1
|
Bordeleau E, Stogios PJ, Evdokimova E, Koteva K, Savchenko A, Wright GD. Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat Chem Biol 2024; 20:234-242. [PMID: 37973888 DOI: 10.1038/s41589-023-01483-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
The efficacy of aminoglycoside antibiotics is waning due to the acquisition of diverse resistance mechanisms by bacteria. Among the most prevalent are aminoglycoside acetyltransferases (AACs) that inactivate the antibiotics through acetyl coenzyme A-mediated modification. Most AACs are members of the GCN5 superfamily of acyltransferases which lack conserved active site residues that participate in catalysis. ApmA is the first reported AAC belonging to the left-handed β-helix superfamily. These enzymes are characterized by an essential active site histidine that acts as an active site base. Here we show that ApmA confers broad-spectrum aminoglycoside resistance with a molecular mechanism that diverges from other detoxifying left-handed β-helix superfamily enzymes and canonical GCN5 AACs. We find that the active site histidine plays different functions depending on the acetyl-accepting aminoglycoside substrate. This flexibility in the mechanism of a single enzyme underscores the plasticity of antibiotic resistance elements to co-opt protein catalysts in the evolution of drug detoxification.
Collapse
Affiliation(s)
- Emily Bordeleau
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kalinka Koteva
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID) University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| |
Collapse
|
2
|
Morgan CE, Kang YS, Green AB, Smith KP, Dowgiallo MG, Miller BC, Chiaraviglio L, Truelson KA, Zulauf KE, Rodriguez S, Kang AD, Manetsch R, Yu EW, Kirby JE. Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome. PLoS Biol 2023; 21:e3002091. [PMID: 37192172 DOI: 10.1371/journal.pbio.3002091] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 03/22/2023] [Indexed: 05/18/2023] Open
Abstract
The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we establish the activity spectrum of nourseothricin and its main components, streptothricin F (S-F, 1 lysine) and streptothricin D (S-D, 3 lysines), purified to homogeneity, against highly drug-resistant, carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii. For CRE, the MIC50 and MIC90 for S-F and S-D were 2 and 4 μM, and 0.25 and 0.5 μM, respectively. S-F and nourseothricin showed rapid, bactericidal activity. S-F and S-D both showed approximately 40-fold greater selectivity for prokaryotic than eukaryotic ribosomes in in vitro translation assays. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain with minimal or no toxicity. Cryo-EM characterization of S-F bound to the A. baumannii 70S ribosome defines extensive hydrogen bonding of the S-F steptolidine moiety, as a guanine mimetic, to the 16S rRNA C1054 nucleobase (Escherichia coli numbering) in helix 34, and the carbamoylated gulosamine moiety of S-F with A1196, explaining the high-level resistance conferred by corresponding mutations at the residues identified in single rrn operon E. coli. Structural analysis suggests that S-F probes the A-decoding site, which potentially may account for its miscoding activity. Based on unique and promising activity, we suggest that the streptothricin scaffold deserves further preclinical exploration as a potential therapeutic for drug-resistant, gram-negative pathogens.
Collapse
Affiliation(s)
- Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alex B Green
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kenneth P Smith
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthew G Dowgiallo
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Brandon C Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Lucius Chiaraviglio
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Katherine A Truelson
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Katelyn E Zulauf
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shade Rodriguez
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Anthony D Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
3
|
Pirrone MG, Ande C, Haldimann K, Hobbie SN, Vasella A, Böttger EC, Crich D. Importance of Co-operative Hydrogen Bonding in the Apramycin-Ribosomal Decoding A-Site Interaction. ChemMedChem 2023; 18:e202200486. [PMID: 36198651 PMCID: PMC10092258 DOI: 10.1002/cmdc.202200486] [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: 09/08/2022] [Revised: 10/05/2022] [Indexed: 01/24/2023]
Abstract
An intramolecular hydrogen bond between the protonated equatorial 7'-methylamino group of apramycin and the vicinal axial 6'-hydroxy group acidifies the 6'-hydroxy group leading to a strong hydrogen bond to A1408 in the ribosomal drug binding pocket in the decoding A site of the small ribosomal subunit. In 6'-epiapramycin, the trans-nature of the 6'-hydroxy group and the 7'-methylamino group results in a much weaker intramolecular hydrogen bond, and a consequently weaker cooperative hydrogen bonding network with A1408, resulting overall in reduced inhibition of protein synthesis and antibacterial activity.
Collapse
Affiliation(s)
- Michael G Pirrone
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, 30602, Athens, GA, USA
| | - Chennaiah Ande
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, 30602, Athens, GA, USA
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28, 8006, Zürich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28, 8006, Zürich, Switzerland
| | - Andrea Vasella
- Organic Chemistry Institute, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28, 8006, Zürich, Switzerland
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, Department of Chemistry, Complex Carbohydrate Research Center, University of Georgia, 250 West Green Street, 30602, Athens, GA, USA
| |
Collapse
|
4
|
Pirrone MG, Hobbie SN, Vasella A, Böttger EC, Crich D. Influence of ring size in conformationally restricted ring I analogs of paromomycin on antiribosomal and antibacterial activity. RSC Med Chem 2021; 12:1585-1591. [PMID: 34671740 DOI: 10.1039/d1md00214g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/03/2021] [Indexed: 11/21/2022] Open
Abstract
In order to further investigate the importance of the conformation of the ring I side chain in aminoglycoside antibiotic binding to the ribosomal target several derivatives of paromomycin were designed with conformationally locked side chains. By changing the size of the appended ring between O-4' and C-6' used to restrict the motion of the side chain, the position of the C-6' hydroxy group was fine tuned to probe for the optimal conformation for inhibition of the ribosome. While the changes in orientation of the 6'-hydroxy group cannot be completely dissociated from the size and hydrophobicity of the conformation-restricting ring, overall, it is apparent that the preferred conformation of the ring I side chain for interaction with A1408 in the decoding A site of the bacterial ribosome is an ideal gt conformation, which results in the highest antimicrobial activity as well as increased selectivity for bacterial over eukaryotic ribosomes.
Collapse
Affiliation(s)
- Michael G Pirrone
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia 250 West Green Street Athens GA 30602 USA .,Complex Carbohydrate Research Center, University of Georgia 315 Riverbend Road Athens GA 30602 USA.,Department of Chemistry, Wayne State University 5101 Cass Avenue Detroit MI 48202 USA
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich Gloriastrasse 28 8006 Zürich Switzerland
| | - Andrea Vasella
- Organic Chemistry Laboratory, ETH Zürich Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich Gloriastrasse 28 8006 Zürich Switzerland
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia 250 West Green Street Athens GA 30602 USA .,Complex Carbohydrate Research Center, University of Georgia 315 Riverbend Road Athens GA 30602 USA.,Department of Chemistry, University of Georgia 140 Cedar Street Athens GA 30602 USA
| |
Collapse
|
5
|
Bassenden AV, Dumalo L, Park J, Blanchet J, Maiti K, Arya DP, Berghuis AM. Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2') enzymes. Sci Rep 2021; 11:11614. [PMID: 34078922 PMCID: PMC8172861 DOI: 10.1038/s41598-021-89446-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/22/2021] [Indexed: 01/20/2023] Open
Abstract
Plazomicin is currently the only next-generation aminoglycoside approved for clinical use that has the potential of evading the effects of widespread enzymatic resistance factors. However, plazomicin is still susceptible to the action of the resistance enzyme AAC(2')-Ia from Providencia stuartii. As the clinical use of plazomicin begins to increase, the spread of resistance factors will undoubtedly accelerate, rendering this aminoglycoside increasingly obsolete. Understanding resistance to plazomicin is an important step to ensure this aminoglycoside remains a viable treatment option for the foreseeable future. Here, we present three crystal structures of AAC(2')-Ia from P. stuartii, two in complex with acetylated aminoglycosides tobramycin and netilmicin, and one in complex with a non-substrate aminoglycoside, amikacin. Together, with our previously reported AAC(2')-Ia-acetylated plazomicin complex, these structures outline AAC(2')-Ia's specificity for a wide range of aminoglycosides. Additionally, our survey of AAC(2')-I homologues highlights the conservation of residues predicted to be involved in aminoglycoside binding, and identifies the presence of plasmid-encoded enzymes in environmental strains that confer resistance to the latest next-generation aminoglycoside. These results forecast the likely spread of plazomicin resistance and highlight the urgency for advancements in next-generation aminoglycoside design.
Collapse
Affiliation(s)
- Angelia V Bassenden
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Linda Dumalo
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Jonathan Blanchet
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | | | - Dev P Arya
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
- Department of Microbiology and Immunology, McGill University, Duff Medical Building, 3775 University Street, Montreal, QC, H3A 2B4, Canada.
| |
Collapse
|
6
|
Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
Collapse
Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
| |
Collapse
|
7
|
Abstract
Apramycin is an aminoglycoside antibiotic with the potential to be developed to combat multidrug-resistant pathogens. Its unique structure evades the clinically widespread mechanisms of aminoglycoside resistance that currently compromise the efficacy of other members in this drug class. Of the aminoglycoside-modifying enzymes that chemically alter these antibiotics, only AAC(3)-IVa has been demonstrated to confer resistance to apramycin through N-acetylation. Knowledge of other modification mechanisms is important to successfully develop apramycin for clinical use. Here, we show that ApmA is structurally unique among the previously described aminoglycoside-modifying enzymes and capable of conferring a high level of resistance to apramycin. In vitro experiments indicated ApmA to be an N-acetyltransferase, but in contrast to AAC(3)-IVa, ApmA has a unique regiospecificity of the acetyl transfer to the N2' position of apramycin. Crystallographic analysis of ApmA conclusively showed that this enzyme is an acetyltransferase from the left-handed β-helix protein superfamily (LβH) with a conserved active site architecture. The success of apramycin will be dependent on consideration of the impact of this potential form of clinical resistance.IMPORTANCE Apramycin is an aminoglycoside antibiotic that has been traditionally used in veterinary medicine. Recently, it has become an attractive candidate to repurpose in the fight against multidrug-resistant pathogens prioritized by the World Health Organization. Its atypical structure circumvents most of the clinically relevant mechanisms of resistance that impact this class of antibiotics. Prior to repurposing apramycin, it is important to understand the resistance mechanisms that could be a liability. Our study characterizes the most recently identified apramycin resistance element, apmA We show ApmA does not belong to the protein families typically associated with aminoglycoside resistance and is responsible for modifying a different site on the molecule. The data presented will be critical in the development of apramycin derivatives that will evade apmA in the event it becomes prevalent in the clinic.
Collapse
|
8
|
Xie Y, Chen J, Wang B, Chen T, Chen J, Zhang Y, Liu X, Chen Q. Activation and enhancement of caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies. Microb Cell Fact 2020; 19:159. [PMID: 32762690 PMCID: PMC7412835 DOI: 10.1186/s12934-020-01418-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Background Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities. Results To well activate the expression of cam, ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development. Conclusions Our results had constructed an ideal CRM A producer. More importantly, our efforts also had demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.
Collapse
Affiliation(s)
- Yunchang Xie
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiawen Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Bo Wang
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Tai Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Junyu Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yuan Zhang
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Xiaoying Liu
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Qi Chen
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
| |
Collapse
|
9
|
Way CM, Lima Cunha D, Moosajee M. Translational readthrough inducing drugs for the treatment of inherited retinal dystrophies. EXPERT REVIEW OF OPHTHALMOLOGY 2020. [DOI: 10.1080/17469899.2020.1762489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christopher M Way
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Dulce Lima Cunha
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| |
Collapse
|
10
|
Mahi-Birjand M, Yaghoubi S, Abdollahpour-Alitappeh M, Keshtkaran Z, Bagheri N, Pirouzi A, Khatami M, Sineh Sepehr K, Peymani P, Karimzadeh I. Protective effects of pharmacological agents against aminoglycoside-induced nephrotoxicity: A systematic review. Expert Opin Drug Saf 2020; 19:167-186. [PMID: 31914328 DOI: 10.1080/14740338.2020.1712357] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Aminoglycosides have been long used for antibacterial treatment and are still commonly used in clinical practice. Despite their extensive application and positive effects, drug-related toxicity is considered as the main obstacle for aminoglycosides. Aminoglycosides induce nephrotoxicity through the endocytosis and accumulation of the antibiotics in the epithelial cells of proximal tubule. Most importantly, however, a number of pharmacological agents were demonstrated to have protective activities against nephrotoxicity in experimental animals.Areas covered: In the present systematic review, the authors provide and discuss the mechanisms and epidemiological features of aminoglycoside-induced nephrotoxicity, and focus mainly on recent discoveries and key features of pharmacological interventions. In total, 39 articles were included in this review.Expert opinion: The majority of studies investigated gentamicin-induced nephrotoxicity in animal models. Antioxidants, chemicals, synthetic drugs, hormones, vitamins, and minerals showed potential values to prevent gentamicin-induced nephrotoxicity. Indicators used to evaluate the effectiveness of nephroprotection included antioxidative indexes, inflammatory responses, and apoptotic markers. Among the nephroprotective agents studied, herbs and natural antioxidant agents showed excellent potential to provide a protective strategy against gentamicin-induced nephrotoxicity.
Collapse
Affiliation(s)
- Motahareh Mahi-Birjand
- Student Research Committee, Department of Clinical Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Infectious Disease Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Sajad Yaghoubi
- Department of Clinical Microbiology, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | | | - Zahra Keshtkaran
- Department of Nursing, School of Nursing and Midwifery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nader Bagheri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Mehrdad Khatami
- NanoBioelectrochemistry Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Koushan Sineh Sepehr
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Payam Peymani
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich-University of Zurich, Switzerland.,Health Policy Research Center, Institute of Heath, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Karimzadeh
- Student Research Committee, Department of Clinical Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
11
|
Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA. Molecules 2019; 25:molecules25010159. [PMID: 31906077 PMCID: PMC6983231 DOI: 10.3390/molecules25010159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 02/04/2023] Open
Abstract
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to those of the wild type and the A1408G antibiotic-resistant mutant. However, significant differences are found in local base stacking interactions including the functionally important A1492 and A1493 residues. In the wild type and the A1408G antibiotic-resistant mutant “off” states, both adenines are exposed to the solvent region. On the other hand, one of the corresponding adenines of the lethal A1408C/U mutants stay deeply inside their A-site helices by forming a purine-pyrimidine AoC or A-U base pair and is sandwiched between the upper and lower bases. Therefore, the ON/OFF switching might unfavorably occur in the lethal mutants compared to the wild type and the A1408G antibiotic-resistant mutant. It is probable that bacteria manage to acquire antibiotic resistance without losing the function of the A-site molecular switch by mutating the position 1408 only from A to G, but not to pyrimidine base C or U.
Collapse
|
12
|
Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
Collapse
Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
| |
Collapse
|
13
|
Matsushita T, Sati GC, Kondasinghe N, Pirrone MG, Kato T, Waduge P, Kumar HS, Sanchon AC, Dobosz-Bartoszek M, Shcherbakov D, Juhas M, Hobbie SN, Schrepfer T, Chow CS, Polikanov YS, Schacht J, Vasella A, Böttger EC, Crich D. Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens. J Am Chem Soc 2019; 141:5051-5061. [PMID: 30793894 DOI: 10.1021/jacs.9b01693] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infectious diseases due to multidrug-resistant pathogens, particularly carbapenem-resistant Enterobacteriaceae (CREs), present a major and growing threat to human health and society, providing an urgent need for the development of improved potent antibiotics for their treatment. We describe the design and development of a new class of aminoglycoside antibiotics culminating in the discovery of propylamycin. Propylamycin is a 4'-deoxy-4'-alkyl paromomycin whose alkyl substituent conveys excellent activity against a broad spectrum of ESKAPE pathogens and other Gram-negative infections, including CREs, in the presence of numerous common resistance determinants, be they aminoglycoside modifying enzymes or rRNA methyl transferases. Importantly, propylamycin is demonstrated not to be susceptible to the action of the ArmA resistance determinant whose presence severely compromises the action of plazomicin and all other 4,6-disubstituted 2-deoxystreptamine aminoglycosides. The lack of susceptibility to ArmA, which is frequently encoded on the same plasmid as carbapenemase genes, ensures that propylamycin will not suffer from problems of cross-resistance when used in combination with carbapenems. Cell-free translation assays, quantitative ribosome footprinting, and X-ray crystallography support a model in which propylamycin functions by interference with bacterial protein synthesis. Cell-free translation assays with humanized bacterial ribosomes were used to optimize the selectivity of propylamycin, resulting in reduced ototoxicity in guinea pigs. In mouse thigh and septicemia models of Escherichia coli, propylamycin shows excellent efficacy, which is better than paromomycin. Overall, a simple novel deoxy alkyl modification of a readily available aminoglycoside antibiotic increases the inherent antibacterial activity, effectively combats multiple mechanisms of aminoglycoside resistance, and minimizes one of the major side effects of aminoglycoside therapy.
Collapse
Affiliation(s)
- Takahiko Matsushita
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Girish C Sati
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Nuwan Kondasinghe
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Michael G Pirrone
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Takayuki Kato
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Prabuddha Waduge
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Harshitha Santhosh Kumar
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - Adrian Cortes Sanchon
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - Malgorzata Dobosz-Bartoszek
- Department of Biological Sciences , University of Illinois at Chicago , 900 South Ashland Avenue , Chicago , Illinois 60607 , United States
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - Mario Juhas
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - Sven N Hobbie
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - Thomas Schrepfer
- Kresge Hearing Research Institute, Department of Otolaryngology , University of Michigan , 1150 West Medical Center Drive , Ann Arbor , Michigan 48109 , United States
| | - Christine S Chow
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Yury S Polikanov
- Department of Biological Sciences , University of Illinois at Chicago , 900 South Ashland Avenue , Chicago , Illinois 60607 , United States.,Department of Medicinal Chemistry and Pharmacognosy , University of Illinois at Chicago , 900 South Ashland Avenue , Chicago , Illinois 60607 , United States
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology , University of Michigan , 1150 West Medical Center Drive , Ann Arbor , Michigan 48109 , United States
| | - Andrea Vasella
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 1-5/10 , 8093 Zürich , Switzerland
| | - Erik C Böttger
- Institut für Medizinische Mikrobiologie , Universität Zürich , 28 Gloriastrasse , 8006 Zürich , Switzerland
| | - David Crich
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| |
Collapse
|
14
|
Martí S, Bastida A, Świderek K. Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase. Front Chem 2019; 6:660. [PMID: 30761287 PMCID: PMC6361787 DOI: 10.3389/fchem.2018.00660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 01/31/2023] Open
Abstract
This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5'-monophosfate) from adenosine 5'-triphosphate (ATP) to a OH-4' hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4'-O-Nucleotidyltransferase [ANT(4')], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol-1 that corresponds to the concerted activation of O4' from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5' atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.
Collapse
Affiliation(s)
- Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
| | - Agatha Bastida
- Departamento de Química Bio-orgánica, Instituto de Química Orgánica General (CSIC), Madrid, Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
| |
Collapse
|
15
|
Smolkin B, Khononov A, Pieńko T, Shavit M, Belakhov V, Trylska J, Baasov T. Towards Catalytic Antibiotics: Redesign of Aminoglycosides To Catalytically Disable Bacterial Ribosomes. Chembiochem 2018; 20:247-259. [DOI: 10.1002/cbic.201800549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Boris Smolkin
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Alina Khononov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Tomasz Pieńko
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
- Department of Drug Chemistry; Faculty of Pharmacy with the Laboratory Medicine Division; Medical University of Warsaw; Banacha 1a 02-097 Warsaw Poland
| | - Michal Shavit
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Valery Belakhov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Joanna Trylska
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| |
Collapse
|
16
|
Sabbavarapu NM, Pieńko T, Zalman BH, Trylska J, Baasov T. Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives. MEDCHEMCOMM 2018; 9:503-508. [PMID: 30108940 DOI: 10.1039/c8md00001h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 01/31/2018] [Indexed: 11/21/2022]
Abstract
New derivatives of aminoglycosides containing 6'-carboxylic acid or 6'-amide on their ring I were designed, synthesized and their ability to readthrough nonsense mutations was examined in vitro, along with the protein translation inhibition in prokaryotic and eukaryotic systems. The observed structure-activity relationships, along with the comparative molecular dynamics simulations within the eukaryotic rRNA decoding site, showed high sensitivity of 6'-position to substitution, indicating that the rational design of potent stop-codon read-through inducers requires consideration of not only the structure and energetics of the drug-RNA interaction but also the dynamics associated with that interaction.
Collapse
Affiliation(s)
- Narayana Murthy Sabbavarapu
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
| | - Tomasz Pieńko
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland . ; Tel: +48 22 554 3683.,Department of Drug Chemistry , Faculty of Pharmacy with the Laboratory Medicine Division , Medical University of Warsaw , Banacha 1a , 02-097 Warsaw , Poland
| | - Bat-Hen Zalman
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland . ; Tel: +48 22 554 3683
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory , Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel . ; Tel: +972 4 829 2590
| |
Collapse
|
17
|
Strain improvement by combined UV mutagenesis and ribosome engineering and subsequent fermentation optimization for enhanced 6'-deoxy-bleomycin Z production. Appl Microbiol Biotechnol 2017; 102:1651-1661. [PMID: 29279956 DOI: 10.1007/s00253-017-8705-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
Abstract
The bleomycins (BLMs) are important clinical drugs extensively used in combination chemotherapy for the treatment of various cancers. Dose-dependent lung toxicity and the development of drug resistance have restricted their wide applications. 6'-Deoxy-BLM Z, a recently engineered BLM analogue with improved antitumor activity, has the potential to be developed into the next-generation BLM anticancer drug. However, its low titer in the recombinant strain Streptomyces flavoviridis SB9026 has hampered current efforts, which require sufficient compound, to pursue preclinical studies and subsequent clinical development. Here, we report the strain improvement by combined UV mutagenesis and ribosome engineering, as well as the fermentation optimization, for enhanced 6'-deoxy-BLM production. A high producer, named S. flavoviridis G-4F12, was successfully isolated, producing 6'-deoxy-BLM at above 70 mg/L under the optimized fermentation conditions, representing a sevenfold increase in comparison with that of the original producer. These findings demonstrated the effectiveness of combined empirical breeding methods in strain improvement and set the stage for sustainable production of 6'-deoxy-BLM via pilot-scale microbial fermentation.
Collapse
|
18
|
Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin. Nat Commun 2017; 8:1589. [PMID: 29150609 PMCID: PMC5693986 DOI: 10.1038/s41467-017-01664-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/05/2017] [Indexed: 12/25/2022] Open
Abstract
Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.
Collapse
|
19
|
Mandhapati AR, Yang G, Kato T, Shcherbakov D, Hobbie SN, Vasella A, Böttger EC, Crich D. Structure-Based Design and Synthesis of Apramycin-Paromomycin Analogues: Importance of the Configuration at the 6'-Position and Differences between the 6'-Amino and Hydroxy Series. J Am Chem Soc 2017; 139:14611-14619. [PMID: 28892368 PMCID: PMC5647259 DOI: 10.1021/jacs.7b07754] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The preparation of a series of four analogues of the aminoglycoside antibiotics neomycin and paromomycin is described in which ring I, involved in critical binding interactions with the ribosomal target, is replaced by an apramycin-like dioxabicyclo[4.4.0]octane system. The effect of this modification is to lock the hydroxymethyl side chain of the neomycin or paromomycin ring I, as part of the dioxabicyclooctane ring, into either the gauche-gauche or the gauche-trans conformation (respectively, axial or equatorial to the bicyclic system). The antiribosomal activity of these compounds is investigated with cell-free translation assays using both bacterial ribosomes and recombinant hybrid ribosomes carrying eukaryotic decoding A site cassettes. Compounds substituted with an equatorial hydroxyl or amino group in the newly formed ring are considerably more active than their axial diastereomers, lending strong support to crystallographically derived models of aminoglycoside-ribosome interactions. One such bicyclic compound carrying an equatorial hydroxyl group has activity equal to that of the parent yet displays better ribosomal selectivity, predictive of an enhanced therapeutic index. A paromomycin analog lacking the hydroxymethyl ring I side chain is considerably less active than the parent. Antibacterial activity against model Gram negative and Gram positive bacteria is reported for selected compounds, as is activity against ESKAPE pathogens and recombinant bacteria carrying specific resistance determinants. Analogues with a bicyclic ring I carrying equatorial amino or hydroxyl groups mimicking the bound side chains of neomycin and paromomycin, respectively, show excellent activity and, by virtue of their novel structure, retain this activity in strains that are insensitive to the parent compounds.
Collapse
Affiliation(s)
- Appi Reddy Mandhapati
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Guanyu Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Takayuki Kato
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Dimitri Shcherbakov
- Institute of Medical Microbiology, University of Zurich , 8006 Zurich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich , 8006 Zurich, Switzerland
| | - Andrea Vasella
- Organic Chemistry Laboratory, ETH Zurich , 8093 Zurich, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich , 8006 Zurich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| |
Collapse
|
20
|
Assis LM, Nedeljković M, Dessen A. New strategies for targeting and treatment of multi-drug resistant Staphylococcus aureus. Drug Resist Updat 2017; 31:1-14. [PMID: 28867240 DOI: 10.1016/j.drup.2017.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is a major cause of bacterial infection in humans, and has been notoriously able to acquire resistance to a variety of antibiotics. An example is methicillin-resistant S. aureus (MRSA), which despite having been initially associated with clinical settings, now is one of the key causative agents of community-acquired infections. Antibiotic resistance in S. aureus involves mechanisms ranging from drug efflux to increased expression or mutation of target proteins, and this has required innovative approaches to develop novel treatment methodologies. This review provides an overview of the major mechanisms of antibiotic resistance developed by S. aureus, and describes the emerging alternatives being sought to circumvent infection and proliferation, including new generations of classic antibiotics, synergistic approaches, antibodies, and targeting of virulence factors.
Collapse
Affiliation(s)
- L Mayrink Assis
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - M Nedeljković
- Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France
| | - A Dessen
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil; Institut de Biologie Structurale (IBS), Univ Grenoble Alpes, CEA, CNRS, Bacterial Pathogenesis Group, 38044 Grenoble, France.
| |
Collapse
|
21
|
Substrate Recognition and Modification by a Pathogen-Associated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antimicrob Agents Chemother 2017; 61:AAC.00077-17. [PMID: 28289026 DOI: 10.1128/aac.00077-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/03/2017] [Indexed: 01/07/2023] Open
Abstract
The pathogen-associated 16S rRNA methyltransferase NpmA catalyzes m1A1408 modification to block the action of structurally diverse aminoglycoside antibiotics. Here, we describe the development of a fluorescence polarization binding assay and its use, together with complementary functional assays, to dissect the mechanism of NpmA substrate recognition. These studies reveal that electrostatic interactions made by the NpmA β2/3 linker collectively are critical for docking of NpmA on a conserved 16S rRNA tertiary surface. In contrast, other NpmA regions (β5/β6 and β6/β7 linkers) contain several residues critical for optimal positioning of A1408 but are largely dispensable for 30S binding. Our data support a model for NpmA action in which 30S binding and adoption of a catalytically competent state are distinct: docking on 16S rRNA via the β2/3 linker necessarily precedes functionally critical 30S substrate-driven conformational changes elsewhere in NpmA. This model is also consistent with catalysis being completely positional in nature, as the most significant effects on activity arise from changes that impact binding or stabilization of the flipped A1408 conformation. Our results provide a molecular framework for aminoglycoside resistance methyltransferase action that may serve as a functional paradigm for related enzymes and a starting point for development of inhibitors of these resistance determinants.
Collapse
|
22
|
Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017; 56:2640-2644. [PMID: 28156044 PMCID: PMC5397316 DOI: 10.1002/anie.201611700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.
Collapse
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| |
Collapse
|
23
|
Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Mark A. Boerneke
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Seergazhi G. Srivatsan
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| |
Collapse
|
24
|
Richardson R, Smart M, Tracey-White D, Webster AR, Moosajee M. Mechanism and evidence of nonsense suppression therapy for genetic eye disorders. Exp Eye Res 2017; 155:24-37. [PMID: 28065590 DOI: 10.1016/j.exer.2017.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
Between 5 and 70% of genetic disease is caused by in-frame nonsense mutations, which introduce a premature termination codon (PTC) within the disease-causing gene. Consequently, during translation, non-functional or gain-of-function truncated proteins of pathological significance, are formed. Approximately 50% of all inherited retinal disorders have been associated with PTCs, highlighting the importance of novel pharmacological or gene correction therapies in ocular disease. Pharmacological nonsense suppression of PTCs could delineate a therapeutic strategy that treats the mutation in a gene- and disease-independent manner. This approach aims to suppress the fidelity of the ribosome during protein synthesis so that a near-cognate aminoacyl-tRNA, which shares two of the three nucleotides of the PTC, can be inserted into the peptide chain, allowing translation to continue, and a full-length functional protein to be produced. Here we discuss the mechanisms and evidence of nonsense suppression agents, including the small molecule drug ataluren (or PTC124) and next generation 'designer' aminoglycosides, for the treatment of genetic eye disease.
Collapse
Affiliation(s)
- Rose Richardson
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Matthew Smart
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Dhani Tracey-White
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Andrew R Webster
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK.
| |
Collapse
|
25
|
Kinetic characterization and molecular docking of novel allosteric inhibitors of aminoglycoside phosphotransferases. Biochim Biophys Acta Gen Subj 2017; 1861:3464-3473. [DOI: 10.1016/j.bbagen.2016.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/07/2016] [Accepted: 09/11/2016] [Indexed: 11/21/2022]
|
26
|
Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 2016; 6:37061. [PMID: 27845431 PMCID: PMC5109232 DOI: 10.1038/srep37061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/24/2016] [Indexed: 12/30/2022] Open
Abstract
Aminoglycosides are broad-spectrum antibiotics that bind to the 30S ribosomal subunit (30S) of bacteria and disrupt protein translation. NpmA, a structurally well-characterized methyltransferase identified in an E. coli clinical isolate, catalyzes methylation of 30S at A1408 of the 16S rRNA and confers aminoglycoside resistance. Using sucrose cushion centrifugation and isothermal titration calorimetry, we first confirmed the binding between NpmA and 30S. Next, we performed amide Hydrogen/Deuterium Exchange Mass Spectrometry (HDXMS) of apo NpmA and in the presence and absence of SAM/SAH. We observed that ligand binding resulted in time-dependent differences in deuterium exchange not only at the ligand-binding pocket (D25–D55 and A86–E112) but also in distal regions (F62-F82 and Y113-S144) of NpmA. These results provide insights into methylation group donor cofactor-mediated allostery in NpmA in the ligand-bound states, which could not be observed in the static endpoint crystal structures. We predict that the two distal sites in NpmA form part of the allosteric sites that importantly are part of the main 16S rRNA binding interface. Thus HDXMS helped uncover allosteric communication relays that couple SAM/SAH binding sites with the ribosome-binding site. This highlights how HDXMS together with X-ray crystallography can provide important allosteric insights in protein-ligand complexes.
Collapse
|
27
|
Herzog IM, Louzoun Zada S, Fridman M. Effects of 5-O-Ribosylation of Aminoglycosides on Antimicrobial Activity and Selective Perturbation of Bacterial Translation. J Med Chem 2016; 59:8008-18. [PMID: 27509271 DOI: 10.1021/acs.jmedchem.6b00793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We studied six pairs of aminoglycosides and their corresponding ribosylated derivatives synthesized by attaching a β-O-linked ribofuranose to the 5-OH of the deoxystreptamine ring of the parent pseudo-oligosaccharide antibiotic. Ribosylation of the 4,6-disubstituted 2-deoxystreptamine aminoglycoside kanamycin B led to improved selectivity for inhibition of prokaryotic relative to cytosolic eukaryotic in vitro translation. For the pseudodisaccharide aminoglycoside scaffolds neamine and nebramine, ribosylated derivatives were both more potent antimicrobials and more selective to inhibition of prokaryotic translation. On the basis of the results of this study, we suggest that modification of the 5-OH position of the streptamine ring of other natural or semisynthetic pseudodisaccharide aminoglycoside scaffolds containing an equatorial amine at the 2' sugar position with a β-O-linked ribofuranose is a promising avenue for the development of novel aminoglycoside antibiotics with improved efficacy and reduced toxicity.
Collapse
Affiliation(s)
- Ido M Herzog
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Sivan Louzoun Zada
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| |
Collapse
|
28
|
Kannan K, Tsvetanova B, Chuang RY, Noskov VN, Assad-Garcia N, Ma L, Hutchison Iii CA, Smith HO, Glass JI, Merryman C, Venter JC, Gibson DG. One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9. Sci Rep 2016; 6:30714. [PMID: 27489041 PMCID: PMC4973257 DOI: 10.1038/srep30714] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 01/04/2023] Open
Abstract
Bacteria are indispensable for the study of fundamental molecular biology processes due to their relatively simple gene and genome architecture. The ability to engineer bacterial chromosomes is quintessential for understanding gene functions. Here we demonstrate the engineering of the small-ribosomal subunit (16S) RNA of Mycoplasma mycoides, by combining the CRISPR/Cas9 system and the yeast recombination machinery. We cloned the entire genome of M. mycoides in yeast and used constitutively expressed Cas9 together with in vitro transcribed guide-RNAs to introduce engineered 16S rRNA genes. By testing the function of the engineered 16S rRNA genes through genome transplantation, we observed surprising resilience of this gene to addition of genetic elements or helix substitutions with phylogenetically-distant bacteria. While this system could be further used to study the function of the 16S rRNA, one could envision the “simple” M. mycoides genome being used in this setting to study other genetic structures and functions to answer fundamental questions of life.
Collapse
Affiliation(s)
| | | | | | | | | | - Li Ma
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Hamilton O Smith
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - J Craig Venter
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Daniel G Gibson
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| |
Collapse
|
29
|
Arenz S, Wilson DN. Blast from the Past: Reassessing Forgotten Translation Inhibitors, Antibiotic Selectivity, and Resistance Mechanisms to Aid Drug Development. Mol Cell 2015; 61:3-14. [PMID: 26585390 DOI: 10.1016/j.molcel.2015.10.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein synthesis is a major target within the bacterial cell for antibiotics. Investigations into ribosome-targeting antibiotics have provided much needed functional and structural insight into their mechanism of action. However, the increasing prevalence of multi-drug-resistant bacteria has limited the utility of our current arsenal of clinically relevant antibiotics, highlighting the need for the development of new classes. Recent structural studies have characterized a number of antibiotics discovered decades ago that have unique chemical scaffolds and/or utilize novel modes of action to interact with the ribosome and inhibit translation. Additionally, structures of eukaryotic cytoplasmic and mitochondrial ribosomes have provided further structural insight into the basis for specificity and toxicity of antibiotics. Together with our increased understanding of bacterial resistance mechanisms, revisiting our treasure trove of "forgotten" antibiotics could pave the way for the next generation of antimicrobial agents.
Collapse
Affiliation(s)
- Stefan Arenz
- Gene Center and Department of Biochemistry, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany
| | - Daniel N Wilson
- Gene Center and Department of Biochemistry, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany; Center for integrated Protein Science Munich, Feodor-Lynenstr. 25, University of Munich, 81377 Munich, Germany.
| |
Collapse
|
30
|
Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| |
Collapse
|
31
|
Matsushita T, Chen W, Juskeviciene R, Teo Y, Shcherbakov D, Vasella A, Böttger EC, Crich D. Influence of 4'-O-Glycoside Constitution and Configuration on Ribosomal Selectivity of Paromomycin. J Am Chem Soc 2015; 137:7706-17. [PMID: 26024064 DOI: 10.1021/jacs.5b02248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of 20 4'-O-glycosides of the aminoglycoside antibiotic paromomycin were synthesized and evaluated for their ability to inhibit protein synthesis by bacterial, mitochondrial and cytosolic ribosomes. Target selectivity, i.e., inhibition of the bacterial ribosome over eukaryotic mitochondrial and cytosolic ribosomes, which is predictive of antibacterial activity with reduced ototoxicity and systemic toxicity, was greater for the equatorial than for the axial pyranosides, and greater for the d-pentopyranosides than for the l-pentopyranosides and d-hexopyranosides. In particular, 4'-O-β-d-xylopyranosyl paromomycin shows antibacterioribosomal activity comparable to that of paromomycin, but is significantly more selective showing considerably reduced affinity for the cytosolic ribosome and for the A1555G mutant mitochondrial ribosome associated with hypersusceptibility to drug-induced ototoxicity. Compound antibacterioribosomal activity correlates with antibacterial activity, and the ribosomally more active compounds show activity against Escherichia coli, Klebsiella pneumonia, Enterobacter cloacae, Acinetobacter baumannii, and methicillin-resistant Staphylococcus aureus (MRSA). The paromomycin glycosides retain activity against clinical strains of MRSA that are resistant to paromomycin, which is demonstrated to be a consequence of 4'-O-glycosylation blocking the action of 4'-aminoglycoside nucleotidyl transferases by the use of recombinant E. coli carrying the specific resistance determinant.
Collapse
Affiliation(s)
- Takahiko Matsushita
- †Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Weiwei Chen
- †Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Reda Juskeviciene
- ‡Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Youjin Teo
- ‡Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Dimitri Shcherbakov
- ‡Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Andrea Vasella
- §Laboratorium für Organische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Erik C Böttger
- ‡Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - David Crich
- †Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| |
Collapse
|
32
|
Maurer FP, Bruderer VL, Castelberg C, Ritter C, Scherbakov D, Bloemberg GV, Böttger EC. Aminoglycoside-modifying enzymes determine the innate susceptibility to aminoglycoside antibiotics in rapidly growing mycobacteria. J Antimicrob Chemother 2015; 70:1412-9. [PMID: 25604746 DOI: 10.1093/jac/dku550] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/08/2014] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Infections caused by the rapidly growing mycobacterium (RGM) Mycobacterium abscessus are notoriously difficult to treat due to the innate resistance of M. abscessus to most clinically available antimicrobials. Aminoglycoside antibiotics (AGA) are a cornerstone of antimicrobial chemotherapy against M. abscessus infections, although little is known about intrinsic drug resistance mechanisms. We investigated the role of chromosomally encoded putative aminoglycoside-modifying enzymes (AME) in AGA susceptibility in M. abscessus. METHODS Clinical isolates of M. abscessus were tested for susceptibility to a series of AGA with different substituents at positions 2', 3' and 4' of ring 1 in MIC assays. Cell-free extracts of M. abscessus type strain ATCC 19977 and Mycobacterium smegmatis strains SZ380 [aac(2')-Id(+)], EP10 [aac(2')-Id(-)] and SZ461 [aac(2')-Id(+), rrs A1408G] were investigated for AGA acetylation activity using thin-layer chromatography (TLC). Cell-free ribosome translation assays were performed to directly study drug-target interaction. RESULTS Cell-free translation assays demonstrated that ribosomes of M. abscessus and M. smegmatis show comparable susceptibility to all tested AGA. MIC assays for M. abscessus and M. smegmatis, however, consistently showed the lowest MIC values for 2'-hydroxy-AGA as compared with 2'-amino-AGA, indicating that an aminoglycoside-2'-acetyltransferase, Aac(2'), contributes to innate AGA susceptibility. TLC experiments confirmed enzymatic activity consistent with Aac(2'). Using M. smegmatis as a model for RGM, acetyltransferase activity was shown to be up-regulated in response to AGA-induced inhibition of protein synthesis. CONCLUSIONS Our findings point to AME as important determinants of AGA susceptibility in M. abscessus.
Collapse
Affiliation(s)
- Florian P Maurer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland Nationales Zentrum für Mykobakterien, Zürich, Switzerland
| | - Vera L Bruderer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Claudio Castelberg
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Claudia Ritter
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland Nationales Zentrum für Mykobakterien, Zürich, Switzerland
| | - Dimitri Scherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Guido V Bloemberg
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland Nationales Zentrum für Mykobakterien, Zürich, Switzerland
| |
Collapse
|
33
|
Duscha S, Boukari H, Shcherbakov D, Salian S, Silva S, Kendall A, Kato T, Akbergenov R, Perez-Fernandez D, Bernet B, Vaddi S, Thommes P, Schacht J, Crich D, Vasella A, Böttger EC. Identification and evaluation of improved 4'-O-(alkyl) 4,5-disubstituted 2-deoxystreptamines as next-generation aminoglycoside antibiotics. mBio 2014; 5:e01827-14. [PMID: 25271289 PMCID: PMC4196235 DOI: 10.1128/mbio.01827-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED The emerging epidemic of drug resistance places the development of efficacious and safe antibiotics in the spotlight of current research. Here, we report the design of next-generation aminoglycosides. Discovery efforts were driven by rational synthesis focusing on 4' alkylations of the aminoglycoside paromomycin, with the goal to alleviate the most severe and disabling side effect of aminoglycosides-irreversible hearing loss. Compounds were evaluated for target activity in in vitro ribosomal translation assays, antibacterial potency against selected pathogens, cytotoxicity against mammalian cells, and in vivo ototoxicity. The results of this study produced potent compounds with excellent selectivity at the ribosomal target, promising antibacterial activity, and little, if any, ototoxicity upon chronic administration. The favorable biocompatibility profile combined with the promising antibacterial activity emphasizes the potential of next-generation aminoglycosides in the treatment of infectious diseases without the risk of ototoxicity. IMPORTANCE The ever-widening epidemic of multidrug-resistant infectious diseases and the paucity of novel antibacterial agents emerging from modern screening platforms mandate the reinvestigation of established drugs with an emphasis on improved biocompatibility and overcoming resistance mechanisms. Here, we describe the preparation and evaluation of derivatives of the established aminoglycoside antibiotic paromomycin that effectively remove its biggest deficiency, ototoxicity, and overcome certain bacterial resistance mechanisms.
Collapse
Affiliation(s)
- Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Sumantha Salian
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Sandrina Silva
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Ann Kendall
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Takayuki Kato
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Bruno Bernet
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | | | - Pia Thommes
- Euprotec Limited, Manchester, United Kingdom
| | - Jochen Schacht
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| |
Collapse
|
34
|
Sanbonmatsu KY. Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics. J Mol Biol 2014; 426:3197-3200. [DOI: 10.1016/j.jmb.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
35
|
Mandhapati AR, Shcherbakov D, Duscha S, Vasella A, Böttger EC, Crich D. Importance of the 6'-hydroxy group and its configuration for apramycin activity. ChemMedChem 2014; 9:2074-83. [PMID: 25045149 DOI: 10.1002/cmdc.201402146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 01/08/2023]
Abstract
A series of apramycin derivatives was prepared and investigated for antibacterial activity and the ability to inhibit protein synthesis in cell-free translation assays. The effect of various modifications at the 6'- and N7'-positions on antiribosomal activity is discussed in terms of their influence on drug binding to specific residues in the decoding A-site. These studies contribute to the development of a structure-activity relationship for the antibacterial activity of the apramycin class of aminoglycosides and to the future design and development of more active and less toxic antibiotics.
Collapse
Affiliation(s)
- Appi Reddy Mandhapati
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (USA)
| | | | | | | | | | | |
Collapse
|
36
|
Dudek M, Romanowska J, Wituła T, Trylska J. Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies. Biochimie 2014; 102:188-202. [PMID: 24769038 DOI: 10.1016/j.biochi.2014.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.
Collapse
Affiliation(s)
- Marta Dudek
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland.
| |
Collapse
|
37
|
Lioy VS, Goussard S, Guerineau V, Yoon EJ, Courvalin P, Galimand M, Grillot-Courvalin C. Aminoglycoside resistance 16S rRNA methyltransferases block endogenous methylation, affect translation efficiency and fitness of the host. RNA (NEW YORK, N.Y.) 2014; 20:382-91. [PMID: 24398977 PMCID: PMC3923132 DOI: 10.1261/rna.042572.113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/06/2013] [Indexed: 05/21/2023]
Abstract
In Gram-negative bacteria, acquired 16S rRNA methyltransferases ArmA and NpmA confer high-level resistance to all clinically useful aminoglycosides by modifying, respectively, G1405 and A1408 in the A-site. These enzymes must coexist with several endogenous methyltransferases that are essential for fine-tuning of the decoding center, such as RsmH and RsmI in Escherichia coli, which methylate C1402 and RsmF C1407. The resistance methyltransferases have a contrasting distribution--ArmA has spread worldwide, whereas a single clinical isolate producing NpmA has been reported. The rate of dissemination of resistance depends on the fitness cost associated with its expression. We have compared ArmA and NpmA in isogenic Escherichia coli harboring the corresponding structural genes and their inactive point mutants cloned under the control of their native constitutive promoter in the stable plasmid pGB2. Growth rate determination and competition experiments showed that ArmA had a fitness cost due to methylation of G1405, whereas NpmA conferred only a slight disadvantage to the host due to production of the enzyme. MALDI MS indicated that ArmA impeded one of the methylations at C1402 by RsmI, and not at C1407 as previously proposed, whereas NpmA blocked the activity of RsmF at C1407. A dual luciferase assay showed that methylation at G1405 and A1408 and lack of methylation at C1407 affect translation accuracy. These results indicate that resistance methyltransferases impair endogenous methylation with different consequences on cell fitness.
Collapse
Affiliation(s)
- Virginia S. Lioy
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
| | - Sylvie Goussard
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
| | - Vincent Guerineau
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Eun-Jeong Yoon
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
| | - Patrice Courvalin
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
| | - Marc Galimand
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
- Corresponding authorsE-mail E-mail
| | - Catherine Grillot-Courvalin
- Institut Pasteur, Unité des Agents Antibactériens, 75724 Paris Cedex 15, France
- Corresponding authorsE-mail E-mail
| |
Collapse
|
38
|
Chen W, Matsushita T, Shcherbakov D, Boukari H, Vasella A, Böttger EC, Crich D. Synthesis, antiribosomal and antibacterial activity of 4′-O-glycopyranosyl paromomycin aminoglycoside antibiotics. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00119b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
4′-O-Glycopyranosylation of the aminoglycoside paromomycin affects differentially the inhibition of prokaryotic and eukaryotic ribosomes and influences antibacterial activity against MRSA.
Collapse
Affiliation(s)
- Weiwei Chen
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| | | | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie
- Universität Zürich
- 8006 Zürich
- Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie
- Universität Zürich
- 8006 Zürich
- Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie
- Universität Zürich
- 8006 Zürich
- Switzerland
| | - David Crich
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| |
Collapse
|
39
|
Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Böttger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun 2014; 5:3112. [PMID: 24473108 PMCID: PMC3942853 DOI: 10.1038/ncomms4112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023] Open
Abstract
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
Collapse
Affiliation(s)
- Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
- These authors contributed equally to this work
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
- These authors contributed equally to this work
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Ng Chyan Leong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- These authors contributed equally to this work
| | - Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashmi Patak
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Srinivas Reddy Dubbaka
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Swapna Vaddi
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - Pia Thommes
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| |
Collapse
|
40
|
Shalev M, Baasov T. When Proteins Start to Make Sense: Fine-tuning Aminoglycosides for PTC Suppression Therapy. MEDCHEMCOMM 2014; 5:1092-1105. [PMID: 25147726 DOI: 10.1039/c4md00081a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aminoglycosides (AGs) are highly potent antibacterial agents, which are known to exert their deleterious effects on bacterial cells by interfering with the translation process, leading to aberrant protein synthesis that usually results in cell death. Nearly 45 years ago, AGs were shown to induce read-through activity in prokaryotic systems by selectively encoding tRNA molecules at premature termination codon (PTC) positions; resulting in the generation of full length functional proteins. However, only in the last 20 years this ability has been demonstrated in eukaryotic systems, highlighting their potential as therapeutic agents to treat PTC induced genetic disorders. Despite the great potential, AGs use in these manners is quite restricted due to relatively high toxicity values observed upon their administration. Over the last few years several synthetic derivatives were developed to overcome some of the enhanced toxicity issues, while in parallel showed significantly improved PTC suppression activity in various in-vitro, ex-vivo and in-vivo models of a variety of different diseases models underling by PTC mutations. Although these derivatives hold great promise to serve as therapeutic candidates they also demonstrate the necessity to further understand the molecular mechanisms of which AGs confer their biological activity in eukaryotic cells for further rational drug design. Recent achievements in structural research shed light on AGs mechanism of action and opened a new avenue in the development of new and improved therapeutic derivatives. The following manuscript highlights these accomplishments and summarizes their contributions to the state of art rational drug design.
Collapse
Affiliation(s)
- Moran Shalev
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
41
|
Jiang J, Sakakibara Y, Chow CS. Helix 69: A Multitasking RNA Motif as a Novel Drug Target. Isr J Chem 2013. [DOI: 10.1002/ijch.201300012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
42
|
Li DG, Liu B, Zhou DW. Structural characterization of enzymatic products in the dTDP-d-Qui4NFo biosynthetic pathway using electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:681-690. [PMID: 23418147 DOI: 10.1002/rcm.6501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 12/04/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
RATIONALE Structural characterization of biosynthetic precursors is very important in assigning enzymatic function to proteins that have been identified as functional homologs on the basis of sequence homology alone. The objective of this study is to demonstrate the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) as a powerful technique for the characterization of enzymatic products in the biosynthetic pathway of deoxythymidine 5'-diphosphate-4-formamido-4,6-dideoxy-D-glucose (dTDP-D-Qui4NFo) in Providencia alcalifaciens O30. METHODS The glucose-1-phosphate thymidyltransferase (RmlA), dTDP-d-glucose 4,6-dehydratase (RmlB), dTDP-4-keto-6-deoxy-d-glucose aminotransferase (VioA), and formyltransferase (VioF) catalyzed reactions were directly monitored by ESI-MS, followed by a detailed structural characterization of the final enzymatic products using ESI-MS/MS in the negative-ion mode after minimal cleanup. RESULTS The biosynthetic pathway of dTDP-D-Qui4NFo, beginning from α-D-glucose-1-phosphate in four reaction steps catalyzed by RmlA, RmlB, VioA and VioF, was characterized solely by ESI-MS/MS. The results obtained were in good agreement with that of traditional high-performance liquid chromatography (HPLC) monitoring and preparation, as well as nuclear magnetic resonance (NMR) and ESI-MS structural characterization. CONCLUSIONS MS provides efficient and simple characterization of important unusual dTDP-sugar biosynthetic pathways in the O-chains of bacterial lipopolysaccharides.
Collapse
Affiliation(s)
- Dian-Ge Li
- TEDA School of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Research Center for Functional Genomics and Biochip, Ministry of Education, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | | | | |
Collapse
|
43
|
Abstract
This is a review of RNA as a target for small molecules (ribosomes, riboswitches, regulatory RNAs) and RNA-derived oligonucleotides as tools (antisense/small interfering RNA, ribozymes, aptamers/decoy RNA and microRNA). This review highlights the present state of research using RNA as a drug target or as a potential drug candidate and explains at which stage and to what extent rational design could eventually be involved. Special attention has been paid to the recent potential clinical applications of RNA either as drugs or drug targets. The review deals mainly with mechanistic approaches rather than with physicochemical or computational aspects of RNA-based drug design.
Collapse
Affiliation(s)
- Irene M Lagoja
- Katholieke Universiteit Leuven, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium +32 16 337396 ; +32 16 337340 ;
| | | |
Collapse
|
44
|
Salian S, Matt T, Akbergenov R, Harish S, Meyer M, Duscha S, Shcherbakov D, Bernet BB, Vasella A, Westhof E, Böttger EC. Structure-activity relationships among the kanamycin aminoglycosides: role of ring I hydroxyl and amino groups. Antimicrob Agents Chemother 2012; 56:6104-8. [PMID: 22948879 PMCID: PMC3497201 DOI: 10.1128/aac.01326-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/26/2012] [Indexed: 11/20/2022] Open
Abstract
The kanamycins form an important subgroup of the 4,6-disubstituted 2-deoxystreptamine aminoglycoside antibiotics, comprising kanamycin A, kanamycin B, tobramycin, and dibekacin. These compounds interfere with protein synthesis by targeting the ribosomal decoding A site, and they differ in the numbers and locations of amino and hydroxy groups of the glucopyranosyl moiety (ring I). We synthesized kanamycin analogues characterized by subtle variations of the 2' and 6' substituents of ring I. The functional activities of the kanamycins and the synthesized analogues were investigated (i) in cell-free translation assays on wild-type and mutant bacterial ribosomes to study drug-target interaction, (ii) in MIC assays to assess antibacterial activity, and (iii) in rabbit reticulocyte translation assays to determine activity on eukaryotic ribosomes. Position 2' forms an intramolecular H bond with O5 of ring II, helping the relative orientations of the two rings with respect to each other. This bond becomes critical for drug activity when a 6'-OH substituent is present.
Collapse
Affiliation(s)
- Sumantha Salian
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Shinde Harish
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Bruno B. Bernet
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire Centre National de la Recherche Scientifique, Strasbourg, France
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| |
Collapse
|
45
|
Bidou L, Allamand V, Rousset JP, Namy O. Sense from nonsense: therapies for premature stop codon diseases. Trends Mol Med 2012; 18:679-88. [PMID: 23083810 DOI: 10.1016/j.molmed.2012.09.008] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 02/04/2023]
Abstract
Ten percent of inherited diseases are caused by premature termination codon (PTC) mutations that lead to degradation of the mRNA template and to the production of a non-functional, truncated polypeptide. In addition, many acquired mutations in cancer introduce similar PTCs. In 1999, proof-of-concept for treating these disorders was obtained in a mouse model of muscular dystrophy, when administration of aminoglycosides restored protein translation by inducing the ribosome to bypass a PTC. Since, many studies have validated this approach, but despite the promise of PTC readthrough therapies, the mechanisms of translation termination remain to be precisely elucidated before even more progress can be made. Here, we review the molecular basis for PTC readthrough in eukaryotes and describe currently available compounds with significant therapeutic potential for treating genetic disorders and cancer.
Collapse
|
46
|
Romanowska J, Reuter N, Trylska J. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins 2012; 81:63-80. [PMID: 22907688 DOI: 10.1002/prot.24163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/02/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022]
Abstract
Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the bacterial ribosomal RNA and interfere with the translation process. However, bacteria produce aminoglycoside modifying enzymes (AME) to resist aminoglycoside actions. AMEs form a variable group and yet they specifically recognize and efficiently bind aminoglycosides, which are also diverse in terms of total net charge and the number of pseudo-sugar rings. Here, we present the results of 25 molecular dynamics simulations of three AME representatives and aminoglycoside ribosomal RNA binding site, unliganded and complexed with an aminoglycoside, kanamycin A. A comparison of the aminoglycoside binding sites in these different receptors revealed that the enzymes efficiently mimic the nucleic acid environment of the ribosomal RNA binding cleft. Although internal dynamics of AMEs and their interaction patterns with aminoglycosides differ, the energetical analysis showed that the most favorable sites are virtually the same in the enzymes and RNA. The most copied interactions were of electrostatic nature, but stacking was also replicated in one AME:kanamycin complex. In addition, we found that some water-mediated interactions were very stable in the simulations of the complexes. We show that our simulations reproduce well findings from NMR or X-ray structural studies, as well as results from directed mutagenesis. The outcomes of our analyses provide new insight into aminoglycoside resistance mechanism that is related to the enzymatic modification of these drugs.
Collapse
Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland.
| | | | | |
Collapse
|
47
|
Studying modification of aminoglycoside antibiotics by resistance-causing enzymes via microarray. Methods Mol Biol 2012; 808:303-20. [PMID: 22057534 DOI: 10.1007/978-1-61779-373-8_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Widespread bacterial resistance to antibiotics is a significant public health concern. To remain a step ahead of evolving bacteria, new methods to study resistance to antibacterials and to uncover novel antibiotics that evade resistance are urgently needed. Herein, microarray-based methods that have been developed to study aminoglycoside modification by resistance-causing enzymes are reviewed. These arrays can also be used to study the binding of aminoglycoside antibiotics to a mimic of their therapeutic target, the rRNA aminoacyl site (A-site), and how modification by resistance-causing enzymes affects their abilities to bind RNA.
Collapse
|
48
|
Kondo J. A Structural Basis for the Antibiotic Resistance Conferred by an A1408G Mutation in 16S rRNA and for the Antiprotozoal Activity of Aminoglycosides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
49
|
Kondo J. A Structural Basis for the Antibiotic Resistance Conferred by an A1408G Mutation in 16S rRNA and for the Antiprotozoal Activity of Aminoglycosides. Angew Chem Int Ed Engl 2011; 51:465-8. [DOI: 10.1002/anie.201106084] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Indexed: 01/05/2023]
|
50
|
Romanowska J, McCammon JA, Trylska J. Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. PLoS Comput Biol 2011; 7:e1002099. [PMID: 21814503 PMCID: PMC3140962 DOI: 10.1371/journal.pcbi.1002099] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/08/2011] [Indexed: 01/15/2023] Open
Abstract
Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations.
Collapse
MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Drug Resistance, Bacterial/drug effects
- Drug Resistance, Bacterial/genetics
- Hydrogen Bonding
- Molecular Dynamics Simulation
- Mutation
- Paromomycin/pharmacology
- Protein Binding
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
Collapse
Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland.
| | | | | |
Collapse
|