1
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Magaña AJ, Sklenicka J, Pinilla C, Giulianotti M, Chapagain P, Santos R, Ramirez MS, Tolmasky ME. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Med Chem 2023; 14:1591-1602. [PMID: 37731693 PMCID: PMC10507813 DOI: 10.1039/d3md00226h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Growing resistance to antimicrobial medicines is a critical health problem that must be urgently addressed. Adding to the increasing number of patients that succumb to infections, there are other consequences to the rise in resistance like the compromise of several medical procedures and dental work that are heavily dependent on infection prevention. Since their introduction in the clinics, aminoglycoside antibiotics have been a critical component of the armamentarium to treat infections. Still, the increase in resistance and their side effects led to a decline in their utilization. However, numerous current factors, like the urgent need for antimicrobials and their favorable properties, led to renewed interest in these drugs. While efforts to design new classes of aminoglycosides refractory to resistance mechanisms and with fewer toxic effects are starting to yield new promising molecules, extending the useful life of those already in use is essential. For this, numerous research projects are underway to counter resistance from different angles, like inhibition of expression or activity of resistance components. This review focuses on selected examples of one aspect of this quest, the design or identification of small molecule inhibitors of resistance caused by enzymatic modification of the aminoglycoside. These compounds could be developed as aminoglycoside adjuvants to overcome resistant infections.
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Affiliation(s)
- Angel J Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Marc Giulianotti
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University Fort Lauderdale FL 33314 USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
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2
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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3
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Uddin R, Siraj B, Rafi S, Azam SS, Wadood A. Structure-based Virtual Screening Approach for the Discovery of Potent Inhibitors of Aminoglycoside 6'-N-Acetyltransferase Type Ib [AAC(6')-Ib] against K. pneumoniae Infections. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817666200108095912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Aminoglycoside 6'-N-acetyltransferase type Ib (AAC(6')-Ib) from
Klebsiella pneumoniae is an established drug target and has conferred insensitivity to
aminoglycosides. Aminoglycosides are often inactivated by aminoglycoside modifying enzymes
encoded by genes present in the chromosome, plasmids, and other genetic elements. The AAC(6′)-
Ib is an enzyme of clinical importance found in a wide variety of gram-negative pathogens. The
AAC(6′)-Ib enzyme is of interest not only because of its ubiquity but also because of other
characteristics e.g., it presents significant microheterogeneity at the N-termini and the aac(6′)-Ib
gene is often present in integrons, transposons, plasmids, genomic islands, and other genetic
structures. The majority of the reported potent inhibitors against the target are substrate analogs.
Therefore, there is a need to develop or discover new scaffolds other than substrate analogs as
AAC(6')-Ib inhibitor.
Objective:
The objective of this study is to set optimum parameters for the structure-based virtual
screening by multiple docking and scoring methods. The multiple scoring of each ligand also
incorporates the ‘Induced Fit’ docking effect that helps to build further confidence in the shortlisted
compounds. The method eventually is able to predict the potential inhibitors that bind to the active
site and can potentially inhibit the activity of the Aminoglycoside 6′-N-acetyltransferase type Ib
[AAC(6’)-Ib] from Klebsiella pneumoniae.
Methods:
Using the available three-dimensional structure of enzyme AAC(6')-Ib inhibitor complex,
a structure-based virtual screening was performed with the hope of prioritizing the promising leads.
In order to set up the protocol, 30,000 drug-like molecules were selected from the ChemBridge
library. Multiple docking programs, i.e. UCSF DOCK6 and AutoDock Vina have been applied in
the current study so that a consensus is developed to the predicted binding modes and thus the
docking accuracy. The Amber scores of the Dock6 – a secondary scoring function was also used to
perform the ‘Induced Fit’ effect and correspondingly re-rank the compounds.
Results:
The top 30 ranked compounds of the most frequent scored were selected from the
histogram. The 2D interactions of those 30 compounds were drawn from the Ligplot+ tool. Six of
the compounds were prioritized as potential inhibitors as they are representing the maximum
number of interactions from the rest of the compounds and also possess the drug-likeness as
predicted by the estimated ADMET properties.
Conclusion:
This study provided useful insight that the proposed compounds have the potential to
bind to the aminoglycoside binding site of AAC(6′)-Ib that may eventually inhibit the Klebsiella
pneumoniae. This study has the potential to propose putative new and novel inhibitors against a
resistant drug target of Klebsiella pneumoniae.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Bushra Siraj
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Sidra Rafi
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Syed Sikander Azam
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
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4
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Duncan D, Auclair K. The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation. Arch Biochem Biophys 2019; 672:108069. [PMID: 31404525 DOI: 10.1016/j.abb.2019.108069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
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5
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Abstract
Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.
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Affiliation(s)
- Anne Witzky
- 1 Department of Molecular Genetics, Ohio State University , Columbus, OH 43210 , USA.,2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA
| | - Rodney Tollerson
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
| | - Michael Ibba
- 2 Center for RNA Biology, Ohio State University , Columbus, OH 43210 , USA.,3 Department of Microbiology, Ohio State University , Columbus, OH 43210 , USA
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6
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Guan J, Vong K, Wee K, Fakhoury J, Dullaghan E, Auclair K. Cellular Studies of an Aminoglycoside Potentiator Reveal a New Inhibitor of Aminoglycoside Resistance. Chembiochem 2018; 19:2107-2113. [DOI: 10.1002/cbic.201800368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Jinming Guan
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Kenward Vong
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Kathleen Wee
- Target Validation Division; The Centre for Drug Research and Development; 2405 Westbrook Mall, 4th Floor Vancouver British Columbia V6T 1Z3 Canada
| | - Johans Fakhoury
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Edie Dullaghan
- Target Validation Division; The Centre for Drug Research and Development; 2405 Westbrook Mall, 4th Floor Vancouver British Columbia V6T 1Z3 Canada
| | - Karine Auclair
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
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7
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Zárate SG, Claure MLDLC, Benito-Arenas R, Revuelta J, Santana AG, Bastida A. Overcoming Aminoglycoside Enzymatic Resistance: Design of Novel Antibiotics and Inhibitors. Molecules 2018; 23:molecules23020284. [PMID: 29385736 PMCID: PMC6017855 DOI: 10.3390/molecules23020284] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/26/2018] [Indexed: 11/17/2022] Open
Abstract
Resistance to aminoglycoside antibiotics has had a profound impact on clinical practice. Despite their powerful bactericidal activity, aminoglycosides were one of the first groups of antibiotics to meet the challenge of resistance. The most prevalent source of clinically relevant resistance against these therapeutics is conferred by the enzymatic modification of the antibiotic. Therefore, a deeper knowledge of the aminoglycoside-modifying enzymes and their interactions with the antibiotics and solvent is of paramount importance in order to facilitate the design of more effective and potent inhibitors and/or novel semisynthetic aminoglycosides that are not susceptible to modifying enzymes.
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Affiliation(s)
- Sandra G. Zárate
- Facultad de Tecnología-Carrera de Ingeniería Química, Universidad Mayor Real y Pontificia de San Francisco Xavier de Chuquisaca, Regimiento Campos 180, Casilla 60-B, Sucre, Bolivia;
| | - M. Luisa De la Cruz Claure
- Facultad de Ciencias Químico Farmacéuticas y Bioquímicas, Universidad Mayor Real y Pontificia de San Francisco Xavier de Chuquisaca, Dalence 51, Casilla 497, Sucre, Bolivia;
| | - Raúl Benito-Arenas
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
| | - Julia Revuelta
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
| | - Andrés G. Santana
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
- Correspondence: (A.G.S.); (A.B.); Tel: +34-915-612-800 (A.B.)
| | - Agatha Bastida
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
- Correspondence: (A.G.S.); (A.B.); Tel: +34-915-612-800 (A.B.)
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8
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Reidl C, Majorek KA, Dang J, Tran D, Jew K, Law M, Payne Y, Minor W, Becker DP, Kuhn ML. Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases. FEBS Lett 2017; 591:2348-2361. [PMID: 28703494 PMCID: PMC5578807 DOI: 10.1002/1873-3468.12753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023]
Abstract
Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor-bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X-ray induced radical-mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely applicable across the GNAT superfamily and can be used to improve the success rate of obtaining liganded structures of other acyltransferases.
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Affiliation(s)
- Cory Reidl
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Joseph Dang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - David Tran
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Kristen Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Yasmine Payne
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Daniel P. Becker
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
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9
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Schillaci D, Spanò V, Parrino B, Carbone A, Montalbano A, Barraja P, Diana P, Cirrincione G, Cascioferro S. Pharmaceutical Approaches to Target Antibiotic Resistance Mechanisms. J Med Chem 2017; 60:8268-8297. [PMID: 28594170 DOI: 10.1021/acs.jmedchem.7b00215] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is urgent need for new therapeutic strategies to fight the global threat of antibiotic resistance. The focus of this Perspective is on chemical agents that target the most common mechanisms of antibiotic resistance such as enzymatic inactivation of antibiotics, changes in cell permeability, and induction/activation of efflux pumps. Here we assess the current landscape and challenges in the treatment of antibiotic resistance mechanisms at both bacterial cell and community levels. We also discuss the potential clinical application of chemical inhibitors of antibiotic resistance mechanisms as add-on treatments for serious drug-resistant infections. Enzymatic inhibitors, such as the derivatives of the β-lactamase inhibitor avibactam, are closer to the clinic than other molecules. For example, MK-7655, in combination with imipenem, is in clinical development for the treatment of infections caused by carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa, which are difficult to treat. In addition, other molecules targeting multidrug-resistance mechanisms, such as efflux pumps, are under development and hold promise for the treatment of multidrug resistant infections.
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Affiliation(s)
- Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Carbone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
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10
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Salah Ud-Din AIM, Tikhomirova A, Roujeinikova A. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Int J Mol Sci 2016; 17:E1018. [PMID: 27367672 PMCID: PMC4964394 DOI: 10.3390/ijms17071018] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Alexandra Tikhomirova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
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11
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Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Potent Inhibitors of Acetyltransferase Eis Overcome Kanamycin Resistance in Mycobacterium tuberculosis. ACS Chem Biol 2016; 11:1639-46. [PMID: 27010218 DOI: 10.1021/acschembio.6b00110] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A major cause of tuberculosis (TB) resistance to the aminoglycoside kanamycin (KAN) is the Mycobacterium tuberculosis (Mtb) acetyltransferase Eis. Upregulation of this enzyme is responsible for inactivation of KAN through acetylation of its amino groups. A 123 000-compound high-throughput screen (HTS) yielded several small-molecule Eis inhibitors that share an isothiazole S,S-dioxide heterocyclic core. These were investigated for their structure-activity relationships. Crystal structures of Eis in complex with two potent inhibitors show that these molecules are bound in the conformationally adaptable aminoglycoside binding site of the enzyme, thereby obstructing binding of KAN for acetylation. Importantly, we demonstrate that several Eis inhibitors, when used in combination with KAN against resistant Mtb, efficiently overcome KAN resistance. This approach paves the way toward development of novel combination therapies against aminoglycoside-resistant TB.
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Affiliation(s)
- Melisa J. Willby
- Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Keith D. Green
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Oleg V. Tsodikov
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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12
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Abstract
Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following Review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery.
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Affiliation(s)
- George P. Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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13
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Chiem K, Jani S, Fuentes B, Lin DL, Rasche ME, Tolmasky ME. Identification of an Inhibitor of the Aminoglycoside 6'- N-Acetyltransferase type Ib [AAC(6')-Ib] by Glide Molecular Docking. MEDCHEMCOMM 2016; 7:184-189. [PMID: 26973774 PMCID: PMC4784703 DOI: 10.1039/c5md00316d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aminoglycoside 6'-N-acetyltransferase type Ib, AAC(6')-Ib, confers resistance to clinically relevant aminoglycosides and is the most widely distributed enzyme among AAC(6')-I-producing Gram-negative pathogens. An alternative to counter the action of this enzyme is the development of inhibitors. Glide is a computational strategy for rapidly docking ligands to protein sites and estimating their binding affinities. We docked a collection of 280,000 compounds from 7 sub-libraries of the Chembridge library as ligands to the aminoglycoside binding site of AAC(6')-Ib. We identified a compound, 1-[3-(2-aminoethyl)benzyl]-3-(piperidin-1-ylmethyl)pyrrolidin-3-ol (compound 1), that inhibited the acetylation of aminoglycosides in vitro with IC50 values of 39.7 and 34.9 µM when the aminoglycoside substrates assayed were kanamycin A or amikacin, respectively. The growth of an amikacin-resistant Acinetobacter baumannii clinical strain was inhibited in the presence of a combination of amikacin and compound 1.
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Affiliation(s)
- Kevin Chiem
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Saumya Jani
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Brooke Fuentes
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - David L. Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Madeline E. Rasche
- Center for Applied Biotechnology Studies, Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
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14
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Bera S, Mondal D, Palit S, Schweizer F. Structural modifications of the neomycin class of aminoglycosides. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00079g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review encompasses comprehensive literature on synthetic modification and biological activities of clinically used neomycin-class aminoglycoside antibiotics to alleviate dose-related toxicity and pathogenic resistance.
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Affiliation(s)
- Smritilekha Bera
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | - Dhananjoy Mondal
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | - Subhadeep Palit
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology Campus
- Kolkata-700 032
- India
| | - Frank Schweizer
- Department of Chemistry and Medical Microbiology
- University of Manitoba
- Winnipeg
- Canada
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15
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Chandrika NT, Garneau-Tsodikova S. A review of patents (2011-2015) towards combating resistance to and toxicity of aminoglycosides. MEDCHEMCOMM 2015; 7:50-68. [PMID: 27019689 PMCID: PMC4806794 DOI: 10.1039/c5md00453e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Since the discovery of the first aminoglycoside (AG), streptomycin, in 1943, these broad-spectrum antibiotics have been extensively used for the treatment of Gram-negative and Gram-positive bacterial infections. The inherent toxicity (ototoxicity and nephrotoxicity) associated with their long-term use as well as the emergence of resistant bacterial strains have limited their usage. Structural modifications of AGs by AG-modifying enzymes, reduced target affinity caused by ribosomal modification, and decrease in their cellular concentration by efflux pumps have resulted in resistance towards AGs. However, the last decade has seen a renewed interest among the scientific community for AGs as exemplified by the recent influx of scientific articles and patents on their therapeutic use. In this review, we use a non-conventional approach to put forth this renaissance on AG development/application by summarizing all patents filed on AGs from 2011-2015 and highlighting some related publications on the most recent work done on AGs to overcome resistance and improving their therapeutic use while reducing ototoxicity and nephrotoxicity. We also present work towards developing amphiphilic AGs for use as fungicides as well as that towards repurposing existing AGs for potential newer applications.
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Affiliation(s)
- Nishad Thamban Chandrika
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. Fax: 859-257-7585; Tel: 859-218-1686
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. Fax: 859-257-7585; Tel: 859-218-1686
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16
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Inhibition of aminoglycoside acetyltransferase resistance enzymes by metal salts. Antimicrob Agents Chemother 2015; 59:4148-56. [PMID: 25941215 DOI: 10.1128/aac.00885-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 11/20/2022] Open
Abstract
Aminoglycosides (AGs) are clinically relevant antibiotics used to treat infections caused by both Gram-negative and Gram-positive bacteria, as well as Mycobacteria. As with all current antibacterial agents, resistance to AGs is an increasing problem. The most common mechanism of resistance to AGs is the presence of AG-modifying enzymes (AMEs) in bacterial cells, with AG acetyltransferases (AACs) being the most prevalent. Recently, it was discovered that Zn(2+) metal ions displayed an inhibitory effect on the resistance enzyme AAC(6')-Ib in Acinetobacter baumannii and Escherichia coli. In this study, we explore a wide array of metal salts (Mg(2+), Cr(3+), Cr(6+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Au(3+) with different counter ions) and their inhibitory effect on a large repertoire of AACs [AAC(2')-Ic, AAC(3)-Ia, AAC(3)-Ib, AAC(3)-IV, AAC(6')-Ib', AAC(6')-Ie, AAC(6')-IId, and Eis]. In addition, we determine the MIC values for amikacin and tobramycin in combination with a zinc pyrithione complex in clinical isolates of various bacterial strains (two strains of A. baumannii, three of Enterobacter cloacae, and four of Klebsiella pneumoniae) and one representative of each species purchased from the American Type Culture Collection.
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17
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Gorityala BK, Guchhait G, Schweizer F. Amphiphilic Aminoglycoside Antimicrobials in Antibacterial Discovery. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Amphiphilic aminoglycoside antimicrobials (AAAs) are an emerging class of polycationic antibacterial agents with broad-spectrum antibacterial activity. In contrast to aminoglycosides, which interfere with protein synthesis by interacting with the 30S ribosomal subunit, AAAs appear to target the bacterial cell wall by interactions with extracellular lipids or proteins or by enhancing the permeability of the bacterial cell wall. The physicochemical similarities between amphiphilic aminoglycosides and antimicrobial peptides, another class of polycationic amphiphiles with broad-spectrum antibacterial activity, suggest similar mode(s) of action. However, in contrast to antimicrobial peptides, AAAs are not composed of peptide bonds and as such promise to display superior metabolic stability. As a result, AAAs may be considered to be a novel class of antimicrobial peptidomimetics. Many AAAs possess impressive potent antibacterial activity against Gram-positive and Gram-negative bacteria, especially against bacterial strains that are resistant to clinically used antibiotics. In summary, AAAs promise to provide a new and rich source of antibacterial lead structures to combat antibiotic-resistant and multidrug-resistant pathogens.
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Affiliation(s)
| | - Goutam Guchhait
- Department of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 Canada
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18
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Freiburger L, Auclair K, Mittermaier A. Global ITC fitting methods in studies of protein allostery. Methods 2015; 76:149-161. [PMID: 25573261 PMCID: PMC5182068 DOI: 10.1016/j.ymeth.2014.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022] Open
Abstract
Allostery is a nearly ubiquitous feature of biological systems in which ligand binding or covalent modification at one site alters the activities of distant sites in a macromolecule or macromolecular complex. The molecular mechanisms underlying this phenomenon have been studied for decades. Nevertheless there are many aspects that remain poorly understood. ITC yields detailed information on the thermodynamics of biomacromolecular interactions and their coupling to additional equilibria, therefore in principle it is a powerful tool for better understanding how allostery is achieved. A particularly powerful approach involves simultaneously fitting multiple ITC data sets together with those of complementary techniques, especially nuclear magnetic resonance and circular dichroism spectroscopies. In this review, we describe several group-fitting methods for discriminating between different binding models and for improving the accuracy of thermodynamic parameters extracted from variable-temperature ITC data. The techniques were applied to the antibiotic resistance-causing enzyme aminoglycoside-6'-acetyltransferase Ii, uncovering the existence of competition between opposing mechanisms and ligand-dependent switching of the underlying mechanism. These novel observations underline the potential of combining ITC and spectroscopic techniques to study allostery.
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Affiliation(s)
- Lee Freiburger
- Technische Universität München, Chair of Biomolecular NMR Spectroscopy, Germany
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19
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Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
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20
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Substrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme. Nat Chem Biol 2014; 10:937-42. [PMID: 25218742 DOI: 10.1038/nchembio.1626] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/21/2014] [Indexed: 11/08/2022]
Abstract
Enzyme activity is commonly controlled by allostery, where ligand binding at one site alters the activities of distant sites. Classical explanations for multisubunit proteins involve conformational transitions that are fundamentally deterministic. For example, in the Monod-Wyman-Changeaux (MWC) paradigm, conformational transitions occur simultaneously in all subunits. In the Koshland-Nemethy-Filmer (KNF) paradigm, conformational transitions only occur in ligand-bound subunits. In contrast, recent models predict conformational changes that are governed by probabilities rather than absolute rules. To better understand allostery at the molecular level, we applied a recently developed spectroscopic and calorimetric method to the interactions of a dimeric enzyme with two different ligands. We found that conformational transitions appear MWC-like for a ligand that binds at the dimer interface and KNF-like for a distal ligand. These results provide strong experimental support for probabilistic allosteric theory predictions that an enzyme can exhibit a mixture of MWC and KNF character, with the balance partly governed by subunit interface energies.
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21
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Tsodikov OV, Green KD, Garneau-Tsodikova S. A random sequential mechanism of aminoglycoside acetylation by Mycobacterium tuberculosis Eis protein. PLoS One 2014; 9:e92370. [PMID: 24699000 PMCID: PMC3974725 DOI: 10.1371/journal.pone.0092370] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
An important cause of bacterial resistance to aminoglycoside antibiotics is the enzymatic acetylation of their amino groups by acetyltransferases, which abolishes their binding to and inhibition of the bacterial ribosome. Enhanced intracellular survival (Eis) protein from Mycobacterium tuberculosis (Mt) is one of such acetyltransferases, whose upregulation was recently established as a cause of resistance to aminoglycosides in clinical cases of drug-resistant tuberculosis. The mechanism of aminoglycoside acetylation by MtEis is not completely understood. A systematic analysis of steady-state kinetics of acetylation of kanamycin A and neomycin B by Eis as a function of concentrations of these aminoglycosides and the acetyl donor, acetyl coenzyme A, reveals that MtEis employs a random-sequential bisubstrate mechanism of acetylation and yields the values of the kinetic parameters of this mechanism. The implications of these mechanistic properties for the design of inhibitors of Eis and other aminoglycoside acetyltransferases are discussed.
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Affiliation(s)
- Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
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22
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Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections. Future Med Chem 2014; 5:1285-309. [PMID: 23859208 DOI: 10.4155/fmc.13.80] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Shortly after the discovery of the first antibiotics, bacterial resistance began to emerge. Many mechanisms give rise to resistance; the most prevalent mechanism of resistance to the aminoglycoside (AG) family of antibiotics is the action of aminoglycoside-modifying enzymes (AMEs). Since the identification of these modifying enzymes, many efforts have been put forth to prevent their damaging alterations of AGs. These diverse strategies are discussed within this review, including: creating new AGs that are unaffected by AMEs; developing inhibitors of AMEs to be co-delivered with AGs; or regulating AME expression. Modern high-throughput methods as well as drug combinations and repurposing are highlighted as recent drug-discovery efforts towards fighting the increasing antibiotic resistance crisis.
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23
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Norris AL, Serpersu EH. Ligand promiscuity through the eyes of the aminoglycoside N3 acetyltransferase IIa. Protein Sci 2014; 22:916-28. [PMID: 23640799 DOI: 10.1002/pro.2273] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 11/08/2022]
Abstract
Aminoglycoside-modifying enzymes (AGMEs) are expressed in many pathogenic bacteria and cause resistance to aminoglycoside (AG) antibiotics. Remarkably, the substrate promiscuity of AGMEs is quite variable. The molecular basis for such ligand promiscuity is largely unknown as there is not an obvious link between amino acid sequence or structure and the antibiotic profiles of AGMEs. To address this issue, this article presents the first kinetic and thermodynamic characterization of one of the least promiscuous AGMEs, the AG N3 acetyltransferase-IIa (AAC-IIa) and its comparison to two highly promiscuous AGMEs, the AG N3-acetyltransferase-IIIb (AAC-IIIb) and the AG phosphotransferase(3')-IIIa (APH). Despite having similar antibiotic selectivities, AAC-IIIb and APH catalyze different reactions and share no homology to one another. AAC-IIa and AAC-IIIb catalyze the same reaction and are very similar in both amino acid sequence and structure. However, they demonstrate strong differences in their substrate profiles and kinetic and thermodynamic properties. AAC-IIa and APH are also polar opposites in terms of ligand promiscuity but share no sequence or apparent structural homology. However, they both are highly dynamic and may even contain disordered segments and both adopt well-defined conformations when AGs are bound. Contrary to this AAC-IIIb maintains a well-defined structure even in apo form. Data presented herein suggest that the antibiotic promiscuity of AGMEs may be determined neither by the flexibility of the protein nor the size of the active site cavity alone but strongly modulated or controlled by the effects of the cosubstrate on the dynamic and thermodynamic properties of the enzyme.
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Affiliation(s)
- Adrianne L Norris
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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24
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Ramirez MS, Nikolaidis N, Tolmasky ME. Rise and dissemination of aminoglycoside resistance: the aac(6')-Ib paradigm. Front Microbiol 2013; 4:121. [PMID: 23730301 PMCID: PMC3656343 DOI: 10.3389/fmicb.2013.00121] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 04/29/2013] [Indexed: 11/21/2022] Open
Abstract
Enzymatic modification is a prevalent mechanism by which bacteria defeat the action of antibiotics. Aminoglycosides are often inactivated by aminoglycoside modifying enzymes encoded by genes present in the chromosome, plasmids, and other genetic elements. The AAC(6′)-Ib (aminoglycoside 6′-N-acetyltransferase type Ib) is an enzyme of clinical importance found in a wide variety of gram-negative pathogens. The AAC(6′)-Ib enzyme is of interest not only because of his ubiquity but also because of other characteristics, it presents significant microheterogeneity at the N-termini and the aac(6′)-Ib gene is often present in integrons, transposons, plasmids, genomic islands, and other genetic structures. Excluding the highly heterogeneous N-termini, there are 45 non-identical AAC(6′)-Ib related entries in the NCBI database, 32 of which have identical name in spite of not having identical amino acid sequence. While some variants conserved similar properties, others show dramatic differences in specificity, including the case of AAC(6′)-Ib-cr that mediates acetylation of ciprofloxacin representing a rare case where a resistance enzyme acquires the ability to utilize an antibiotic of a different class as substrate. Efforts to utilize antisense technologies to turn off expression of the gene or to identify enzymatic inhibitors to induce phenotypic conversion to susceptibility are under way.
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Affiliation(s)
- María S Ramirez
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton, CA, USA
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25
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Zhang W, Chen Y, Liang Q, Li H, Jin H, Zhang L, Meng X, Li Z. Design, Synthesis, and Antibacterial Activities of Conformationally Constrained Kanamycin A Derivatives. J Org Chem 2012; 78:400-9. [DOI: 10.1021/jo302247x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wenxuan Zhang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Ying Chen
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Qingzhao Liang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Hui Li
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Hongwei Jin
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Liangren Zhang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xiangbao Meng
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Zhongjun Li
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
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26
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Dorfmueller HC, Fang W, Rao FV, Blair DE, Attrill H, van Aalten DMF. Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase 1. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1019-29. [PMID: 22868768 PMCID: PMC3413214 DOI: 10.1107/s0907444912019592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 05/02/2012] [Indexed: 01/31/2023]
Abstract
Glucosamine-6-phosphate N-acetyltransferase is an essential enzyme of the eukaryotic UDP-GlcNAc biosynthetic pathway. A crystal structure at 1.55 Å resolution revealed a highly unusual covalent product complex and biochemical studies investigated the function of a fully conserved active-site cysteine. Glucosamine-6-phosphate N-acetyltransferase 1 (GNA1) produces GlcNAc-6-phosphate from GlcN-6-phosphate and acetyl coenzyme A. Early mercury-labelling experiments implicated a conserved cysteine in the reaction mechanism, whereas recent structural data appear to support a mechanism in which this cysteine plays no role. Here, two crystal structures of Caenorhabditis elegans GNA1 are reported, revealing an unusual covalent complex between this cysteine and the coenzyme A product. Mass-spectrometric and reduction studies showed that this inactive covalent complex can be reactivated through reduction, yet mutagenesis of the cysteine supports a previously reported bi-bi mechanism. The data unify the apparently contradictory earlier reports on the role of a cysteine in the GNA1 active site.
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Affiliation(s)
- Helge C Dorfmueller
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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27
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Vong K, Auclair K. Understanding and overcoming aminoglycoside resistance caused by N-6'-acetyltransferase. MEDCHEMCOMM 2012; 3:397-407. [PMID: 28018574 PMCID: PMC5179255 DOI: 10.1039/c2md00253a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminoglycosides occupy a special niche amongst antibiotics in part because of their broad spectrum of action. Bacterial resistance is however menacing to render these drugs obsolete. A significant amount of work has been devoted to understand and overcome aminoglycoside resistance. This mini-review will discuss aminoglycoside-modifying enzymes (AMEs), with a special emphasis on the efforts to comprehend and block resistance caused by aminoglycoside 6'-N-acetyltransferase (AAC(6')).
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Affiliation(s)
- Kenward Vong
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
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28
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Vong K, Tam IS, Yan X, Auclair K. Inhibitors of aminoglycoside resistance activated in cells. ACS Chem Biol 2012; 7:470-5. [PMID: 22217014 DOI: 10.1021/cb200366u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The most common mechanism of resistance to aminoglycoside antibiotics entails bacterial expression of drug-metabolizing enzymes, such as the clinically widespread aminoglycoside N-6'-acetyltransferase (AAC(6')). Aminoglycoside-CoA bisubstrates are highly potent AAC(6') inhibitors; however, their inability to penetrate cells precludes in vivo studies. Some truncated bisubstrates are known to cross cell membranes, yet their activities against AAC(6') are in the micromolar range at best. We report here the synthesis and biological activity of aminoglycoside-pantetheine derivatives that, although devoid of AAC(6') inhibitory activity, can potentiate the antibacterial activity of kanamycin A against an aminoglycoside-resistant strain of Enterococcus faecium. Biological studies demonstrate that these molecules are potentially extended to their corresponding full-length bisubstrates by enzymes of the coenzyme A biosynthetic pathway. This work provides a proof-of-concept for the utility of prodrug compounds activated by enzymes of the coenzyme A biosynthetic pathway, to resensitize resistant strains of bacteria to aminoglycoside antibiotics.
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Affiliation(s)
- Kenward Vong
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Ingrid S. Tam
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Xuxu Yan
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
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29
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Matesanz R, Diaz JF, Corzana F, Santana AG, Bastida A, Asensio JL. Multiple keys for a single lock: the unusual structural plasticity of the nucleotidyltransferase (4')/kanamycin complex. Chemistry 2012; 18:2875-89. [PMID: 22298309 DOI: 10.1002/chem.201101888] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 12/05/2011] [Indexed: 11/09/2022]
Abstract
The most common mode of bacterial resistance to aminoglycoside antibiotics is the enzyme-catalysed chemical modification of the drug. Over the last two decades, significant efforts in medicinal chemistry have been focused on the design of non- inactivable antibiotics. Unfortunately, this strategy has met with limited success on account of the remarkably wide substrate specificity of aminoglycoside-modifying enzymes. To understand the mechanisms behind substrate promiscuity, we have performed a comprehensive experimental and theoretical analysis of the molecular-recognition processes that lead to antibiotic inactivation by Staphylococcus aureus nucleotidyltransferase 4'(ANT(4')), a clinically relevant protein. According to our results, the ability of this enzyme to inactivate structurally diverse polycationic molecules relies on three specific features of the catalytic region. First, the dominant role of electrostatics in aminoglycoside recognition, in combination with the significant extension of the enzyme anionic regions, confers to the protein/antibiotic complex a highly dynamic character. The motion deduced for the bound antibiotic seem to be essential for the enzyme action and probably provide a mechanism to explore alternative drug inactivation modes. Second, the nucleotide recognition is exclusively mediated by the inorganic fragment. In fact, even inorganic triphosphate can be employed as a substrate. Third, ANT(4') seems to be equipped with a duplicated basic catalyst that is able to promote drug inactivation through different reactive geometries. This particular combination of features explains the enzyme versatility and renders the design of non-inactivable derivatives a challenging task.
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Affiliation(s)
- Ruth Matesanz
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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30
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Szychowski J, Kondo J, Zahr O, Auclair K, Westhof E, Hanessian S, Keillor JW. Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues. ChemMedChem 2011; 6:1961-6. [PMID: 21905229 DOI: 10.1002/cmdc.201100346] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Janek Szychowski
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, QC, H3C 3J7, Canada
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31
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Xu H, Hegde SS, Blanchard JS. Reversible acetylation and inactivation of Mycobacterium tuberculosis acetyl-CoA synthetase is dependent on cAMP. Biochemistry 2011; 50:5883-92. [PMID: 21627103 DOI: 10.1021/bi200156t] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recent proteomics studies have revealed that protein acetylation is an abundant and evolutionarily conserved post-translational modification from prokaryotes to eukaryotes. Although an astonishing number of acetylated proteins have been identified in those studies, the acetyltransferases that target these proteins remain largely unknown. Here we characterized MSMEG_5458, one of the GCN5-related N-acetyltransferases (GNAT's) in Mycobacterium smegmatis, and show that it is a protein acetyltransferase (MsPat) that specifically acetylates the ε-amino group of a highly conserved lysine residue in acetyl-CoA synthetase (ACS) with a k(cat)/K(m) of nearly 10(4) M(-1) s(-1). This acetylation results in the inactivation of ACS activity. Lysine acetylation by MsPat is dependent on 3',5'-cyclic adenosine monophosphate (cAMP), an important second messenger, indicating that MsPat is a downstream target of the intracellular cAMP signaling pathway. To the best of our knowledge, this is the first protein acetyltransferase in mycobacteria that both is dependent on cAMP and targets a central metabolic enzyme by a specific post-translational modification. Since cAMP is synthesized by adenylate cyclases (AC's) that sense various environmental signals, we hypothesize that the acetylation and inactivation of ACS is important for mycobacteria to adjust to environmental changes. In addition, we show that Rv1151c, a sirtuin-like deacetylase in Mycobacterium tuberculosis, reactivates acetylated ACS through an NAD(+)-dependent deacetylation. Therefore, Pat and the sirtuin-like deacetylase in mycobacteria constitute a reversible acetylation system that regulates the activity of ACS.
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Affiliation(s)
- Hua Xu
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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32
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Yan X, Akinnusi TO, Larsen AT, Auclair K. Synthesis of 4'-aminopantetheine and derivatives to probe aminoglycoside N-6'-acetyltransferase. Org Biomol Chem 2011; 9:1538-46. [PMID: 21225062 PMCID: PMC3084192 DOI: 10.1039/c0ob01018a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient synthesis of 4'-aminopantetheine from commercial D-pantethine is reported. The amino group was introduced by reductive amination in order to avoid substitution at a sterically congested position. Derivatives of 4'-aminopantetheine were also prepared to evaluate the effect of O-to-N substitution on inhibitors of the resistance-causing enzyme aminoglycoside N-6'-acetyltransferase. The biological results combined with docking studies indicate that in spite of its reported unusual flexibility and ability to adopt different folds, this enzyme is highly specific for AcCoA.
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Affiliation(s)
- Xuxu Yan
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - T. Olukayode Akinnusi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - Aaron T. Larsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
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33
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Competing allosteric mechanisms modulate substrate binding in a dimeric enzyme. Nat Struct Mol Biol 2011; 18:288-94. [PMID: 21278754 DOI: 10.1038/nsmb.1978] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/16/2010] [Indexed: 11/08/2022]
Abstract
Allostery has been studied for many decades, yet it remains challenging to determine experimentally how it occurs at a molecular level. We have developed an approach combining isothermal titration calorimetry, circular dichroism and nuclear magnetic resonance spectroscopy to quantify allostery in terms of protein thermodynamics, structure and dynamics. This strategy was applied to study the interaction between aminoglycoside N-(6')-acetyltransferase-Ii and one of its substrates, acetyl coenzyme A. It was found that homotropic allostery between the two active sites of the homodimeric enzyme is modulated by opposing mechanisms. One follows a classical Koshland-Némethy-Filmer (KNF) paradigm, whereas the other follows a recently proposed mechanism in which partial unfolding of the subunits is coupled to ligand binding. Competition between folding, binding and conformational changes represents a new way to govern energetic communication between binding sites.
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34
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Shaul P, Green KD, Rutenberg R, Kramer M, Berkov-Zrihen Y, Breiner-Goldstein E, Garneau-Tsodikova S, Fridman M. Assessment of 6′- and 6′′′-N-acylation of aminoglycosides as a strategy to overcome bacterial resistance. Org Biomol Chem 2011; 9:4057-63. [DOI: 10.1039/c0ob01133a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Rational design and synthesis of potent aminoglycoside antibiotics against resistant bacterial strains. Bioorg Med Chem 2011; 19:30-40. [DOI: 10.1016/j.bmc.2010.11.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 11/27/2010] [Accepted: 11/30/2010] [Indexed: 11/20/2022]
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36
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Abstract
Aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. Unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. In some cases the levels of resistance reached the point that rendered them virtually useless. Among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. Aminoglycoside modifying enzymes catalyze the modification at different -OH or -NH₂ groups of the 2-deoxystreptamine nucleus or the sugar moieties and can be nucleotidyltransferases, phosphotransferases, or acetyltransferases. The number of aminoglycoside modifying enzymes identified to date as well as the genetic environments where the coding genes are located is impressive and there is virtually no bacteria that is unable to support enzymatic resistance to aminoglycosides. Aside from the development of new aminoglycosides refractory to as many as possible modifying enzymes there are currently two main strategies being pursued to overcome the action of aminoglycoside modifying enzymes. Their successful development would extend the useful life of existing antibiotics that have proven effective in the treatment of infections. These strategies consist of the development of inhibitors of the enzymatic action or of the expression of the modifying enzymes.
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37
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Vacas T, Corzana F, Jiménez-Osés G, González C, Gómez AM, Bastida A, Revuelta J, Asensio JL. Role of Aromatic Rings in the Molecular Recognition of Aminoglycoside Antibiotics: Implications for Drug Design. J Am Chem Soc 2010; 132:12074-90. [DOI: 10.1021/ja1046439] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatiana Vacas
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Francisco Corzana
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Carlos González
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Julia Revuelta
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
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38
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Revuelta J, Corzana F, Bastida A, Asensio J. The Unusual Nucleotide Recognition Properties of the Resistance Enzyme ANT(4′): Inorganic Tri/Polyphosphate as a Substrate for Aminoglycoside Inactivation. Chemistry 2010; 16:8635-40. [DOI: 10.1002/chem.201000641] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Houghton JL, Green KD, Chen W, Garneau-Tsodikova S. The future of aminoglycosides: the end or renaissance? Chembiochem 2010; 11:880-902. [PMID: 20397253 DOI: 10.1002/cbic.200900779] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 11/05/2022]
Abstract
Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.
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Affiliation(s)
- Jacob L Houghton
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
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40
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Le Calvez PB, Scott CJ, Migaud ME. Multisubstrate adduct inhibitors: drug design and biological tools. J Enzyme Inhib Med Chem 2010; 24:1291-318. [PMID: 19912064 DOI: 10.3109/14756360902843809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In drug discovery, different methods exist to create new inhibitors possessing satisfactory biological activity. The multisubstrate adduct inhibitor (MAI) approach is one of these methods, which consists of a covalent combination between analogs of the substrate and the cofactor or of the multiple substrates used by the target enzyme. Adopted as the first line of investigation for many enzymes, this method has brought insights into the enzymatic mechanism, structure, and inhibitory requirements. In this review, the MAI approach, applied to different classes of enzyme, is reported from the point of view of biological activity.
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41
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Gao F, Yan X, Auclair K. Synthesis of a phosphonate-linked aminoglycoside-coenzyme a bisubstrate and use in mechanistic studies of an enzyme involved in aminoglycoside resistance. Chemistry 2009; 15:2064-70. [PMID: 19152351 DOI: 10.1002/chem.200802172] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Just five steps! The synthesis of a phosphonate-linked aminoglycoside-coenzyme A derivative (see scheme) that includes a Michael addition in water has been realized in just five steps. Aminoglycoside N-6'-acetyltransferases (AAC(6')s) are important determinants of antibiotic resistance. A good mechanistic understanding of these enzymes is essential to overcome aminoglycoside resistance. We have previously reported the synthesis of amide- and sulfonamide-linked aminoglycoside-coenzyme A conjugates, which were useful mechanistic and structural probes of AAC(6')s. We report here the synthesis of a phosphonate-linked aminoglycoside-coenzyme A variant, which is expected to be a superior mimic of the tetrahedral intermediate proposed for catalysis by AAC(6')s. This synthetic target is especially challenging for a number of reasons, including the presence of multiple functional groups, the water solubility of both starting materials, and incompatibility of P(III) chemistry with water. We have overcome these challenges by adding the expensive coenzyme A in the last step by means of an elegant Michael-type addition onto a vinylphosphonate in water. Overall, a single protection step was needed. The decreased inhibitory potency of this bisubstrate compared to that of the amide-linked analogue suggests that Enterococcus faecium AAC(6')-Ii may not stabilize the proposed tetrahedral intermediate, and may act mainly through proximity catalysis.
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Affiliation(s)
- Feng Gao
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada
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42
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Wu J, Xie N, Wu Z, Zhang Y, Zheng YG. Bisubstrate Inhibitors of the MYST HATs Esa1 and Tip60. Bioorg Med Chem 2008; 17:1381-6. [PMID: 19114310 DOI: 10.1016/j.bmc.2008.12.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2008] [Revised: 11/30/2008] [Accepted: 12/07/2008] [Indexed: 01/03/2023]
Abstract
Esa1 (essential Sas2-related acetyltransferase 1) and Tip60 (HIV-1 TAT-interactive protein, 60 kDa) are key members of the MYST family of histone acetyltransferases (HATs) and play important functions in many cellular processes. In this work, we designed, synthesized and evaluated a series of substrate-based analogs for the inhibition of Esa1 and Tip60. The structures of these analogs feature that coenzyme A is covalently linked to the side chain amino group of the acetyl lysine residues in the histone peptide substrates. These bisubstrate analogs exhibit stronger potency in the inhibition of Esa1 and Tip60 compared to the small molecules curcumin and anacardic acid. In particular, H4K16CoA was tested as one of the most potent inhibitors for both Esa1 and Tip60. These substrate-based analog inhibitors will be useful mechanistic tools for analyzing biochemical mechanisms of Esa1 and Tip60, defining their functional roles in particular biological pathways, and facilitating protein crystallization and structural determination.
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Affiliation(s)
- Jiang Wu
- Department of Chemistry, Georgia State University, PO Box 4098, Atlanta, GA 30302, USA
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43
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Gao F, Yan X, Zahr O, Larsen A, Vong K, Auclair K. Synthesis and use of sulfonamide-, sulfoxide-, or sulfone-containing aminoglycoside-CoA bisubstrates as mechanistic probes for aminoglycoside N-6'-acetyltransferase. Bioorg Med Chem Lett 2008; 18:5518-22. [PMID: 18805003 PMCID: PMC3084191 DOI: 10.1016/j.bmcl.2008.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
Aminoglycoside-coenzyme A conjugates are challenging synthetic targets because of the wealth of functional groups and high polarity of the starting materials. We previously reported a one-pot synthesis of amide-linked aminoglycoside-CoA bisubstrates. These molecules are nanomolar inhibitors of aminoglycoside N-6'-acetyltransferase Ii (AAC(6')-Ii), an important enzyme involved in bacterial resistance to aminoglycoside antibiotics. We report here the synthesis and biological activity of five new aminoglycoside-CoA bisubstrates containing sulfonamide, sulfoxide, or sulfone groups. Interestingly, the sulfonamide-linked bisubstrate, which was expected to best mimic the tetrahedral intermediate, does not show improved inhibition when compared with amide-linked bisubstrates. On the other hand, most of the sulfone- and sulfoxide-containing bisubstrates prepared are nanomolar inhibitors of AAC(6')-Ii.
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Affiliation(s)
| | | | - Omar Zahr
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Aaron Larsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Kenward Vong
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
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44
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Lombès T, Bégis G, Maurice F, Turcaud S, Lecourt T, Dardel F, Micouin L. NMR-guided fragment-based approach for the design of AAC(6')-Ib ligands. Chembiochem 2008; 9:1368-71. [PMID: 18464231 DOI: 10.1002/cbic.200700677] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Lombès
- Chimie Thérapeutique, UMR 8638, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
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45
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Magalhães MLB, Vetting MW, Gao F, Freiburger L, Auclair K, Blanchard JS. Kinetic and structural analysis of bisubstrate inhibition of the Salmonella enterica aminoglycoside 6'-N-acetyltransferase. Biochemistry 2007; 47:579-84. [PMID: 18095712 DOI: 10.1021/bi701957c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminoglycosides are antibacterial compounds that act by binding to the A site of the small 30S bacterial ribosomal subunit and inhibiting protein translation. Clinical resistance to aminoglycosides is generally the result of the expression of enzymes that covalently modify the antibiotic, including phosphorylation, adenylylation, and acetylation. Bisubstrate analogs for the aminoglycoside N-acetyltransferases are nanomolar inhibitors of Enterococcus faecium AAC(6')-Ii. However, in the case of the Salmonella enterica aac(6')-Iy-encoded aminoglycoside N-acetyltransferase, we demonstrate that a series of bisubstrate analogs are only micromolar inhibitors. In contrast to studies with AAC(6')-Ii, the inhibition constants toward AAC(6')-Iy are essentially independent of both the identity of the aminoglycoside component of the bisubstrate and the number of carbon atoms that are used to link the CoA and aminoglycoside components. The patterns of inhibition suggest that the CoA portion of the bisubstrate analog can bind to the enzyme-aminoglycoside substrate complex and that the aminoglycoside portion can bind to the enzyme-CoA product complex. However, at the high concentrations of bisubstrate analog used in crystallization experiments, we could crystallize and solve the three-dimensional structure of the enzyme-bisubstrate complex. The structure reveals that both the CoA and aminoglycoside portions bind in essentially the same positions as those previously observed for the enzyme-CoA-ribostamycin complex, with only a modest adjustment to accommodate the "linker". These results are compared to previous studies of the interaction of similar bisubstrate analogs with other aminoglycoside N-acetyltransferases.
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Affiliation(s)
- Maria L B Magalhães
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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46
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Hegde SS, Chandler J, Vetting MW, Yu M, Blanchard JS. Mechanistic and structural analysis of human spermidine/spermine N1-acetyltransferase. Biochemistry 2007; 46:7187-95. [PMID: 17516632 PMCID: PMC2518666 DOI: 10.1021/bi700256z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N1-acetylation of spermidine and spermine by spermidine/spermine acetyltransferase (SSAT) is a crucial step in the regulation of the cellular polyamine levels in eukaryotic cells. Altered polyamine levels are associated with a variety of cancers as well as other diseases, and key enzymes in the polyamine pathway, including SSAT, are being explored as potential therapeutic drug targets. We have expressed and purified human SSAT in Escherichia coli and characterized its kinetic and chemical mechanism. Initial velocity and inhibition studies support a random sequential mechanism for the enzyme. The bisubstrate analogue, N1-spermine-acetyl-coenzyme A, exhibited linear, competitive inhibition against both substrates with a true Ki of 6 nM. The pH-activity profile was bell-shaped, depending on the ionization state of two groups exhibiting apparent pKa values of 7.27 and 8.87. The three-dimensional crystal structure of SSAT with bound bisubstrate inhibitor was determined at 2.3 A resolution. The structure of the SSAT-spermine-acetyl-coenzyme A complex suggested that Tyr140 acts as general acid and Glu92, through one or more water molecules, acts as the general base during catalysis. On the basis of kinetic properties, pH dependence, and structural information, we propose an acid/base-assisted reaction catalyzed by SSAT, involving a ternary complex.
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Affiliation(s)
- Subray S. Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | | | - Matthew W. Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Michael Yu
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - John S. Blanchard
- *Corresponding author: phone: (718) 430-3096; fax: (718) 430-8565 E-mail:
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47
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Yan X, Gao F, Yotphan S, Bakirtzian P, Auclair K. The use of aminoglycoside derivatives to study the mechanism of aminoglycoside 6'-N-acetyltransferase and the role of 6'-NH2 in antibacterial activity. Bioorg Med Chem 2007; 15:2944-51. [PMID: 17317190 PMCID: PMC5173354 DOI: 10.1016/j.bmc.2007.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 01/30/2007] [Accepted: 02/08/2007] [Indexed: 11/20/2022]
Abstract
Aminoglycoside antibiotics act by binding to 16S rRNA. Resistance to these antibiotics occurs via drug modifications by enzymes such as aminoglycoside 6'-N-acetyltransferases (AAC(6')s). We report here the regioselective and efficient synthesis of N-6'-acylated aminoglycosides and their use as probes to study AAC(6')-Ii and aminoglycoside-RNA complexes. Our results emphasize the central role of N-6' nucleophilicity for transformation by AAC(6')-Ii and the importance of hydrogen bonding between 6'-NH(2) and 16S rRNA for antibacterial activity.
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Affiliation(s)
- Xuxu Yan
- Department of Chemistry McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Feng Gao
- Department of Chemistry McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Sirilata Yotphan
- Department of Chemistry McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Parseh Bakirtzian
- Department of Chemistry McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Karine Auclair
- Department of Chemistry McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
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48
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Umehara S, Pourmand N, Webb CD, Davis RW, Yasuda K, Karhanek M. Current rectification with poly-l-lysine-coated quartz nanopipettes. NANO LETTERS 2006; 6:2486-92. [PMID: 17090078 PMCID: PMC2948113 DOI: 10.1021/nl061681k] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ion current rectification with quartz nanopipette electrodes was investigated through the control of the surface charge. The presence and absence of a positively charged poly-l-lysine (PLL) coating resulted in the rectified current with opposite polarity. The results agreed with the theories developed for current-rectifying conical nanopores, suggesting the similar underlying mechanism among asymmetric nanostructure in general. This surface condition dependence can be used as the fundamental principle of multi-purpose real-time in vivo biosensors.
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Affiliation(s)
- Senkei Umehara
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 California Avenue, Palo Alto, California 94304
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902 Japan
| | - Nader Pourmand
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 California Avenue, Palo Alto, California 94304
| | - Chris D. Webb
- Stanford University School of Medicine, Stanford University, 855 California Avenue, Palo Alto, California 94304
| | - Ronald W. Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 California Avenue, Palo Alto, California 94304
| | - Kenji Yasuda
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 California Avenue, Palo Alto, California 94304
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902 Japan
| | - Miloslav Karhanek
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 855 California Avenue, Palo Alto, California 94304
- Corresponding author. . Tel: +1 650 812 1960. Fax: +1 650 812 1975
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Rodolfa KT, Bruckbauer A, Zhou D, Schevchuk AI, Korchev YE, Klenerman D. Nanoscale pipetting for controlled chemistry in small arrayed water droplets using a double-barrel pipet. NANO LETTERS 2006; 6:252-7. [PMID: 16464045 DOI: 10.1021/nl052215i] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We present a new methodology which provides for the miniaturization of one of the most common tools in use in chemistry and biology laboratories today-the micropipet. We have used glass-fabricated double-barrel nanopipets to controllably produce arrayed water droplets with volumes as small as a few attoliters under an organic layer. We have addressed individual droplets and added controlled amounts of either additional volume or reagents from one of the barrels of the pipet. We demonstrate that this method can be used for miniaturized cell-free protein expression.
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Affiliation(s)
- Kit T Rodolfa
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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