. Results In cell culture, both CMC 2.24 and curcumin appeared similarly effective in suppressing LPS-induced cytokine (IL-1β and TNF-α) secretion by mononuclear inflammatory cells; however, CMC 2.24 significantly reduced MMP-9 secretion by 78% (P<0.05) whereas curcumin was ineffective. In vivo, CMC 2.24 administration was more effective than curcumin in suppressing (a) IL-1β in gingival tissue and (b) MMP-9 in both gingiva and plasma, the latter indicating a reduced severity of systemic inflammation. The difference in primary clinical outcome between the two treatments was that CMC 2.24 reduced the pathologically excessive alveolar bone loss, assessed morphometrically at multiple sites, by 80%-90% (P<0.01), whereas curcumin, surprisingly, either increased (P<0.05) or had no effect on alveolar bone loss at these sites. Conclusion These data, plus that from previous studies, support the therapeutic potential of CMC 2.24 in the management of inflammatory periodontal disease and its ability to reduce the risk of associated systemic diseases. The current study also indicates that the MMP-9 inhibitor efficacy is associated with the ability of CMC 2.24 (but not curcumin) to inhibit alveolar bone loss in this rat model of periodontitis.
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Affiliation(s)
- Howard H Wang
- Department of Periodontology and Endodontology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - Hsi-Ming Lee
- Department of Oral Biology and Pathology, School of Dental Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Veena Raja
- Department of Oral Biology and Pathology, School of Dental Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Wei Hou
- Department of Preventive Medicine, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Vincent J Iacono
- Department of Periodontology, School of Dental Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Francis Johnson
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Lorne M Golub
- Department of Oral Biology and Pathology, School of Dental Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Ying Gu
- Department of General Dentistry, School of Dental Medicine, Stony Brook University, Stony Brook, NY, USA,
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12
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Kürkçüoğlu Ö. Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis. Turk J Biol 2018; 42:392-404. [PMID: 30930623 PMCID: PMC6438126 DOI: 10.3906/biy-1802-77] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Antibiotic resistance is one of the most important problems of our era and hence the discovery of new effective therapeutics is urgent. At this point, studying the allosteric communication pathways in the bacterial ribosome and revealing allosteric sites/residues is critical for designing new inhibitors or repurposing readily approved drugs for this enormous machine. To shed light onto molecular details of the allosteric mechanisms, here we construct residue networks of the bacterial ribosomal complex at four different states of translation by using an effective description of the intermolecular interactions. Centrality analysis of these networks highlights the functional roles of structural components and critical residues on the ribosomal complex. High betweenness scores reveal pathways of residues connecting numerous sites on the structure. Interestingly, these pathways assemble highly conserved residues, drug binding sites, and known allosterically linked regions on the same structure. This study proposes a new residue-level model to test how distant sites on the molecular machine may be linked through hub residues that are critically located on the contact topology to inherently form communication pathways. Findings also indicate intersubunit bridges B1b, B3, B5, B7, and B8 as critical targets to design novel antibiotics.
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Affiliation(s)
- Özge Kürkçüoğlu
- Department of Chemical Engineering, Faculty of Chemical-Metallurgical Engineering, İstanbul Technical University , İstanbul , Turkey
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13
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Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
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Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
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14
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Identification of potential allosteric communication pathways between functional sites of the bacterial ribosome by graph and elastic network models. Biochim Biophys Acta Gen Subj 2017; 1861:3131-3141. [PMID: 28917952 DOI: 10.1016/j.bbagen.2017.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Accumulated evidence indicates that bacterial ribosome employs allostery throughout its structure for protein synthesis. The nature of the allosteric communication between remote functional sites remains unclear, but the contact topology and dynamics of residues may play role in transmission of a perturbation to distant sites. METHODS/RESULTS We employ two computationally efficient approaches - graph and elastic network modeling to gain insights about the allosteric communication in ribosome. Using graph representation of the structure, we perform k-shortest pathways analysis between peptidyl transferase center-ribosomal tunnel, decoding center-peptidyl transferase center - previously reported functional sites having allosteric communication. Detailed analysis on intact structures points to common and alternative shortest pathways preferred by different states of translation. All shortest pathways capture drug target sites and allosterically important regions. Elastic network model further reveals that residues along all pathways have the ability of quickly establishing pair-wise communication and to help the propagation of a perturbation in long-ranges during functional motions of the complex. CONCLUSIONS Contact topology and inherent dynamics of ribosome configure potential communication pathways between functional sites in different translation states. Inter-subunit bridges B2a, B3 and P-tRNA come forward for their high potential in assisting allostery during translation. Especially B3 emerges as a potential druggable site. GENERAL SIGNIFICANCE This study indicates that the ribosome topology forms a basis for allosteric communication, which can be disrupted by novel drugs to kill drug-resistant bacteria. Our computationally efficient approach not only overlaps with experimental evidence on allosteric regulation in ribosome but also proposes new druggable sites.
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15
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
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16
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Thoduka SG, Zaleski PA, Dąbrowska Z, Równicki M, Stróżecka J, Górska A, Olejniczak M, Trylska J. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides. Biopolymers 2017; 107. [PMID: 27858985 DOI: 10.1002/bip.23004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/06/2016] [Accepted: 11/10/2016] [Indexed: 01/15/2023]
Abstract
The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Based on these properties we selected rRNA targets for hybridization with complementary 2'-O-methyl oligoribonucleotides (2'-OMe RNAs). Further, the inhibition efficiencies of the designed ribosome-interfering 2'-OMe RNAs were tested using a β-galactosidase assay in a translation system based on the E. coli extract. Several of the oligonucleotides displayed IC50 values below 1 μM, which were in a similar range as those determined for known ribosome inhibitors, tetracycline and pactamycin. The calculated opening and van der Waals stacking energies of the rRNA targets correlated best with the inhibitory efficiencies of 2'-OMe RNAs. Moreover, the binding affinities of several oligonucleotides to both 70S ribosomes and isolated 30S and 50S subunits were measured using a double-filter retention assay. Further, we applied heat-shock chemical transformation to introduce 2'-OMe RNAs to E. coli cells and verify inhibition of bacterial growth. We observed high correlation between IC50 in the cell-free extract and bacterial growth inhibition. Overall, the results suggest that the computational analysis of potential rRNA targets within the conformationally dynamic regions of inter-subunit bridges can help design efficient antisense oligomers to probe the ribosome function.
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Affiliation(s)
- Sapna G Thoduka
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Paul A Zaleski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Zofia Dąbrowska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
| | - Joanna Stróżecka
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Anna Górska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
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17
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Dremann DN, Chow CS. The development of peptide ligands that target helix 69 rRNA of bacterial ribosomes. Bioorg Med Chem 2016; 24:4486-4491. [PMID: 27492196 PMCID: PMC4992606 DOI: 10.1016/j.bmc.2016.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 12/19/2022]
Abstract
Antibiotic resistance prevents successful treatment of common bacterial infections, making it clear that new target locations and drugs are required to resolve this ongoing challenge. The bacterial ribosome is a common target for antibacterials due to its essential contribution to cell viability. The focus of this work is a region of the ribosome called helix 69 (H69), which was recently identified as a secondary target site for aminoglycoside antibiotics. H69 has key roles in essential ribosomal processes such as subunit association, ribosome recycling, and tRNA selection. Conserved across phylogeny, bacterial H69 also contains two pseudouridines and one 3-methylpseudouridine. Phage display revealed a heptameric peptide sequence that targeted H69. Using solid-phase synthesis, peptide variants with higher affinity and improved selectivity to modified H69 were generated. Electrospray ionization mass spectrometry was used to determine relative apparent dissociation constants of the RNA-peptide complexes.
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Affiliation(s)
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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18
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Arenz S, Wilson DN. Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025361. [PMID: 27481773 DOI: 10.1101/cshperspect.a025361] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein synthesis occurs on macromolecular machines, called ribosomes. Bacterial ribosomes and the translational machinery represent one of the major targets for antibiotics in the cell. Therefore, structural and biochemical investigations into ribosome-targeting antibiotics provide not only insight into the mechanism of action and resistance of antibiotics, but also insight into the fundamental process of protein synthesis. This review summarizes the recent advances in our understanding of protein synthesis, particularly with respect to X-ray and cryoelectron microscopy (cryo-EM) structures of ribosome complexes, and highlights the different steps of translation that are targeted by the diverse array of known antibiotics. Such findings will be important for the ongoing development of novel and improved antimicrobial agents to combat the rapid emergence of multidrug resistant pathogenic bacteria.
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Affiliation(s)
- Stefan Arenz
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Daniel N Wilson
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
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19
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Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, Matzov D, Metz M, Rufayda M, Peretz M, Pick O, Pyetan E, Rozenberg H, Shalev-Benami M, Wekselman I, Zarivach R, Zimmerman E, Assis N, Bloch J, Israeli H, Kalaora R, Lim L, Sade-Falk O, Shapira T, Taha-Salaime L, Tang H, Yonath A. Ribosomal Antibiotics: Contemporary Challenges. Antibiotics (Basel) 2016; 5:antibiotics5030024. [PMID: 27367739 PMCID: PMC5039520 DOI: 10.3390/antibiotics5030024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/07/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022] Open
Abstract
Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.
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Affiliation(s)
- Tamar Auerbach-Nevo
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - David Baram
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Matthew Belousoff
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Elinor Breiner
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Chen Davidovich
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Giuseppe Cimicata
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Zohar Eyal
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Markus Metz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Mruwat Rufayda
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moshe Peretz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ophir Pick
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Erez Pyetan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Raz Zarivach
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Nofar Assis
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Joel Bloch
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hadar Israeli
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Rinat Kalaora
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Lisha Lim
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ofir Sade-Falk
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Tal Shapira
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Leena Taha-Salaime
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hua Tang
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
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20
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Gagnon MG, Roy RN, Lomakin IB, Florin T, Mankin AS, Steitz TA. Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Nucleic Acids Res 2016; 44:2439-50. [PMID: 26809677 PMCID: PMC4797290 DOI: 10.1093/nar/gkw018] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/07/2016] [Indexed: 12/20/2022] Open
Abstract
With bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (AMPs) have become a promising area of focus in antibiotic research. AMPs are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. Proline-rich antimicrobial peptides (PrAMPs) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. Recently, it was reported that some PrAMPs, such as Bac71 -35, oncocins and apidaecins, bind and inactivate the bacterial ribosome. Here we report the crystal structures of Bac71 -35, Pyrrhocoricin, Metalnikowin and two oncocin derivatives, bound to the Thermus thermophilus 70S ribosome. Each of the PrAMPs blocks the peptide exit tunnel of the ribosome by simultaneously occupying three well characterized antibiotic-binding sites and interferes with the initiation step of translation, thereby revealing a common mechanism of action used by these PrAMPs to inactivate protein synthesis. Our study expands the repertoire of PrAMPs and provides a framework for designing new-generation therapeutics.
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Affiliation(s)
- Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA
| | - Raktim N Roy
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Ivan B Lomakin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Tanja Florin
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607-7173, USA
| | - Alexander S Mankin
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607-7173, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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21
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Arenz S, Wilson DN. Blast from the Past: Reassessing Forgotten Translation Inhibitors, Antibiotic Selectivity, and Resistance Mechanisms to Aid Drug Development. Mol Cell 2015; 61:3-14. [PMID: 26585390 DOI: 10.1016/j.molcel.2015.10.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein synthesis is a major target within the bacterial cell for antibiotics. Investigations into ribosome-targeting antibiotics have provided much needed functional and structural insight into their mechanism of action. However, the increasing prevalence of multi-drug-resistant bacteria has limited the utility of our current arsenal of clinically relevant antibiotics, highlighting the need for the development of new classes. Recent structural studies have characterized a number of antibiotics discovered decades ago that have unique chemical scaffolds and/or utilize novel modes of action to interact with the ribosome and inhibit translation. Additionally, structures of eukaryotic cytoplasmic and mitochondrial ribosomes have provided further structural insight into the basis for specificity and toxicity of antibiotics. Together with our increased understanding of bacterial resistance mechanisms, revisiting our treasure trove of "forgotten" antibiotics could pave the way for the next generation of antimicrobial agents.
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Affiliation(s)
- Stefan Arenz
- Gene Center and Department of Biochemistry, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany
| | - Daniel N Wilson
- Gene Center and Department of Biochemistry, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany; Center for integrated Protein Science Munich, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany.
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22
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Donner CD. Naphthopyranones--isolation, bioactivity, biosynthesis and synthesis. Nat Prod Rep 2015; 32:578-604. [PMID: 25531639 DOI: 10.1039/c4np00127c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 1H-naphtho[2,3-c]pyran-1-one (naphthopyranone) moiety forms the structural framework of a group of secondary metabolites that have been isolated from a range of organisms including fungi, bacteria, lichen and plants. This review documents the known naturally occurring naphthopyranones - their isolation, biosynthesis and biological activity. A survey of methods reported for the synthesis of naphthopyranone natural products is presented.
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23
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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24
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Panecka J, Mura C, Trylska J. Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study. PLoS One 2014; 9:e111811. [PMID: 25379961 PMCID: PMC4224418 DOI: 10.1371/journal.pone.0111811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/07/2014] [Indexed: 12/28/2022] Open
Abstract
The conformational properties of the aminoacyl-tRNA binding site (A-site), and its surroundings in the Escherichia coli 30S ribosomal subunit, are of great relevance in designing antibacterial agents. The 30S subunit A-site is near ribosomal protein S12, which neighbors helices h27 and H69; this latter helix, of the 50S subunit, is a functionally important component of an intersubunit bridge. Experimental work has shown that specific point mutations in S12 (K42A, R53A) yield hyper-accurate ribosomes, which in turn confers resistance to the antibiotic 'paromomycin' (even when this aminoglycoside is bound to the A-site). Suspecting that these effects can be elucidated in terms of the local atomic interactions and detailed dynamics of this region of the bacterial ribosome, we have used molecular dynamics simulations to explore the motion of a fragment of the E. coli ribosome, including the A-site. We found that the ribosomal regions surrounding the A-site modify the conformational space of the flexible A-site adenines 1492/93. Specifically, we found that A-site mobility is affected by stacking interactions between adenines A1493 and A1913, and by contacts between A1492 and a flexible side-chain (K43) from the S12 protein. In addition, our simulations reveal possible indirect pathways by which the R53A and K42A mutations in S12 are coupled to the dynamical properties of the A-site. Our work extends what is known about the atomistic dynamics of the A-site, and suggests possible links between the biological effects of hyper-accurate mutations in the S12 protein and conformational properties of the ribosome; the implications for S12 dynamics help elucidate how the miscoding effects of paromomycin may be evaded in antibiotic-resistant mutants of the bacterial ribosome.
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Affiliation(s)
- Joanna Panecka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States of America
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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25
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Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 2014; 3:e02030. [PMID: 24842992 PMCID: PMC4034769 DOI: 10.7554/elife.02030] [Citation(s) in RCA: 444] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein–protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter. DOI:http://dx.doi.org/10.7554/eLife.02030.001 Proteins are considered the ‘workhorse molecules’ of life and they are involved in virtually everything that cells do. Proteins are strings of amino acids that have folded into a specific three-dimensional shape. Proteins must have the correct shape to function properly, as they often work by binding to other proteins or molecules—much like a key fitting into a lock. Working out the structure of a protein can, therefore, provide major insights into how the protein does its job. Two or more proteins can bind together and form a complex to perform various tasks; and solving the structures of these complexes can be challenging, even if the structures of the protein subunits are known. Now, Ovchinnikov, Kamisetty, and Baker have developed a method for predicting which parts of the proteins make contact with each other in a two-protein complex. Different species can have copies of the same proteins; but a copy from one species might have different amino acids at certain positions when compared to a related copy from another species. As such, when pairs of interacting proteins from different species are compared, there will be many positions in the two proteins that vary. However, if the amino acid at a position in one protein (let's call it ‘X’) varies, and the amino acid at, say, position ‘Y’ in the other protein also varies such that for any given amino acid at position Y there is often a specific amino acid at position X; positions X and Y are said to ‘co-vary’. Ovchinnikov et al. noticed that when a pair of amino acids (one from each protein in a two-protein complex) co-varied, these two amino acids tended to make contact with each other at the protein–protein interface. Ovchinnikov et al. used the new method to make predictions about the protein–protein interfaces in 28 protein complexes found in bacteria, and also to make a prediction about the interface between protein subunits in the bacterial ribosome. When these predictions were checked against the actual structures, which were all known beforehand, they were found to be accurate if the number of copies of each protein being compared is greater than the average length of the two proteins. Ovchinnikov et al. went on to predict the amino acids on the protein–protein interfaces for another 36 bacterial protein complexes with unknown structures, and to present models for four larger complexes. The next challenge is to extend the method to protein complexes that are found only in eukaryotes (i.e., not in bacteria). Since the number of related copies for eukaryotic proteins tends to be smaller, there are fewer proteins to compare and it is therefore harder to detect ‘covariation’ when it occurs. DOI:http://dx.doi.org/10.7554/eLife.02030.002
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Affiliation(s)
- Sergey Ovchinnikov
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Hetunandan Kamisetty
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States Facebook Inc., Seattle, United States
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States
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26
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Abstract
The ribosome is one of the main antibiotic targets in the bacterial cell. Crystal structures of naturally produced antibiotics and their semi-synthetic derivatives bound to ribosomal particles have provided unparalleled insight into their mechanisms of action, and they are also facilitating the design of more effective antibiotics for targeting multidrug-resistant bacteria. In this Review, I discuss the recent structural insights into the mechanism of action of ribosome-targeting antibiotics and the molecular mechanisms of bacterial resistance, in addition to the approaches that are being pursued for the production of improved drugs that inhibit bacterial protein synthesis.
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27
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Kondo J, Westhof E. Aminoglycoside Antibiotics: Structural Decoding of Inhibitors Targeting the Ribosomal Decoding A Site. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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28
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Jiang J, Sakakibara Y, Chow CS. Helix 69: A Multitasking RNA Motif as a Novel Drug Target. Isr J Chem 2013. [DOI: 10.1002/ijch.201300012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kaur M, Rupasinghe CN, Klosi E, Spaller MR, Chow CS. Selection of heptapeptides that bind helix 69 of bacterial 23S ribosomal RNA. Bioorg Med Chem 2013; 21:1240-7. [PMID: 23375098 DOI: 10.1016/j.bmc.2012.12.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 12/13/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022]
Abstract
Helix 69 of Escherichia coli 23S rRNA has important roles in specific steps of translation, such as subunit association, translocation, and ribosome recycling. An M13 phage library was used to identify peptide ligands with affinity for helix 69. One selected sequence, NQVANHQ, was shown through a bead assay to interact with helix 69. Electrospray ionization mass spectroscopy revealed an apparent dissociation constant for the amidated peptide and helix 69 in the low micromolar range. This value is comparable to that of aminoglycoside antibiotics binding to the A site of 16S rRNA or helix 69. Helix 69 variants (human) and unrelated RNAs (helix 31 or A site of 16S rRNA) showed two- to fourfold lower affinity for NQVANHQ-NH(2). These results suggest that the peptide has desirable features for development as a lead compound for novel antimicrobials.
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Affiliation(s)
- Moninderpal Kaur
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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30
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Blaha GM, Polikanov YS, Steitz TA. Elements of ribosomal drug resistance and specificity. Curr Opin Struct Biol 2012; 22:750-8. [PMID: 22981944 DOI: 10.1016/j.sbi.2012.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/19/2012] [Accepted: 07/19/2012] [Indexed: 10/27/2022]
Abstract
The structures of ribosomes in complex with inhibitors of translation have not only shed light on the interactions of antibiotics with the ribosome but also on the underlying mechanisms by which they interfere with the ribosome function. Several recent papers [1(•),2(••),3,4] have correlated the available ribosome structures with the wealth of biochemical data [5(•)]. In this review we shall focus on the lessons learned for drug specificity rather than presenting a comprehensive survey of the known structures of ribosome complexes with antibiotics.
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Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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31
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Wang L, Pulk A, Wasserman MR, Feldman MB, Altman RB, Cate JHD, Blanchard SC. Allosteric control of the ribosome by small-molecule antibiotics. Nat Struct Mol Biol 2012; 19:957-63. [PMID: 22902368 PMCID: PMC3645490 DOI: 10.1038/nsmb.2360] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/13/2012] [Indexed: 12/15/2022]
Abstract
Protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. Using single-molecule imaging and X-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer RNA (aa-tRNA) selection and translocation as well as ribosome recycling by binding to helix 69 (H69) of 23S ribosomal RNA within the large subunit of the Escherichia coli ribosome. There, neomycin prevents the remodeling of intersubunit bridges that normally accompanies the process of subunit rotation to stabilize a partially rotated ribosome configuration in which peptidyl (P)-site tRNA is constrained in a previously unidentified hybrid position. Direct measurements show that this neomycin-stabilized intermediate is incompatible with the translation factor binding that is required for distinct protein synthesis reactions. These findings reveal the functional importance of reversible intersubunit rotation to the translation mechanism and shed new light on the allosteric control of ribosome functions by small-molecule antibiotics.
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MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/drug effects
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Models, Molecular
- Neomycin/chemistry
- Neomycin/pharmacology
- Protein Biosynthesis/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/drug effects
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/drug effects
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Leyi Wang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
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Monshupanee T, Johansen SK, Dahlberg AE, Douthwaite S. Capreomycin susceptibility is increased by TlyA-directed 2'-O-methylation on both ribosomal subunits. Mol Microbiol 2012; 85:1194-203. [PMID: 22779429 DOI: 10.1111/j.1365-2958.2012.08168.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The binding site of the cyclic peptide antibiotics capreomycin and viomycin is located on the ribosomal subunit interface close to nucleotides C1409 in 16S rRNA and C1920 in 23S rRNA. In Mycobacterium tuberculosis, the 2'-hydroxyls of both nucleotides are methylated by the enzyme TlyA. Loss of these methylations through inactivation of TlyA confers resistance to capreomycin and viomycin. We report here that TlyA orthologues occur in diverse bacteria and fall into two distinct groups. One group, now termed TlyA(I) , has shorter N- and C-termini and methylates only C1920; the second group (now TlyA(II) ) includes the mycobacterial enzyme, and these longer orthologues methylate at both C1409 and C1920. Ribosomal subunits are the preferred substrates for both groups of orthologues. Amino acid substitutions at the N-terminus of TlyA(II) reduce its ability to methylate these substrates. Growing pairs of recombinant TlyA(II) Escherichia coli strains in competition shows that even subtle changes in the level of rRNA methylation lead to significant differences in susceptibility to sub-inhibitory concentrations of capreomycin. The findings reveal that 2'-O-methyls at both C1409 and C1920 play a role in facilitating the inhibitory effects of capreomycin and viomycin on the bacterial ribosome.
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Affiliation(s)
- Tanakarn Monshupanee
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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