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Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG. Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun 2023; 14:4666. [PMID: 37537169 PMCID: PMC10400623 DOI: 10.1038/s41467-023-40416-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Narayan P Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Arindam De Tarafder
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Microbiology and Immunology, 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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2
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Shapovalova K, Zatonsky G, Grammatikova N, Osterman I, Razumova E, Shchekotikhin A, Tevyashova A. Synthesis of 6″-Modified Kanamycin A Derivatives and Evaluation of Their Antibacterial Properties. Pharmaceutics 2023; 15:pharmaceutics15041177. [PMID: 37111662 PMCID: PMC10141514 DOI: 10.3390/pharmaceutics15041177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Aminoglycosides are one of the first classes of antibiotics to have been used clinically, and they are still being used today. They have a broad spectrum of antimicrobial activity, making them effective against many different types of bacteria. Despite their long history of use, aminoglycosides are still considered promising scaffolds for the development of new antibacterial agents, particularly as bacteria continue to develop resistances to existing antibiotics. We have synthesized a series of 6″-deoxykanamycin A analogues with additional protonatable groups (amino-, guanidino or pyridinium) and tested their biological activities. For the first time we have demonstrated the ability of the tetra-N-protected-6″-O-(2,4,6-triisopropylbenzenesulfonyl)kanamycin A to interact with a weak nucleophile, pyridine, resulting in the formation of the corresponding pyridinium derivative. Introducing small diamino-substituents at the 6″-position of kanamycin A did not significantly alter the antibacterial activity of the parent antibiotic, but further modification by acylation resulted in a complete loss of the antibacterial activity. However, introducing a guanidine residue led to a compound with improved activity against S. aureus. Moreover, most of the obtained 6″-modified kanamycin A derivatives were less influenced by the resistant mechanism associated with mutations of the elongation factor G than the parent kanamycin A. This suggests that modifying the 6″-position of kanamycin A with protonatable groups is a promising direction for the further development of new antibacterial agents with reduced resistances.
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Affiliation(s)
- Kseniya Shapovalova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia
| | - Georgy Zatonsky
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia
| | | | - Ilya Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
| | - Elizaveta Razumova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | | | - Anna Tevyashova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia
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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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Singh S, Lahry K, Mandava CS, Singh J, Shah RA, Sanyal S, Varshney U. Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli. RNA Biol 2023; 20:681-692. [PMID: 37676049 PMCID: PMC10486304 DOI: 10.1080/15476286.2023.2253395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast kinetics assay, the in vivo experiments show that Ltg causes accumulation of the 17S precursor of 16S rRNA and leads to a decrease in polysome levels in E. coli. IF2 overexpression in E. coli increases Ltg toxicity. However, the overexpression of initiator tRNA (i-tRNA) protects it from the Ltg toxicity. The depletion of i-tRNA or overexpression of its 3GC mutant (lacking the characteristic 3GC base pairs in anticodon stem) enhances Ltg toxicity, and this enhancement in toxicity is synthetic with IF2 overexpression. The Ltg treatment itself causes a detectable increase in IF2 levels in E. coli and allows initiation with an elongator tRNA, suggesting compromise in the fidelity/specificity of IF2 function. Also, Ltg causes increased accumulation of ribosome-binding factor A (RbfA) on 30S ribosomal subunit. Based on our genetic and biochemical investigations, we show that Ltg compromises the function of i-tRNA/IF2 complex in ribosome maturation.
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Affiliation(s)
- Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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5
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Webster CM, Shepherd M. A mini-review: environmental and metabolic factors affecting aminoglycoside efficacy. World J Microbiol Biotechnol 2023; 39:7. [PMID: 36350431 PMCID: PMC9646598 DOI: 10.1007/s11274-022-03445-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
Following the discovery of streptomycin from Streptomyces griseus in the 1940s by Selman Waksman and colleagues, aminoglycosides were first used to treat tuberculosis and then numerous derivatives have since been used to combat a wide variety of bacterial infections. These bactericidal antibiotics were used as first-line treatments for several decades but were largely replaced by ß-lactams and fluoroquinolones in the 1980s, although widespread emergence of antibiotic-resistance has led to renewed interest in aminoglycosides. The primary site of action for aminoglycosides is the 30 S ribosomal subunit where they disrupt protein translation, which contributes to widespread cellular damage through a number of secondary effects including rapid uptake of aminoglycosides via elevated proton-motive force (PMF), membrane damage and breakdown, oxidative stress, and hyperpolarisation of the membrane. Several factors associated with aminoglycoside entry have been shown to impact upon bacterial killing, and more recent work has revealed a complex relationship between metabolic states and the efficacy of different aminoglycosides. Hence, it is imperative to consider the environmental conditions and bacterial physiology and how this can impact upon aminoglycoside entry and potency. This mini-review seeks to discuss recent advances in this area and how this might affect the future use of aminoglycosides.
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Affiliation(s)
- Calum M Webster
- School of Biosciences, RAPID Group, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mark Shepherd
- School of Biosciences, RAPID Group, University of Kent, Canterbury, CT2 7NJ, UK.
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Cusack R, Garduno A, Elkholy K, Martín-Loeches I. Novel investigational treatments for ventilator-associated pneumonia and critically ill patients in the intensive care unit. Expert Opin Investig Drugs 2022; 31:173-192. [PMID: 35040388 DOI: 10.1080/13543784.2022.2030312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Ventilator-associated pneumonia (VAP) is common; its prevalence has been highlighted by the Covid-19 pandemic. Even young patients can suffer severe nosocomial infection and prolonged mechanical ventilation. Multidrug-resistant bacteria can spread alarmingly fast around the globe and new antimicrobials are struggling to keep pace; hence physicians must stay abreast of new developments in the treatment of nosocomial pneumonia and VAP. AREAS COVERED This narrative review examines novel antimicrobial investigational drugs and their implementation in the ICU setting for VAP. The paper highlights novel approaches such as monoclonal antibody treatments for P. aeruginosa and S. aureus, and phage antibiotic synthesis. The paper also examines mechanisms of resistance in gram-negative bacteria, virulence factors and inhaled antibiotics and questions what may be on the horizon in terms of emerging treatment strategies. EXPERT OPINION The post-antibiotic era is rapidly approaching and the need for personalised medicine, point-of-care microbial sensitivity testing and development of biomarkers for severe infections is clear. Results from emerging and new antibiotics are encouraging, but infection control measures and de-escalation protocols must be employed to prolong their usefulness in critical illness.
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Affiliation(s)
- Rachael Cusack
- Department of Clinical Medicine, Trinity College Dublin.,Department of Intensive Care Medicine, St. James's Hospital, Dublin, (Ireland)
| | - Alexis Garduno
- Department of Clinical Medicine, Trinity College Dublin.,Intensive Care Translational Research, Trinity College Dublin
| | - Khalid Elkholy
- Department of Intensive Care Medicine, St. James's Hospital, Dublin, (Ireland)
| | - Ignacio Martín-Loeches
- Department of Clinical Medicine, Trinity College Dublin.,Department of Intensive Care Medicine, St. James's Hospital, Dublin, (Ireland).,Multidisciplinary Intensive Care Research Organization (MICRO), St. James's Hospital, Dublin, (Ireland)
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