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Ngiwsara L, Sawangareetrakul P, Wattanasirichaigoon D, Tim-Aroon T, Dejkhamron P, Champattanachai V, Ketudat-Cairns JR, Svasti J. Effects of gentamicin inducing readthrough premature stop Codons: A study of alpha-L-iduronidase nonsense variants in COS-7 Cells. Biochem Biophys Res Commun 2022; 636:147-154. [DOI: 10.1016/j.bbrc.2022.10.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/23/2022] [Indexed: 11/02/2022]
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2
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Gao Y, Chen Y, Cao Y, Mo A, Peng Q. Potentials of nanotechnology in treatment of methicillin-resistant Staphylococcus aureus. Eur J Med Chem 2020; 213:113056. [PMID: 33280899 DOI: 10.1016/j.ejmech.2020.113056] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/05/2023]
Abstract
Abuse of antibiotics has led to the emergence of drug-resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) was reported just two years after the clinical use of methicillin, which can cause severe infections with high morbidity and mortality in both community and hospital. The treatment of MRSA infection is greatly challenging since it has developed the resistance to almost all types of antibiotics. As such, it is of great significance and importance to develop novel therapeutic approaches. The fast development of nanotechnology provides a promising solution to this dilemma. Functional nanomaterials and nanoparticles can act either as drug carriers or as antibacterial agents for antibacterial therapy. Herein, we aim to provide a comprehensive understanding of the drug resistance mechanisms of MRSA and discuss the potential applications of some functionalized nanomaterials in anti-MRSA therapy. Also, the concerns and possible solutions for the nanomaterials-based anti-MRSA therapy are discussed.
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Affiliation(s)
- Yujie Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China; Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuan Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China; Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yubin Cao
- Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Anchun Mo
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Qiang Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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3
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Assis LM, Nedeljković M, Dessen A. New strategies for targeting and treatment of multi-drug resistant Staphylococcus aureus. Drug Resist Updat 2017; 31:1-14. [PMID: 28867240 DOI: 10.1016/j.drup.2017.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is a major cause of bacterial infection in humans, and has been notoriously able to acquire resistance to a variety of antibiotics. An example is methicillin-resistant S. aureus (MRSA), which despite having been initially associated with clinical settings, now is one of the key causative agents of community-acquired infections. Antibiotic resistance in S. aureus involves mechanisms ranging from drug efflux to increased expression or mutation of target proteins, and this has required innovative approaches to develop novel treatment methodologies. This review provides an overview of the major mechanisms of antibiotic resistance developed by S. aureus, and describes the emerging alternatives being sought to circumvent infection and proliferation, including new generations of classic antibiotics, synergistic approaches, antibodies, and targeting of virulence factors.
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Affiliation(s)
- L Mayrink Assis
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - M Nedeljković
- Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France
| | - A Dessen
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil; Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France.
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4
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Kato T, Yang G, Teo Y, Juskeviciene R, Perez-Fernandez D, Shinde HM, Salian S, Bernet B, Vasella A, Böttger EC, Crich D. Synthesis and Antiribosomal Activities of 4'-O-, 6'-O-, 4″-O-, 4',6'-O- and 4″,6″-O-Derivatives in the Kanamycin Series Indicate Differing Target Selectivity Patterns between the 4,5- and 4,6-Series of Disubstituted 2-Deoxystreptamine Aminoglycoside Antibiotics. ACS Infect Dis 2015; 1:479-86. [PMID: 27623314 DOI: 10.1021/acsinfecdis.5b00069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Chemistry for the efficient modification of the kanamycin class of 4,6-aminoglycosides at the 4'-position is presented. In all kanamycins but kanamycin B, 4'-O-alkylation is strongly detrimental to antiribosomal and antibacterial activity. Ethylation of kanamycin B at the 4″-position entails little loss of antiribosomal and antibacterial activity, but no increase of ribosomal selectivity. These results are contrasted with those for the 4,5-aminoglycosides, where 4'-O-alkylation of paromomycin causes only a minimal loss of activity but results in a significant increase in selectivity with a concomitant loss of ototoxicity.
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Affiliation(s)
- Takayuki Kato
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Guanyu Yang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Reda Juskeviciene
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | | | - Harish M. Shinde
- Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Sumanth Salian
- Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Bruno Bernet
- Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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5
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Duscha S, Boukari H, Shcherbakov D, Salian S, Silva S, Kendall A, Kato T, Akbergenov R, Perez-Fernandez D, Bernet B, Vaddi S, Thommes P, Schacht J, Crich D, Vasella A, Böttger EC. Identification and evaluation of improved 4'-O-(alkyl) 4,5-disubstituted 2-deoxystreptamines as next-generation aminoglycoside antibiotics. mBio 2014; 5:e01827-14. [PMID: 25271289 PMCID: PMC4196235 DOI: 10.1128/mbio.01827-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED The emerging epidemic of drug resistance places the development of efficacious and safe antibiotics in the spotlight of current research. Here, we report the design of next-generation aminoglycosides. Discovery efforts were driven by rational synthesis focusing on 4' alkylations of the aminoglycoside paromomycin, with the goal to alleviate the most severe and disabling side effect of aminoglycosides-irreversible hearing loss. Compounds were evaluated for target activity in in vitro ribosomal translation assays, antibacterial potency against selected pathogens, cytotoxicity against mammalian cells, and in vivo ototoxicity. The results of this study produced potent compounds with excellent selectivity at the ribosomal target, promising antibacterial activity, and little, if any, ototoxicity upon chronic administration. The favorable biocompatibility profile combined with the promising antibacterial activity emphasizes the potential of next-generation aminoglycosides in the treatment of infectious diseases without the risk of ototoxicity. IMPORTANCE The ever-widening epidemic of multidrug-resistant infectious diseases and the paucity of novel antibacterial agents emerging from modern screening platforms mandate the reinvestigation of established drugs with an emphasis on improved biocompatibility and overcoming resistance mechanisms. Here, we describe the preparation and evaluation of derivatives of the established aminoglycoside antibiotic paromomycin that effectively remove its biggest deficiency, ototoxicity, and overcome certain bacterial resistance mechanisms.
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Affiliation(s)
- Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Sumantha Salian
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Sandrina Silva
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Ann Kendall
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Takayuki Kato
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Bruno Bernet
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | | | - Pia Thommes
- Euprotec Limited, Manchester, United Kingdom
| | - Jochen Schacht
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 2014; 426:3201-3213. [PMID: 24813122 DOI: 10.1016/j.jmb.2014.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/13/2014] [Accepted: 04/14/2014] [Indexed: 11/22/2022]
Abstract
Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near-cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA.
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Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Böttger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun 2014; 5:3112. [PMID: 24473108 PMCID: PMC3942853 DOI: 10.1038/ncomms4112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023] Open
Abstract
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
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Affiliation(s)
- Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
- These authors contributed equally to this work
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
- These authors contributed equally to this work
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Ng Chyan Leong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- These authors contributed equally to this work
| | - Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashmi Patak
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Srinivas Reddy Dubbaka
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Swapna Vaddi
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - Pia Thommes
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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Lu J, Zhao L, Xia A, Xia T, Qi X. Dissect conformational distribution and drug-induced population shift of prokaryotic rRNA A-site. Biochemistry 2013; 52:1651-3. [PMID: 23427980 DOI: 10.1021/bi400053s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The dynamic behavior of the rRNA A-site plays an important functional role. We have employed femtosecond time-resolved spectroscopy to investigate the nature of the conformational dynamics. In the drug-free state, the A-site samples multiple distinct conformations. Drug binding shifts the population distribution in a drug-specific manner. Motions of bases on nanosecond and picosecond time scales are differentially affected by the drug binding. Our results underscore the importance of understanding the detailed dynamic picture of molecular recognition by resolving dynamics in the distinct picosecond time regime and facilitate development of antimicrobial drugs targeting dynamic RNAs.
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Affiliation(s)
- Jia Lu
- Department of Molecular and Cell Biology, The University of Texas at Dallas , Richardson, Texas 75080, United States
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9
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Abstract
Several disease states create conditions that lead to opportunistic Gram-negative respiratory infections. Inhalation is the most direct and, until recently, underutilized means of antimicrobial drug targeting for respiratory tract infections. All approved antimicrobial agents for administration by inhalation are indicated for Pseudomonas aeruginosa infections in patients with cystic fibrosis. These inhaled therapies have directly contributed to a significant reduction in exacerbations and hospitalizations in this patient population over the last few decades. The relentless adaptation of pathogenic organisms to current treatment options demands that the pharmaceutical industry continue designing next-generation antimicrobial agents over 70 years after they were first introduced. Recent technological advances in inhalation devices and drug formulation techniques have broadened the scope of antimicrobial structural classes that can be investigated by inhalation; however, there is an urgent need to discover novel compounds with improved resistance profiles relative to those drugs that are already marketed.
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McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:209-32. [DOI: 10.1002/wrna.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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