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Xiao J, Chen C, Fu Z, Wang S, Luo F. Assessment of the Safety and Probiotic Properties of Enterococcus faecium B13 Isolated from Fermented Chili. Microorganisms 2024; 12:994. [PMID: 38792822 PMCID: PMC11123876 DOI: 10.3390/microorganisms12050994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety of B13 were evaluated at the genetic and phenotype levels in vitro and then confirmed in vivo. The genome of B13 contains one chromosome and two plasmids. The average nucleotide identity indicated that B13 was most closely related to the fermentation-plant-derived strain. The strain does not carry the major virulence genes of the clinical E. faecium strains but contains aac(6')-Ii, ant (6)-Ia, msrC genes. The strain had a higher tolerance to acid at pH 3.0, 4.0, and 0.3% bile salt and a 32.83% free radical DPPH clearance rate. It can adhere to Caco-2 cells and reduce the adhesion of E. coli to Caco-2 cells. The safety assessment revealed that the strain showed no hemolysis and did not exhibit gelatinase, ornithine decarboxylase, lysine decarboxylase, or tryptophanase activity. It was sensitive to twelve antibiotics but was resistant to erythromycin, rifampicin, tetracycline, doxycycline, and minocycline. Experiments in vivo have shown that B13 can be located in the ileum and colon and has no adverse effects on experiment animals. After 28 days of feeding, B13 did not remarkable change the α-diversity of the gut flora or increase the virulence genes. Our study demonstrated that E. faecium B13 may be used as a probiotic candidate.
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Affiliation(s)
- Jingmin Xiao
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Cai Chen
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Zhuxian Fu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; (J.X.); (C.C.); (Z.F.)
| | - Shumin Wang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China;
| | - Fan Luo
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China;
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2
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Denissen J, Reyneke B, Barnard T, Khan S, Khan W. Risk assessment of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa in environmental water sources: Development of surrogate models for antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166217. [PMID: 37604372 DOI: 10.1016/j.scitotenv.2023.166217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023]
Abstract
The presence of Enterococcus faecium (E. faecium), Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), and the aminoglycoside resistance genes, aac(6')-Ib and aac(6')-aph(2″), was investigated in environmental water sources obtained from informal settlements in the Western Cape (South Africa). Using ethidium monoazide bromide quantitative polymerase chain reaction (EMA-qPCR) analysis, E. faecium, K. pneumoniae, and P. aeruginosa were detected in 88.9 %, 100 %, and 93.3 % of the samples (n = 45), respectively, with a significantly higher mean concentration recorded for K. pneumoniae (7.83 × 104 cells/100 mL) over the sampling period. The aac(6')-Ib gene was detected in 95.6 % (43/45) of the environmental water samples [mean concentration of 7.07 × 106 gene copies (GC)/100 mL], while the aac(6')-aph(2″) gene was detected in 100 % (n = 45) of the samples [mean concentration of 6.68 × 105 GC/100 mL]. Quantitative microbial risk assessment (QMRA) subsequently indicated that the risks posed by K. pneumoniae and P. aeruginosa were linked to intentional drinking, washing/bathing, cleaning of the home, and swimming, in the samples collected from the various sampling sites. Surrogate risk assessment models were then designed and applied for Gram-positive [aac(6')-aph(2″) gene] and Gram-negative [aac(6')-Ib gene] pathogens that may exhibit aminoglycoside resistance. The results indicated that only the Gram-negative pathogens posed a risk (>10-4) in all the samples for cleaning of the home and intentional drinking, as well as for washing laundry by hand, garden hosing, garden work, washing/bathing, accidental consumption, and swimming at the stream and marsh sites. Thus, while environmental waters may pose a health risk of exposure to pathogenic bacteria, the results obtained indicate that screening for antibiotic resistant genes, associated with multiple genera/species, could serve as a surrogate model for estimating risks with the target group under investigation.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Tobias Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein 7305, South Africa
| | - Sehaam Khan
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein 7305, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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Xu F, Zhang X, Liu L, Ke X, Wu J, Guo Y, Tian X, Chu J. Engineering the methyltransferase through inactivation of the genK and genL leads to a significant increase of gentamicin C1a production in an industrial strain of Micromonospora echinospora 49-92S. Bioprocess Biosyst Eng 2022; 45:1693-1703. [PMID: 36029348 DOI: 10.1007/s00449-022-02774-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/06/2022] [Indexed: 05/31/2023]
Abstract
In this study, a single-component high-yielding Micromonospora echinospora strain 49-92S-KL01 was constructed by deleting methyltransferase-encoding genes genK and genL. In 5-L fermentation trials, gentamicin C1a titers in the mutant strain were 3.22-fold higher than that in the parental strain (211 U/mL vs. 50 U/mL). The glycolysis pathway and tricarboxylic acid cycle fluxes were reduced by 26.8% and 26.6%, respectively, compared to the parental strain according to the metabolic flux analysis during the stationary phase, resulting in lower levels of energy supplements required for the cellular maintenance. Meanwhile, a significant enhancement in precursor (paromamine) accumulation and availability was observed in 49-92S-KL01 compared to parental strain. These results indicate that genK and genL significantly affect the synthesis of gentamicin C1a. In addition, this study provides a more rational strategy for gentamicin C1a production.
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Affiliation(s)
- Feng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xinyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ling Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jie Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yuanxin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Wang Q, Zhu L, Yu Y, Guan H, Xu Z. Microbial Screening of Marine Natural Product Inhibitors for the 6′-Aminoglycoside Acetyltransferase 2″-Aminoglycoside Phosphotransferase [AAC(6′)-APH(2″)] Bifunctional Enzyme by Ultra-High Performance Liquid Chromatography–Mass Spectrometry (UHPLC-MS). ANAL LETT 2021. [DOI: 10.1080/00032719.2021.1903025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Qian Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yi Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhe Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Exclusive Production of Gentamicin C1a from Micromonospora purpurea by Metabolic Engineering. Antibiotics (Basel) 2019; 8:antibiotics8040267. [PMID: 31847403 PMCID: PMC6963548 DOI: 10.3390/antibiotics8040267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Gentamicin C1a is an important precursor to the synthesis of etimicin, a potent antibiotic. Wild type Micromonospora purpurea Gb1008 produces gentamicin C1a, besides four other gentamicin C components: C1, C2, C2a, and C2b. While the previously reported engineered strain M. purpurea GK1101 can produce relatively high titers of C1a by blocking the genK pathway, a small amount of undesirable C2b is still being synthesized in cells. Gene genL (orf6255) is reported to be responsible for converting C1a to C2b and C2 to C1 in Micromonospora echinospora ATCC15835. In this work, we identify the genL that is also responsible for the same methylation in Micromonospora purpurea. Based on M. purpurea GK1101, we construct a new strain with genL inactivated and show that no C2b is produced in this strain. Therefore, we successfully engineer a strain of M. purpurea that solely produces gentamicin C1a. This strain can potentially be used in the industrial production of C1a for the synthesis of etimicin.
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Takenoya M, Shimamura T, Yamanaka R, Adachi Y, Ito S, Sasaki Y, Nakamura A, Yajima S. Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus. Acta Crystallogr F Struct Biol Commun 2019; 75:599-607. [PMID: 31475927 PMCID: PMC6718145 DOI: 10.1107/s2053230x19011105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/09/2019] [Indexed: 10/14/2023] Open
Abstract
Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7''-phosphotransferase-Ia [APH(7'')-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7'' and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7'')-Ia and APH(4)-Ia, the crystal structure of APH(7'')-Ia complexed with HygB is reported. The overall structure of APH(7'')-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7'')-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7'')-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.
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Affiliation(s)
- Mihoko Takenoya
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryuji Yamanaka
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuya Adachi
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinsaku Ito
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
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7
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Zhu L, Liu R, Liu T, Zou X, Xu Z, Guan H. A novel strategy to screen inhibitors of multiple aminoglycoside-modifying enzymes with ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry. J Pharm Biomed Anal 2018; 164:520-527. [PMID: 30458385 DOI: 10.1016/j.jpba.2018.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022]
Abstract
Resistance to aminoglycoside antibiotics occurs primarily as a result of aminoglycoside-modification enzymes (AMEs) that modify the antibiotics. In this work, a novel strategy to combat the effects of antibiotic resistance was developed by screening multiple AMEs inhibitors with ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF MS). The method screened inhibitors of three AMEs (AAC(6')-APH(2"), AAC(6') and APH(2")) simultaneously through measuring the acetyltransferase activity and phosphotransferase activity of AAC(6')-APH(2") enzyme in a single assay. Screening inhibitors of multiple targets could greatly improve the screening efficiency at early-stages of drug discovery. In this study, enzyme reaction conditions including cosubstrate, enzyme concentration and cosubstrate concentration were optimized. The inhibition constants (Ki) for two known inhibitors, paromomycin and quercetin, were determined to be 1.23 and 20.27 μM, respectively. The assay was further validated through the determination of a high Z' factor value of 0.73. The developed assay was applied to screen a chemical library against bifunctional AAC(6')-APH(2'') enzyme. Using this assay, two pyrimidinyl indole derivatives were found to be potent, and effective AAC(6')-APH(2'') inhibitors. The assay of exploring the selective inhibitory effect on two AAC(6')-APH(2'') active sites was further performed. Two pyrimidinyl indole derivatives were found to exhibit striking inhibitory activities on AAC(6').
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Affiliation(s)
- Li Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Ruonan Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Tangrong Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xuan Zou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhe Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266071, China.
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266071, China
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8
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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Amikacin: Uses, Resistance, and Prospects for Inhibition. Molecules 2017; 22:molecules22122267. [PMID: 29257114 PMCID: PMC5889950 DOI: 10.3390/molecules22122267] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
Aminoglycosides are a group of antibiotics used since the 1940s to primarily treat a broad spectrum of bacterial infections. The primary resistance mechanism against these antibiotics is enzymatic modification by aminoglycoside-modifying enzymes that are divided into acetyl-transferases, phosphotransferases, and nucleotidyltransferases. To overcome this problem, new semisynthetic aminoglycosides were developed in the 70s. The most widely used semisynthetic aminoglycoside is amikacin, which is refractory to most aminoglycoside modifying enzymes. Amikacin was synthesized by acylation with the l-(-)-γ-amino-α-hydroxybutyryl side chain at the C-1 amino group of the deoxystreptamine moiety of kanamycin A. The main amikacin resistance mechanism found in the clinics is acetylation by the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib], an enzyme coded for by a gene found in integrons, transposons, plasmids, and chromosomes of Gram-negative bacteria. Numerous efforts are focused on finding strategies to neutralize the action of AAC(6')-Ib and extend the useful life of amikacin. Small molecules as well as complexes ionophore-Zn+2 or Cu+2 were found to inhibit the acetylation reaction and induced phenotypic conversion to susceptibility in bacteria harboring the aac(6')-Ib gene. A new semisynthetic aminoglycoside, plazomicin, is in advance stage of development and will contribute to renewed interest in this kind of antibiotics.
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Ngo HX, Garneau-Tsodikova S. Flipping the Switch "On" for Aminoglycoside-Resistance Enzymes: The Mechanism Is Finally Revealed! Structure 2017; 24:1011-3. [PMID: 27387794 DOI: 10.1016/j.str.2016.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In a recent issue of Structure, Caldwell et al. (2016) determined crystal structures of APH(2″)-Ia in complex with various combinations of aminoglycosides and nucleosides, which compellingly revealed that the catalytic activity of this resistance enzyme is regulated by a conformational change of the triphosphate of GTP, a mechanism previously unknown for antibiotic kinases.
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Affiliation(s)
- Huy X Ngo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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11
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Stogios PJ, Kuhn ML, Evdokimova E, Law M, Courvalin P, Savchenko A. Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes. ACS Infect Dis 2017; 3:132-143. [PMID: 27785912 DOI: 10.1021/acsinfecdis.6b00058] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modification of aminoglycosides by N-acetyltransferases (AACs) is one of the major mechanisms of resistance to these antibiotics in human bacterial pathogens. More than 50 enzymes belonging to the AAC(6') subfamily have been identified in Gram-negative and Gram-positive clinical isolates. Our understanding of the molecular function and evolutionary origin of these resistance enzymes remains incomplete. Here we report the structural and enzymatic characterization of AAC(6')-Ig and AAC(6')-Ih from Acinetobacter spp. The crystal structure of AAC(6')-Ig in complex with tobramycin revealed a large substrate-binding cleft remaining partially unoccupied by the substrate, which is in stark contrast with the previously characterized AAC(6')-Ib enzyme. Enzymatic analysis indicated that AAC(6')-Ig and -Ih possess a broad specificity against aminoglycosides but with significantly lower turnover rates as compared to other AAC(6') enzymes. Structure- and function-informed phylogenetic analysis of AAC(6') enzymes led to identification of at least three distinct subfamilies varying in oligomeric state, active site composition, and drug recognition mode. Our data support the concept of AAC(6') functionality originating through convergent evolution from diverse Gcn5-related-N-acetyltransferase (GNAT) ancestral enzymes, with AAC(6')-Ig and -Ih representing enzymes that may still retain ancestral nonresistance functions in the cell as provided by their particular active site properties.
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Affiliation(s)
- Peter J. Stogios
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Elena Evdokimova
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Patrice Courvalin
- Institut Pasteur, Unité des Agents Antibactériens, 25 rue du Docteur Roux, 75724 Cedex 15 Paris, France
| | - Alexei Savchenko
- Department of Chemical
Engineering and Applied Chemistry, University of Toronto, 200 College
Street, Toronto, Ontario M5G 1L6, Canada
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12
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Garzan A, Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Sulfonamide-Based Inhibitors of Aminoglycoside Acetyltransferase Eis Abolish Resistance to Kanamycin in Mycobacterium tuberculosis. J Med Chem 2016; 59:10619-10628. [PMID: 27933949 DOI: 10.1021/acs.jmedchem.6b01161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A two-drug combination therapy where one drug targets an offending cell and the other targets a resistance mechanism to the first drug is a time-tested, yet underexploited approach to combat or prevent drug resistance. By high-throughput screening, we identified a sulfonamide scaffold that served as a pharmacophore to generate inhibitors of Mycobacterium tuberculosis acetyltransferase Eis, whose upregulation causes resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN) in Mycobacterium tuberculosis. Rational systematic derivatization of this scaffold to maximize Eis inhibition and abolish the Eis-mediated KAN resistance of M. tuberculosis yielded several highly potent agents. A crystal structure of Eis in complex with one of the most potent inhibitors revealed that the inhibitor bound Eis in the AG-binding pocket held by a conformationally malleable region of Eis (residues 28-37) bearing key hydrophobic residues. These Eis inhibitors are promising leads for preclinical development of innovative AG combination therapies against resistant TB.
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Affiliation(s)
- Atefeh Garzan
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Melisa J Willby
- Mycobacteriology Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States
| | - Keith D Green
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Chathurada S Gajadeera
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Oleg V Tsodikov
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - James E Posey
- Mycobacteriology Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States
| | - Sylvie Garneau-Tsodikova
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
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13
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Holbrook SYL, Garneau-Tsodikova S. Expanding Aminoglycoside Resistance Enzyme Regiospecificity by Mutation and Truncation. Biochemistry 2016; 55:5726-5737. [PMID: 27618454 DOI: 10.1021/acs.biochem.6b00770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics famous for their antibacterial activity against Gram-positive and Gram-negative bacteria, as well as mycobacteria. In the United States, the most prescribed AGs, including amikacin (AMK), gentamicin (GEN), and tobramycin (TOB), are vital components of the treatment for resistant bacterial infections. Arbekacin (ABK), a semisynthetic AG, is widely used for the treatment of resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus in Asia. However, the rapid emergence and development of bacterial resistance are limiting the clinical application of AG antibiotics. Of all bacterial resistance mechanisms against AGs, the acquisition of AG-modifying enzymes (AMEs) by bacteria is the most common. It was previously reported that a variant of a bifunctional AME, the 6'-N-AG acetyltransferase-Ie/2″-O-AG phosphotransferase-Ia [AAC(6')-Ie/APH(2″)-Ia], containing a D80G point mutation and a truncation after amino acid 240 modified ABK and AMK at a new position, the 4‴-amine, therefore displaying a change in regiospecificity. In this study, we aimed to verify the altered regiospecificity of this bifunctional enzyme by mutation and truncation for the potential of derivatizing AGs with chemoenzymatic reactions. With the three variant enzymes in this study that contained either mutation only (D80G), truncation only (1-240), or mutation and truncation (D80G-1-240), we characterized their activity by profiling their substrate promiscuity, determined their kinetics parameters, and performed mass spectrometry to determine how and where ABK and AMK were acetylated by these enzymes. We found that the three mutant enzymes possessed distinct acetylation regiospecificity compared to that of the bifunctional AAC(6')-Ie/APH(2″)-Ia enzyme and the functional AAC(6')-Ie domain [AAC(6')/APH(2″)-1-194].
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Affiliation(s)
- Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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14
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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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15
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Caldwell SJ, Huang Y, Berghuis AM. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2″)-Ia. Structure 2016; 24:935-45. [PMID: 27161980 DOI: 10.1016/j.str.2016.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 04/04/2016] [Indexed: 11/28/2022]
Abstract
APH(2″)-Ia is a widely disseminated resistance factor frequently found in clinical isolates of Staphylococcus aureus and pathogenic enterococci, where it is constitutively expressed. APH(2″)-Ia confers high-level resistance to gentamicin and related aminoglycosides through phosphorylation of the antibiotic using guanosine triphosphate (GTP) as phosphate donor. We have determined crystal structures of the APH(2″)-Ia in complex with GTP analogs, guanosine diphosphate, and aminoglycosides. These structures collectively demonstrate that aminoglycoside binding to the GTP-bound kinase drives conformational changes that bring distant regions of the protein into contact. These changes in turn drive a switch of the triphosphate cofactor from an inactive, stabilized conformation to a catalytically competent active conformation. This switch has not been previously reported for antibiotic kinases or for the structurally related eukaryotic protein kinases. This catalytic triphosphate switch presents a means by which the enzyme can curtail wasteful hydrolysis of GTP in the absence of aminoglycosides, providing an evolutionary advantage to this enzyme.
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Affiliation(s)
- Shane J Caldwell
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Yue Huang
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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16
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von Wintersdorff CJH, Wolffs PFG, Savelkoul PHM, Nijsen RRR, Lau S, Gerhold K, Hamelmann E, Penders J. The gut resistome is highly dynamic during the first months of life. Future Microbiol 2016; 11:501-10. [PMID: 27064174 DOI: 10.2217/fmb.15.154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
AIM We investigated the longitudinal development of several antibiotic resistance genes (ARGs) of the infant gut resistome during the first months after birth. MATERIALS & METHODS Fecal samples from 120 infants collected at the ages of 5, 13 and 31 weeks were analyzed and subjected to qPCR for the detection of several ARGs. RESULTS The prevalence of ARGs significantly increased for ermB, tetM and tetQ, while it decreased for aac(6')-aph(2'). Birth mode and breastfeeding significantly affected tetQ prevalence. Correlations to bacterial taxa suggest that fluctuations in some ARGs are (partly) attributed to shifts in bacteroides colonization rates. CONCLUSION Acquisition of ARGs in the gut microbiota occurs shortly after birth and resistome composition fluctuates over the course of several months, reflecting changes in microbial community structure.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam
| | - Rianne R R Nijsen
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Susanne Lau
- Department of Pediatrics, Pneumology & Immunology, Charité Medical University Berlin, Berlin, Germany
| | - Kerstin Gerhold
- Department of Pediatrics & Child Health, Section of Pediatric Rheumatology, Winnipeg, Manitoba, Canada
| | - Eckard Hamelmann
- Children's Hospital, Ev. Hospital Bielefeld (EvKB), Bielefeld, Germany
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
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17
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Jin Y, Watkins D, Degtyareva NN, Green KD, Spano MN, Garneau-Tsodikova S, Arya DP. Arginine-linked neomycin B dimers: synthesis, rRNA binding, and resistance enzyme activity. MEDCHEMCOMM 2016; 7:164-169. [PMID: 26811742 PMCID: PMC4722958 DOI: 10.1039/c5md00427f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The nucleotides comprising the ribosomal decoding center are highly conserved, as they are important for maintaining translational fidelity. The bacterial A-site has a small base variation as compared with the human analogue, allowing aminoglycoside (AG) antibiotics to selectively bind within this region of the ribosome and negatively affect microbial protein synthesis. Here, by using a fluorescence displacement screening assay, we demonstrate that neomycin B (NEO) dimers connected by L-arginine-containing linkers of varying length and composition bind with higher affinity to model A-site RNAs compared to NEO, with IC50 values ranging from ~40-70 nM, and that a certain range of linker lengths demonstrates a clear preference for the bacterial A-site RNA over the human analogue. Furthermore, AG-modifying enzymes (AMEs), such as AG O-phosphotransferases, which are responsible for conferring antibiotic resistance in many types of infectious bacteria, demonstrate markedly reduced activity against several of the L-arginine-linked NEO dimers in vitro. The antimicrobial activity of these dimers against several bacterial strains is weaker than that of the parent NEO.
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Affiliation(s)
- Yi Jin
- Clemson University, Department of Chemistry, Clemson, SC, 29634, USA
| | | | | | - Keith D. Green
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, 40536-0596, 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, 40536-0596, USA. Fax: 859-257-7585; Tel: 859-218-1686
| | - Dev P. Arya
- Clemson University, Department of Chemistry, Clemson, SC, 29634, USA
- NUBAD, LLC, Greenville, SC, 29605, USA
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18
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Emerging resistance to aminoglycosides in lactic acid bacteria of food origin—an impending menace. Appl Microbiol Biotechnol 2015; 100:1137-1151. [DOI: 10.1007/s00253-015-7184-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023]
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19
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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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20
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Garneau-Tsodikova S, Labby KJ. Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives. MEDCHEMCOMM 2015; 7:11-27. [PMID: 26877861 DOI: 10.1039/c5md00344j] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.
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Affiliation(s)
- Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. ; Tel: 859-218-1686
| | - Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI, USA. ; Tel: 608-363-2273
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21
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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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22
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Jaimee G, Halami PM. High level aminoglycoside resistance in Enterococcus, Pediococcus and Lactobacillus species from farm animals and commercial meat products. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1086-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Smith CA, Toth M, Weiss TM, Frase H, Vakulenko SB. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2754-64. [PMID: 25286858 PMCID: PMC4188014 DOI: 10.1107/s1399004714017635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/31/2014] [Indexed: 11/11/2022]
Abstract
Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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24
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Delgado-Valverde M, Sojo-Dorado J, Pascual A, Rodríguez-Baño J. Clinical management of infections caused by multidrug-resistant Enterobacteriaceae. Ther Adv Infect Dis 2014; 1:49-69. [PMID: 25165544 DOI: 10.1177/2049936113476284] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Enterobacteriaceae showing resistance to cephalosporins due to extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC enzymes, and those producing carbapenemases have spread worldwide during the last decades. Many of these isolates are also resistant to other first-line agents such as fluoroquinolones or aminoglycosides, leaving few available options for therapy. Thus, older drugs such as colistin and fosfomycin are being increasingly used. Infections caused by these bacteria are associated with increased morbidity and mortality compared with those caused by their susceptible counterparts. Most of the evidence supporting the present recommendations is from in vitro data, animal studies, and observational studies. While carbapenems are considered the drugs of choice for ESBL and AmpC producers, recent data suggest that certain alternatives may be suitable for some types of infections. Combined therapy seems superior to monotherapy in the treatment of invasive infections caused by carbapenemase-producing Enterobacteriaceae. Optimization of dosage according to pharmacokinetics/pharmacodynamics data is important for the treatment of infections caused by isolates with borderline minimum inhibitory concentration due to low-level resistance mechanisms. The increasing frequency and the rapid spread of multidrug resistance among the Enterobacteriaceae is a true and complex public health problem.
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Affiliation(s)
- Mercedes Delgado-Valverde
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, Seville, Spain
| | - Jesús Sojo-Dorado
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, Seville, Spain
| | - Alvaro Pascual
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, and Department of Microbiology, University of Seville, Seville, Spain
| | - Jesús Rodríguez-Baño
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, Avda Dr Fedriani 3, 41009 Seville, Spain
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25
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Abstract
The human food chain begins with upwards of 1,000 species of bacteria that inhabit the intestinal tracts of poultry and livestock. These intestinal denizens are responsible for the health and safety of a major protein source for humans. The use of antibiotics to treat animal diseases was followed by the surprising discovery that antibiotics enhanced food animal growth, and both led to six decades of antibiotic use that has shaped food animal management practices. Perhaps the greatest impact of antibiotic feeding in food animals has been as a selective force in the evolution of their intestinal bacteria, particularly by increasing the prevalence and diversity of antibiotic resistance genes. Future antibiotic use will likely be limited to prudent applications in both human and veterinary medicine. Improved knowledge of antibiotic effects, particularly of growth-promoting antibiotics, will help overcome the challenges of managing animal health and food safety.
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Affiliation(s)
- Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa 50010; ,
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26
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Smith CA, Toth M, Bhattacharya M, Frase H, Vakulenko SB. Structure of the phosphotransferase domain of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1561-71. [PMID: 24914967 PMCID: PMC4051501 DOI: 10.1107/s1399004714005331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/07/2014] [Indexed: 01/04/2023]
Abstract
The bifunctional acetyltransferase(6')-Ie-phosphotransferase(2'')-Ia [AAC(6')-Ie-APH(2'')-Ia] is the most important aminoglycoside-resistance enzyme in Gram-positive bacteria, conferring resistance to almost all known aminoglycoside antibiotics in clinical use. Owing to its importance, this enzyme has been the focus of intensive research since its isolation in the mid-1980s but, despite much effort, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. The structure of the Mg2GDP complex of the APH(2'')-Ia domain of the bifunctional enzyme has now been determined at 2.3 Å resolution. The structure of APH(2'')-Ia is reminiscent of the structures of other aminoglycoside phosphotransferases, having a two-domain architecture with the nucleotide-binding site located at the junction of the two domains. Unlike the previously characterized APH(2'')-IIa and APH(2'')-IVa enzymes, which are capable of utilizing both ATP and GTP as the phosphate donors, APH(2'')-Ia uses GTP exclusively in the phosphorylation of the aminoglycoside antibiotics, and in this regard closely resembles the GTP-dependent APH(2'')-IIIa enzyme. In APH(2'')-Ia this GTP selectivity is governed by the presence of a `gatekeeper' residue, Tyr100, the side chain of which projects into the active site and effectively blocks access to the adenine-binding template. Mutation of this tyrosine residue to a less bulky phenylalanine provides better access for ATP to the NTP-binding template and converts APH(2'')-Ia into a dual-specificity enzyme.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Monolekha Bhattacharya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Green KD, Garneau-Tsodikova S. Domain dissection and characterization of the aminoglycoside resistance enzyme ANT(3″)-Ii/AAC(6')-IId from Serratia marcescens. Biochimie 2013; 95:1319-25. [PMID: 23485681 DOI: 10.1016/j.biochi.2013.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/18/2013] [Indexed: 01/19/2023]
Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics whose constant use and presence in growth environments has led bacteria to develop resistance mechanisms to aid in their survival. A common mechanism of resistance to AGs is their chemical modification (nucleotidylation, phosphorylation, or acetylation) by AG-modifying enzymes (AMEs). Through evolution, fusion of two AME-encoding genes has resulted in bifunctional enzymes with broader spectrum of activity. Serratia marcescens, a human enteropathogen, contains such a bifunctional enzyme, ANT(3″)-Ii/AAC(6')-IId. To gain insight into the role, effect, and importance of the union of ANT(3″)-Ii and AAC(6')-IId in this bifunctional enzyme, we separated the two domains and compared their activity to that of the full-length enzyme. We performed a thorough comparison of the substrate and cosubstrate profiles as well as kinetic characterization of the bifunctional ANT(3″)-Ii/AAC(6')-IId and its individually expressed components.
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Affiliation(s)
- Keith D Green
- Life Sciences Institute, 210 Washtenaw Ave, University of Michigan, Ann Arbor, MI 48109-2216, USA
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Abstract
Aminoglycoside antibiotics were among the first antibiotics discovered and used clinically. Although they have never completely fallen out of favor, their importance has waned due to the emergence of other broad-spectrum antibiotics with fewer side effects. Today, with the dramatically increasing rate of infections caused by multidrug-resistant bacteria, focus has returned to aminoglycoside antibiotics as one of the few remaining treatment options, particularly for Gram-negative pathogens. Although the mechanisms of resistance are reasonably well understood, our knowledge about the mode of action of aminoglycosides is still far from comprehensive. In the face of emerging bacterial infections that are virtually untreatable, it is time to have a fresh look at this old class to reinvigorate the struggle against multidrug-resistant pathogens.
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Affiliation(s)
- Bernd Becker
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane,
Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane,
Queensland 4072, Australia
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29
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Frase H, Toth M, Vakulenko SB. Revisiting the nucleotide and aminoglycoside substrate specificity of the bifunctional aminoglycoside acetyltransferase(6')-Ie/aminoglycoside phosphotransferase(2'')-Ia enzyme. J Biol Chem 2012; 287:43262-9. [PMID: 23115238 DOI: 10.1074/jbc.m112.416453] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bifunctional aminoglycoside-modifying enzyme aminoglycoside acetyltransferase(6')-Ie/aminoglycoside phosphotransferase(2″)-Ia, or AAC(6')-Ie/APH(2″)-Ia, is the major source of aminoglycoside resistance in gram-positive bacterial pathogens. In previous studies, using ATP as the cosubstrate, it was reported that the APH(2″)-Ia domain of this enzyme is unique among aminoglycoside phosphotransferases, having the ability to inactivate an unusually broad spectrum of aminoglycosides, including 4,6- and 4,5-disubstituted and atypical. We recently demonstrated that GTP, and not ATP, is the preferred cosubstrate of this enzyme. We now show, using competition assays between ATP and GTP, that GTP is the exclusive phosphate donor at intracellular nucleotide levels. In light of these findings, we reevaluated the substrate profile of the phosphotransferase domain of this clinically important enzyme. Steady-state kinetic characterization using the phosphate donor GTP demonstrates that AAC(6')-Ie/APH(2″)-Ia phosphorylates 4,6-disubstituted aminoglycosides with high efficiency (k(cat)/K(m) = 10(5)-10(7) M(-1) s(-1)). Despite this proficiency, no resistance is conferred to some of these antibiotics by the enzyme in vivo. We now show that phosphorylation of 4,5-disubstituted and atypical aminoglycosides are negligible and thus these antibiotics are not substrates. Instead, these aminoglycosides tend to stimulate an intrinsic GTPase activity of the enzyme. Taken together, our data show that the bifunctional enzyme efficiently phosphorylates only 4,6-disubstituted antibiotics; however, phosphorylation does not necessarily result in bacterial resistance. Hence, the APH(2″)-Ia domain of the bifunctional AAC(6')-Ie/APH(2″)-Ia enzyme is a bona fide GTP-dependent kinase with a narrow substrate profile, including only 4,6-disubstituted aminoglycosides.
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Affiliation(s)
- Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Chaudhary M, Kesava Naidu G, Kumar S, Payasi A. Comparative antibacterial activity of a novel semisynthetic antibiotic: etimicin sulphate and other aminoglycosides. World J Microbiol Biotechnol 2012; 28:3365-71. [PMID: 22983905 DOI: 10.1007/s11274-012-1148-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022]
Abstract
Etimicin is a novel fourth generation semisynthetic aminoglycoside. It has good antimicrobial activity against both gram-positive and gram-negative bacterial infections and also against aminoglycoside resistant strains. In the present study, in vitro antibacterial activity of etimicin was determined by minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and time kill curve tests against type strains and 407 clinical isolates (obtained in a surveillance study), in comparison to other aminoglycosides. Test results revealed that etimicin has potential antimicrobial activity and MIC, MBC values for etimicin were low compared to other aminoglycosides. In MBC test etimicin has exhibited potential bactericidal effect ranging from 0.25 to 2 mg/L. The time kill-curve study further demonstrated the rapid, concentration dependent killing and comparative study showed etimicin to exhibit long and effective bactericidal activity over amikacin. The interesting fact is that most of the tested aminoglycoside resistant clinical isolates were susceptible to etimicin. In view of its potent in vitro antibacterial activity and efficacy profiles, it can be concluded that etimicin can be a potent injectable agent for the treatment of severe bacterial infections.
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Affiliation(s)
- Manu Chaudhary
- Venus Medicine Research Centre, Hill Top Industrial Estate, Bhatoli Kalan, Baddi, H.P., 173205, India.
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31
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Cosubstrate tolerance of the aminoglycoside resistance enzyme Eis from Mycobacterium tuberculosis. Antimicrob Agents Chemother 2012; 56:5831-8. [PMID: 22948873 DOI: 10.1128/aac.00932-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously demonstrated that aminoglycoside acetyltransferases (AACs) display expanded cosubstrate promiscuity. The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis is responsible for the resistance of this pathogen to kanamycin A in a large fraction of clinical isolates. Recently, we discovered that Eis is a unique AAC capable of acetylating multiple amine groups on a large pool of aminoglycoside (AG) antibiotics, an unprecedented property among AAC enzymes. Here, we report a detailed study of the acyl-coenzyme A (CoA) cosubstrate profile of Eis. We show that, in contrast to other AACs, Eis efficiently uses only 3 out of 15 tested acyl-CoA derivatives to modify a variety of AGs. We establish that for almost all acyl-CoAs, the number of sites acylated by Eis is smaller than the number of sites acetylated. We demonstrate that the order of n-propionylation of the AG neamine by Eis is the same as the order of its acetylation. We also show that the 6' position is the first to be n-propionylated on amikacin and netilmicin. By sequential acylation reactions, we show that AGs can be acetylated after the maximum possible n-propionylation of their scaffolds by Eis. The information reported herein will advance our understanding of the multiacetylation mechanism of inactivation of AGs by Eis, which is responsible for M. tuberculosis resistance to some AGs.
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32
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Caldwell SJ, Berghuis AM. Small-angle X-ray scattering analysis of the bifunctional antibiotic resistance enzyme aminoglycoside (6') acetyltransferase-ie/aminoglycoside (2'') phosphotransferase-ia reveals a rigid solution structure. Antimicrob Agents Chemother 2012; 56:1899-906. [PMID: 22290965 PMCID: PMC3318351 DOI: 10.1128/aac.06378-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 01/20/2012] [Indexed: 11/20/2022] Open
Abstract
Aminoglycoside (6') acetyltransferase-Ie/aminoglycoside (2″) phosphotransferase-Ia [AAC(6')-Ie/APH(2″)-Ia] is one of the most problematic aminoglycoside resistance factors in clinical pathogens, conferring resistance to almost every aminoglycoside antibiotic available to modern medicine. Despite 3 decades of research, our understanding of the structure of this bifunctional enzyme remains limited. We used small-angle X-ray scattering (SAXS) to model the structure of this bifunctional enzyme in solution and to study the impact of substrate binding on the enzyme. It was observed that the enzyme adopts a rigid conformation in solution, where the N-terminal AAC domain is fixed to the C-terminal APH domain and not loosely tethered. The addition of acetyl-coenzyme A, coenzyme A, GDP, guanosine 5'-[β,γ-imido]triphosphate (GMPPNP), and combinations thereof to the protein resulted in only modest changes to the radius of gyration (R(G)) of the enzyme, which were not consistent with any large changes in enzyme structure upon binding. These results imply some selective advantage to the bifunctional enzyme beyond coexpression as a single polypeptide, likely linked to an improvement in enzymatic properties. We propose that the rigid structure contributes to improved electrostatic steering of aminoglycoside substrates toward the two active sites, which may provide such an advantage.
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Affiliation(s)
| | - Albert M. Berghuis
- Department of Biochemistry
- Department of Microbiology and Immunology, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec, Canada
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Toth M, Vakulenko SB, Smith CA. Purification, crystallization and preliminary X-ray analysis of the aminoglycoside-6'-acetyltransferase AAC(6')-Im. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:472-5. [PMID: 22505423 PMCID: PMC3325823 DOI: 10.1107/s1744309112007117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 02/16/2012] [Indexed: 11/10/2022]
Abstract
Bacterial resistance to the aminoglycoside antibiotics is primarily the result of enzymatic deactivation of the drugs. The aminoglycoside N-acetyltransferases (AACs) are a large family of bacterial enzymes that are responsible for coenzyme-A-facilitated acetylation of aminoglycosides. The gene encoding one of these enzymes, AAC(6')-Im, has been cloned and the protein (comprising 178 amino-acid residues) was expressed in Escherichia coli, purified and crystallized as the kanamycin complex. Synchrotron diffraction data to approximately 2.0 Å resolution were collected from a crystal of this complex on beamline BL12-2 at SSRL (Stanford, California, USA). The crystals belonged to the hexagonal space group P6(5), with approximate unit-cell parameters a = 107.75, c = 37.33 Å, and contained one molecule in the asymmetric unit. Structure determination is under way using molecular replacement.
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Affiliation(s)
- Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Light Source, Stanford University, Menlo Park, CA 94025, USA
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34
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Green KD, Chen W, Garneau-Tsodikova S. Identification and characterization of inhibitors of the aminoglycoside resistance acetyltransferase Eis from Mycobacterium tuberculosis. ChemMedChem 2012; 7:73-7. [PMID: 21898832 PMCID: PMC3401626 DOI: 10.1002/cmdc.201100332] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/18/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Keith D. Green
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
| | - Wenjing Chen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
| | - Sylvie Garneau-Tsodikova
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
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35
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Susceptibility of vertilmicin to modifications by three types of recombinant aminoglycoside-modifying enzymes. Antimicrob Agents Chemother 2011; 55:3950-3. [PMID: 21646489 DOI: 10.1128/aac.00300-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The susceptibilities of vertilmicin and seven reference aminoglycosides to modifications by six recombinant aminoglycoside-modifying enzymes, AAC(6')-Ie, APH(2'')-Ia, AAC(6')-Ie-APH(2'')-Ia, ANT(2'')-Ia, AAC(6')-Ib, and AAC(6')-Ib-cr, were studied by coupled spectrophotometric assays in microtiter plates. In comparison to other aminoglycosides, the susceptibility of vertilmicin was 45.8- to 250.0-fold lower for AAC(6')-Ie acetylation, 39.2- to 116.7-fold lower for AAC(6')-Ie-APH(2'')-Ia acetylation, and 1.8- to 7.5-fold lower for ANT(2'')-Ia adenylation (except that shown by amikacin) while relatively comparable for AAC(6')-Ib acetylation, AAC(6')-Ib-cr acetylation, APH(2'')-Ia phosphorylation, and AAC(6')-Ie-APH(2'')-Ia phosphorylation.
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36
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Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB. Proc Natl Acad Sci U S A 2011; 108:9804-8. [PMID: 21628583 DOI: 10.1073/pnas.1105379108] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis (TB) is a serious global threat. Aminoglycoside antibiotics are used as a last resort to treat XDR-TB. Resistance to the aminoglycoside kanamycin is a hallmark of XDR-TB. Here, we reveal the function and structure of the mycobacterial protein Eis responsible for resistance to kanamycin in a significant fraction of kanamycin-resistant Mycobacterium tuberculosis clinical isolates. We demonstrate that Eis has an unprecedented ability to acetylate multiple amines of many aminoglycosides. Structural and mutagenesis studies of Eis indicate that its acetylation mechanism is enabled by a complex tripartite fold that includes two general control non-derepressible 5 (GCN5)-related N-acetyltransferase regions. An intricate negatively charged substrate-binding pocket of Eis is a potential target of new antitubercular drugs expected to overcome aminoglycoside resistance.
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37
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Effects of altering aminoglycoside structures on bacterial resistance enzyme activities. Antimicrob Agents Chemother 2011; 55:3207-13. [PMID: 21537023 DOI: 10.1128/aac.00312-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aminoglycoside-modifying enzymes (AMEs) constitute the most prevalent mechanism of resistance to aminoglycosides by bacteria. We show that aminoglycosides can be doubly modified by the sequential actions of AMEs, with the activity of the second AME in most cases unaffected, decreased, or completely abolished. We demonstrate that the bifunctional enzyme AAC(3)-Ib/AAC(6')-Ib' can diacetylate gentamicin. Since single acetylation does not always inactivate the parent drugs completely, two modifications likely provide more-robust inactivation in vivo.
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38
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Affiliation(s)
- Jonas J. Forsman
- Laboratory of Organic Chemistry, Åbo Akademi University, FI-20500 Åbo, Finland
| | - Reko Leino
- Laboratory of Organic Chemistry, Åbo Akademi University, FI-20500 Åbo, Finland
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39
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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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40
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Abstract
Antibiotic kinases, which include aminoglycoside and macrolide phosphotransferases (APHs and MPHs), pose a serious threat to currently used antimicrobial therapies. These enzymes show structural and functional homology with Ser/Thr/Tyr kinases, which is suggestive of a common ancestor. Surprisingly, recent in vitro studies using purified antibiotic kinase enzymes have revealed that a number are able to utilize GTP as the antibiotic phospho donor, either preferentially or exclusively compared to ATP, the canonical phosphate donor in most biochemical reactions. To further explore this phenomenon, we examined three enzymes, APH(3')-IIIa, APH(2'')-Ib, and MPH(2')-I, using a competitive assay that mimics in vivo nucleotide triphosphate (NTP) concentrations and usage by each enzyme. Downstream analysis of reaction products by high-performance liquid chromatography enabled the determination of partitioning of phosphate flux from NTP donors to antibiotics. Using this ratio along with support from kinetic analysis and inhibitor studies, we find that under physiologic concentrations of NTPs, APH(3')-IIIa exclusively uses ATP, MPH(2')-I exclusively uses GTP, and APH(2'')-Ib is able to use both species with a preference for GTP. These differences reveal likely different pathways in antibiotic resistance enzyme evolution and can be exploited in selective inhibitor design to counteract resistance.
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Zhang W, Fisher JF, Mobashery S. The bifunctional enzymes of antibiotic resistance. Curr Opin Microbiol 2009; 12:505-11. [PMID: 19615931 DOI: 10.1016/j.mib.2009.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/09/2009] [Indexed: 11/29/2022]
Abstract
The evolutionary union of two genes--each encoding proteins of complementary enzymatic activity--into a single gene so as to allow the coordinated expression of these activities as a fusion polypeptide, is an increasingly recognized biological occurrence. The result of this genetic union is the bifunctional enzyme. This fusion of separate catalytic activities into a single protein, whose gene is regulated by a single promoter, is seen especially where the coordinated expression of the separate activities is highly desirable. Increasingly, a circumstance driving the evolution of the bifunctional enzyme in bacteria is the resistance response of bacteria to antibiotic chemotherapy. We summarize the knowledge on bifunctional antibiotic-resistance enzymes, as possible harbingers of clinically significant resistance mechanisms of the future.
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Affiliation(s)
- Weilie Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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42
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Pokrovskaya V, Belakhov V, Hainrichson M, Yaron S, Baasov T. Design, Synthesis, and Evaluation of Novel Fluoroquinolone−Aminoglycoside Hybrid Antibiotics. J Med Chem 2009; 52:2243-54. [DOI: 10.1021/jm900028n] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Varvara Pokrovskaya
- The Edith and Joseph Fisher Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, and Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Valery Belakhov
- The Edith and Joseph Fisher Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, and Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Mariana Hainrichson
- The Edith and Joseph Fisher Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, and Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Sima Yaron
- The Edith and Joseph Fisher Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, and Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Timor Baasov
- The Edith and Joseph Fisher Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, and Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
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43
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Li CR, Yang XY, Lou RH, Zhang WX, Wang YM, Yuan M, Li Y, Chen HZ, Hong B, Sun CH, Zhao LX, Li ZR, Jiang JD, You XF. In vitro antibacterial activity of vertilmicin and its susceptibility to modifications by the recombinant AAC6'-APH2'' enzyme. Antimicrob Agents Chemother 2008; 52:3875-82. [PMID: 18710917 PMCID: PMC2573110 DOI: 10.1128/aac.01400-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 02/23/2008] [Accepted: 08/03/2008] [Indexed: 11/20/2022] Open
Abstract
Vertilmicin is a new semisynthetic aminoglycoside with a structure similar to that of netilmicin except for a methyl group at the C-6' position. In the present study, the in vitro antibacterial activity of vertilmicin was studied, and its susceptibility to modifications by the recombinant aminoglycoside bifunctional modifying enzyme AAC(6')-APH(2'') was compared with those of verdamicin and netilmicin. A total of 1,185 clinical isolates collected from hospitals in Beijing between 2000 and 2001 were subjected to the in vitro antibacterial activity evaluations, including MIC, minimum bactericidal concentration (MBC), and time-kill curve tests. The MICs were evaluated in non-gentamicin-resistant (gentamicin-susceptible and gentamicin-intermediate) strains and gentamicin-resistant strains, respectively. For most of the non-gentamicin-resistant bacteria (except for the isolates of Pseudomonas spp.), the MIC(90)s of vertilmicin were in the range of 0.5 to 8 microg/ml, comparable to those of the reference aminoglycosides. For the gentamicin-resistant isolates, the three semisynthetic aminoglycosides (vertilmicin, netilmicin, and amikacin) demonstrated low MIC(50)s and/or MIC(90)s, as well as high percent susceptibility values. Among the study drugs, vertilmicin showed the lowest MIC(90)s, 16 microg/ml, for the gram-positive gentamicin-resistant isolates of Staphylococcus aureus and Staphylococcus epidermidis. Meanwhile, vertilmicin was a potent bactericidal agent, with MBC/MIC ratios in the range of 1 to 2 for Escherichia coli, Klebsiella pneumoniae, and S. aureus and 1 to 4 for S. epidermidis. The time-kill curve determination further demonstrated that this effect was rapid and concentration dependent. In evaluations of susceptibility to modifications by the recombinant AAC(6')-APH(2'') with maximum rate of metabolism/K(m) measurements, vertilmicin exhibited susceptibilities to both acetylation and phosphorylation lower than those of netilmicin and verdamicin.
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Affiliation(s)
- Cong-Ran Li
- Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Hainrichson M, Nudelman I, Baasov T. Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases. Org Biomol Chem 2007; 6:227-39. [PMID: 18174989 DOI: 10.1039/b712690p] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminoglycosides are highly potent, broad-spectrum antibiotics that exert their bactericidal therapeutic effect by selectively binding to the decoding aminoacyl site (A-site) of the bacterial 16 S rRNA, thereby interfering with translational fidelity during protein synthesis. The appearance of bacterial strains resistant to these drugs, as well as their relative toxicity, have inspired extensive searches towards the goal of obtaining novel molecular designs with improved antibacterial activity and reduced toxicity. In the last few years, a new, aminoglycoside dependent therapeutic approach for the treatment of certain human genetic diseases has been identified. These treatments rely on the ability of certain aminoglycosides to induce mammalian ribosomes to readthrough premature stop codon mutations. This new and challenging task has introduced fresh research avenues in the field of aminoglycoside research. Recent observations and current challenges in the design of aminoglycosides with improved antibacterial activity and the treatment of human genetic diseases are discussed.
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Affiliation(s)
- Mariana Hainrichson
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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45
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Pich OQ, Burgos R, Planell R, Querol E, Piñol J. Comparative analysis of antibiotic resistance gene markers in Mycoplasma genitalium: application to studies of the minimal gene complement. MICROBIOLOGY-SGM 2006; 152:519-527. [PMID: 16436439 DOI: 10.1099/mic.0.28287-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycoplasma genitalium has been proposed as a suitable model for an in-depth understanding of the biology of a free-living organism. This paper reports that the expression of the aminoglycoside resistance gene aac(6')-aph(2''), the only selectable marker hitherto available for M. genitalium genetic studies, correlates with a growth impairment of the resistant strains. In light of this finding, a tetM438 construction based on the tetracycline resistance gene tetM was developed; it can be used efficiently in M. genitalium and confers multiple advantages when compared to aac(6')-aph(2''). The use of tetM438 significantly improves transformation efficiency and generates visible colonies faster. Finally, the improvements in the pMTnTetM438 construction made it possible to obtain insertions in genes which have not been previously considered to be dispensable under laboratory growth conditions.
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Affiliation(s)
- Oscar Q Pich
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Raul Burgos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Raquel Planell
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Jana S, Deb JK. Molecular understanding of aminoglycoside action and resistance. Appl Microbiol Biotechnol 2006; 70:140-50. [PMID: 16391922 DOI: 10.1007/s00253-005-0279-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 11/23/2005] [Accepted: 11/27/2005] [Indexed: 11/26/2022]
Abstract
Aminoglycosides are potent bactericidal antibiotics targeting the bacterial ribosome, where they bind to the A-site and disrupt protein synthesis. They are particularly active against aerobic, Gram-negative bacteria and act synergistically against certain Gram-positive organisms. Aminoglycosides are used in the treatment of severe infections of the abdomen and urinary tract, bacteremia, and endocarditis. They are also used for prophylaxis, especially against endocarditis. Bacterial resistance to aminoglycosides continues to escalate and is widely recognized as a serious health threat. This might be the reason for the interest in understanding the mechanisms of resistance. It is now clear that the resistance occurs by different mechanisms such as prevention of drug entry, active extrusion of drugs, alteration of the drug target (mutational modification of 16S rRNA and mutational modification of ribosomal proteins), and enzymatic inactivation through the expression of enzymes, which covalently modify these antibiotics. Enzymatic inactivation is normally due to acetyltransferases, nucleotidyltransferases, and phosphotransferases. In this review, we focus on the recent concept of molecular understanding of aminoglycoside action and resistance.
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Affiliation(s)
- S Jana
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi
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