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Roy D, Kaul G, Akhir A, Sharma AK, Saha S, Chopra S, Panda G. Discovery and Biological Evaluation of Novel Diarylmethyl Amines Active against Drug Resistant
S. aureus
and
Enterococcus. ChemistrySelect 2022. [DOI: 10.1002/slct.202103904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Deblina Roy
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
- Department of Chemistry Institute of Science Banaras Hindu University Varanasi 221005 UP India
| | - Grace Kaul
- Division of Microbiology CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
- Academy of Scientific and Innovative Research New Delhi 110001 India
| | - Abdul Akhir
- Division of Microbiology CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
| | - Ashok Kumar Sharma
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
| | - Satyen Saha
- Department of Chemistry Institute of Science Banaras Hindu University Varanasi 221005 UP India
| | - Sidharth Chopra
- Division of Microbiology CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
- Academy of Scientific and Innovative Research New Delhi 110001 India
| | - Gautam Panda
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031 India
- Academy of Scientific and Innovative Research New Delhi 110001 India
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2
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Bollu R, Banu S, Bantu R, Reddy AG, Nagarapu L, Sirisha K, Kumar CG, Gunda SK, Shaik K. Potential antimicrobial agents from triazole-functionalized 2 H -benzo[ b ][1,4]oxazin-3(4 H )-ones. Bioorg Med Chem Lett 2017; 27:5158-5162. [DOI: 10.1016/j.bmcl.2017.10.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/13/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022]
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4
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Cui P, Li X, Zhu M, Wang B, Liu J, Chen H. Design, synthesis and antimicrobial activities of thiouracil derivatives containing triazolo-thiadiazole as SecA inhibitors. Eur J Med Chem 2016; 127:159-165. [PMID: 28039774 DOI: 10.1016/j.ejmech.2016.12.053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 11/28/2022]
Abstract
A series of novel thiouracil derivatives containing a triazolo-thiadiazole moiety (7a-7l) have been synthesized by structural modifications on a lead SecA inhibitor, 2. All the compounds have been evaluated for their antibacterial activities against Bacillus amyloliquefaciens, Staphylococcus aureus, and Bacillus subtilis. Compounds 7d and 7g were also tested for their inhibitory activities against SecA ATPase due to their promising antimicrobial activities. The inhibitory activity of compound 7d was found to be higher than that of 2. Molecular docking work suggests that compound 7d might bind at a pocket close to the ATPase ATP-binding domain.
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Affiliation(s)
- Penglei Cui
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China; College of Science, Agricultural University of Hebei, Baoding 071001, China
| | - Xiaoliu Li
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
| | - Mengyuan Zhu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Jing Liu
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Hua Chen
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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5
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Czarny TL, Brown ED. A Small-Molecule Screening Platform for the Discovery of Inhibitors of Undecaprenyl Diphosphate Synthase. ACS Infect Dis 2016; 2:489-99. [PMID: 27626101 DOI: 10.1021/acsinfecdis.6b00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The bacterial cell wall has long been a celebrated target for antibacterial drug discovery due to its critical nature in bacteria and absence in mammalian systems. At the heart of the cell wall biosynthetic pathway lies undecaprenyl phosphate (Und-P), the lipid-linked carrier upon which the bacterial cell wall is built. This study exploits recent insights into the link between late-stage wall teichoic acid inhibition and Und-P production, in Gram-positive organisms, to develop a cell-based small-molecule screening platform that enriches for inhibitors of undecaprenyl diphosphate synthase (UppS). Screening a chemical collection of 142,000 small molecules resulted in the identification of 6 new inhibitors of UppS. To date, inhibitors of UppS have generally shown off-target effects on membrane potential due to their physical-chemical characteristics. We demonstrate that MAC-0547630, one of the six inhibitors identified, exhibits selective, nanomolar inhibition against UppS without off-target effects on membrane potential. Such characteristics make it a unique chemical probe for exploring the inhibition of UppS in bacterial cell systems.
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Affiliation(s)
- Tomasz L. Czarny
- Department
of Biochemistry and Biomedical Sciences and ‡Michael G. DeGroote Institute of
Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Eric D. Brown
- Department
of Biochemistry and Biomedical Sciences and ‡Michael G. DeGroote Institute of
Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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6
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Antibacterial activity of Mannich bases derived from 2-naphthols, aromatic aldehydes and secondary aliphatic amines. Bioorg Med Chem Lett 2016; 26:2498-2502. [DOI: 10.1016/j.bmcl.2016.03.098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 01/14/2023]
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7
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Liu X, Lei Z, Liu D, Wang Z. Development of a sandwiched microarray platform for studying the interactions of antibiotics with Staphylococcus aureus. Anal Chim Acta 2016; 917:93-100. [PMID: 27026605 DOI: 10.1016/j.aca.2016.02.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/18/2022]
Abstract
It still confronts an outstanding challenge to screen efficient antibacterial drugs from millions of potential antibiotic candidates. In this regard, a sandwiched microarray platform has been developed to culture live bacteria and carry out high-throughput screening antibacterial drugs. The optimized lectin-hydrogel microarray can be used as an efficient bacterial capturing and culturing platform, which is beneficial to identify spots and collect data. At the same time, a matching drug-laden polyacrylamide microarray with Luria-Bertani (LB) culture medium can be generated automatically and accurately by using a standard non-contacting procedure. A large number of microscale culture chambers (more than 100 individual samples) between two microarrays can be formed by linking two aligned hydrogel spots using LB culture medium, where live bacteria can be co-cultured with drug candidates. Using Staphylococcus aureus (S. aureus) and four well-known antibiotics (amoxicillin, vancomycin, streptomycin and chloramphenicol) as model system, the MIC (minimum inhibitory concentration) values of the antibiotics can be determined by the drug induced change of bacterial growth, and the results demonstrate that the MIC values of amoxicillin, vancomycin and streptomycin are 1.7 μg mL(-1), 3.3 μg mL(-1) and 10.3 μg mL(-1), respectively.
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Affiliation(s)
- Xia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China
| | - Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China.
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8
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Using adjuvants and environmental factors to modulate the activity of antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:926-35. [PMID: 26751595 DOI: 10.1016/j.bbamem.2015.12.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 12/12/2022]
Abstract
The increase in antibiotic resistant and multi-drug resistant bacterial infections has serious implications for the future of health care. The difficulty in finding both new microbial targets and new drugs against existing targets adds to the concern. The use of combination and adjuvant therapies are potential strategies to counter this threat. Antimicrobial peptides (AMPs) are a promising class of antibiotics (ABs), particularly for topical and surface applications. Efforts have been directed toward a number of strategies, including the use of conventional ABs combined with AMPs, and the use of potentiating agents to increase the performance of AMPs. This review focuses on combination strategies such as adjuvants and the manipulation of environmental variables to improve the efficacy of AMPs as potential therapeutic agents. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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9
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Chemical inhibition of bacterial ribosome biogenesis shows efficacy in a worm infection model. Antimicrob Agents Chemother 2015; 59:2918-20. [PMID: 25712357 DOI: 10.1128/aac.04690-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/14/2015] [Indexed: 11/20/2022] Open
Abstract
The development of antibacterial compounds that perturb novel processes is an imperative in the challenge presented by widespread antibiotic resistance. While many antibiotics target the ribosome, molecules that inhibit ribosome assembly have yet to be used in this manner. Here we show that a novel inhibitor of ribosome biogenesis, lamotrigine, is capable of rescuing Caenorhabditis elegans from an established Salmonella infection, revealing that ribosome biogenesis is a promising target for the development of new antibiotics.
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10
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McPhillie MJ, Cain RM, Narramore S, Fishwick CWG, Simmons KJ. Computational Methods to Identify New Antibacterial Targets. Chem Biol Drug Des 2014; 85:22-9. [DOI: 10.1111/cbdd.12385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 01/09/2023]
Affiliation(s)
| | - Ricky M. Cain
- School of Chemistry; University of Leeds; Leeds LS2 9JT UK
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11
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Bloes DA, Kretschmer D, Peschel A. Enemy attraction: bacterial agonists for leukocyte chemotaxis receptors. Nat Rev Microbiol 2014; 13:95-104. [PMID: 25534805 DOI: 10.1038/nrmicro3390] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The innate immune system recognizes conserved microorganism-associated molecular patterns (MAMPs), some of which are sensed by G protein-coupled receptors (GPCRs), and this leads to chemotactic leukocyte influx. Recent studies have indicated that these processes are crucial for host defence and rely on a larger set of chemotactic MAMPs and corresponding GPCRs than was previously thought. Agonists, such as bacterial formyl peptides, enterococcal pheromone peptides, staphylococcal peptide toxins, bacterial fermentation products and the Helicobacter pylori peptide HP(2-20), stimulate specific GPCRs. The importance of leukocyte chemotaxis in host defence is highlighted by the fact that some bacterial pathogens produce chemotaxis inhibitors. How the various chemoattractants, receptors and antagonists shape antibacterial host defence represents an important topic for future research.
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Affiliation(s)
- Dominik Alexander Bloes
- Cellular and Molecular Microbiology Division, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
| | - Dorothee Kretschmer
- Cellular and Molecular Microbiology Division, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
| | - Andreas Peschel
- Cellular and Molecular Microbiology Division, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
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Kollipara R, Downing C, Lee M, Guidry J, Curtis S, Tyring S. Current and emerging drugs for acute bacterial skin and skin structure infections: an update. Expert Opin Emerg Drugs 2014; 19:431-40. [DOI: 10.1517/14728214.2014.955015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Shapiro AB, Gu RF, Gao N. Dimerization of isolated Pseudomonas aeruginosa lipopolysaccharide transporter component LptA. Biochem Biophys Res Commun 2014; 450:1327-32. [DOI: 10.1016/j.bbrc.2014.06.138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/26/2014] [Indexed: 11/16/2022]
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14
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Discovery of novel cell wall-active compounds using P ywaC, a sensitive reporter of cell wall stress, in the model gram-positive bacterium Bacillus subtilis. Antimicrob Agents Chemother 2014; 58:3261-9. [PMID: 24687489 DOI: 10.1128/aac.02352-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of antibiotic resistance in recent years has radically reduced the clinical efficacy of many antibacterial treatments and now poses a significant threat to public health. One of the earliest studied well-validated targets for antimicrobial discovery is the bacterial cell wall. The essential nature of this pathway, its conservation among bacterial pathogens, and its absence in human biology have made cell wall synthesis an attractive pathway for new antibiotic drug discovery. Herein, we describe a highly sensitive screening methodology for identifying chemical agents that perturb cell wall synthesis, using the model of the Gram-positive bacterium Bacillus subtilis. We report on a cell-based pilot screen of 26,000 small molecules to look for cell wall-active chemicals in real time using an autonomous luminescence gene cluster driven by the promoter of ywaC, which encodes a guanosine tetra(penta)phosphate synthetase that is expressed under cell wall stress. The promoter-reporter system was generally much more sensitive than growth inhibition testing and responded almost exclusively to cell wall-active antibiotics. Follow-up testing of the compounds from the pilot screen with secondary assays to verify the mechanism of action led to the discovery of 9 novel cell wall-active compounds.
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15
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Donkor ES. Sequencing of bacterial genomes: principles and insights into pathogenesis and development of antibiotics. Genes (Basel) 2013; 4:556-72. [PMID: 24705262 PMCID: PMC3927574 DOI: 10.3390/genes4040556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/24/2013] [Accepted: 08/27/2013] [Indexed: 11/17/2022] Open
Abstract
The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics.
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Affiliation(s)
- Eric S Donkor
- Department of Microbiology, University of Ghana Medical School, P. O. Box 4236, Accra, Ghana.
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Abstract
AbstractBacterial resistance to commonly used antibiotics is constantly increasing. Bacteria particularly dangerous for human life are methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium and fluoroquinolone-resistant Pseudomonas aeruginosa. Hence, there is an incessant need for developing compounds with new modes of action and seeking alternate drug targets. In this review, the authors discuss the current situation of antibacterial medicines and present data on new antibiotic targets. Moreover, alternatives to antibiotics, such as bacteriophages, antimicrobial peptides and monoclonal antibodies, are presented. The authors also draw attention to the valuable features of natural sources in developing antibacterial compounds. The need to prevent and control infections as well as the reasonable use of currently available antibiotics is also emphasized.
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Lei EK, Pereira MP, Kelley SO. Tuning the intracellular bacterial targeting of peptidic vectors. Angew Chem Int Ed Engl 2013; 52:9660-3. [PMID: 23893882 DOI: 10.1002/anie.201302265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 06/20/2013] [Indexed: 01/07/2023]
Affiliation(s)
- Eric K Lei
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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18
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Lei EK, Pereira MP, Kelley SO. Tuning the Intracellular Bacterial Targeting of Peptidic Vectors. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat Struct Mol Biol 2013; 20:843-50. [DOI: 10.1038/nsmb.2615] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/15/2013] [Indexed: 12/23/2022]
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20
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Tanouchi Y, Lee AJ, Meredith H, You L. Programmed cell death in bacteria and implications for antibiotic therapy. Trends Microbiol 2013; 21:265-70. [PMID: 23684151 DOI: 10.1016/j.tim.2013.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
It is now well appreciated that programmed cell death (PCD) plays critical roles in the life cycle of diverse bacterial species. It is an apparently paradoxical behavior as it does not benefit the cells undergoing PCD. However, growing evidence suggests that PCD can be 'altruistic': the dead cells may directly or indirectly benefit survivors through generation of public goods. This property provides a potential explanation on how PCD can evolve as an extreme form of cooperation, although many questions remain to be addressed. From another perspective, as PCD plays a critical role in bacterial pathogenesis, it has been proposed as a potential target for new antibacterial therapy. To this end, understanding the population and evolutionary dynamics resulting from PCD and public goods production may be a key to the success of designing effective antibiotic treatment.
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Affiliation(s)
- Yu Tanouchi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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Abstract
INTRODUCTION Natural products have long been instrumental for discovering antibiotics, but many pharmaceutical companies abandoned this field and new antibiotics declined. In contrast, microbial resistance to current antibiotics has approached critical levels. AREAS COVERED This article gives historical perspectives by providing background about present-day economic realities and medical needs for antibiotic research, whose pipeline is mostly focused toward older known agents and newer semi-synthetic derivatives. Future research trends and projected technological developments open many innovative opportunities to discover novel antibacterials and find ways to control pathogenic bacteria without conventional antibiotics that provoke resistance. EXPERT OPINION The successful registration of daptomycin, retapamulin and fidaxomicin indicate the re-emergence of natural products has already begun. Semi-synthetic derivatives from other under-explored classes are progressing. More effort is being put into approaches such as total synthesis, discovery of new structural scaffolds for synthesis, alterations of biosynthetic pathways, combinatorial biosynthesis, new screening targets and new resources from which to isolate natural products. A return to successful screening of actinomycetes depends on solving the rate-limiting dereplication obstacle. Long-term solutions need to come from greater exploration of the massive numbers of uncultured microbes. An ultimate solution to the antibiotic-promoted microbial resistance cycle may lie in finding ways to control bacteria by non-lethal means.
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Abstract
The United States GAIN (Generating Antibiotic Incentives Now) Act is a call to action for new antibiotic discovery and development that arises from a ground swell of concern over declining activity in this therapeutic area in the pharmaceutical sector. The GAIN Act aims to provide economic incentives for antibiotic drug discovery in the form of market exclusivity and accelerated drug approval processes. The legislation comes on the heels of nearly two decades of failure using the tools of modern drug discovery to find new antibiotic drugs. The lessons of failure are examined herein as are the prospects for a renewed effort in antibiotic drug discovery and development stimulated by new investments in both the public and private sector.
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Affiliation(s)
- Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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Gao J, Cheng Y, Cui W, Zhang F, Zhang H, Du Y, Ji M. Prediction of the binding modes between macrolactin N and peptide deformylase from Staphylococcus aureus by molecular docking and molecular dynamics simulations. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0303-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shapiro AB, Ross PL, Gao N, Livchak S, Kern G, Yang W, Andrews B, Thresher J. A high-throughput-compatible fluorescence anisotropy-based assay for competitive inhibitors of Escherichia coli UDP-N-acetylglucosamine acyltransferase (LpxA). ACTA ACUST UNITED AC 2012; 18:341-7. [PMID: 23015018 DOI: 10.1177/1087057112462062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
LpxA, the first enzyme in the biosynthetic pathway for the Lipid A component of the outer membrane lipopolysaccharide in Gram-negative bacteria, is a potential target for novel antibacterial drug discovery. A fluorescence polarization assay was developed to facilitate high-throughput screening for competitive inhibitors of LpxA. The assay detects displacement of a fluorescently labeled peptide inhibitor, based on the previously reported inhibitor peptide 920, by active site ligands. The affinity of the fluorescent ligand was increased ~10-fold by acyl carrier protein (ACP). Competition with peptide binding was observed with UDP-N-acetylglucosamine (IC(50) ~6 mM), UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine (IC(50) ~200 nM), and DL-3-hydroxymyristic acid (IC(50) ~50 µM) and peptide 920 (IC(50) ~600 nM). The IC(50)s were not significantly affected by the presence of ACP.
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de Lima Procópio RE, da Silva IR, Martins MK, de Azevedo JL, de Araújo JM. Antibiotics produced by Streptomyces. Braz J Infect Dis 2012; 16:466-71. [DOI: 10.1016/j.bjid.2012.08.014] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/06/2012] [Indexed: 10/27/2022] Open
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Compounds of Alpinia katsumadai as potential efflux inhibitors in Mycobacterium smegmatis. Bioorg Med Chem 2012; 20:2701-6. [PMID: 22459211 DOI: 10.1016/j.bmc.2012.02.039] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/22/2022]
Abstract
Efflux pumps are one of the well established mechanisms that contribute to antibiotic resistance in bacteria, such as mycobacteria. As a result, the identification of efflux pump inhibitors is an attractive target in antimicrobial therapy. The isolated compounds, three diarylheptanoids, trans,trans-1,7-diphenylhepta-4,6-dien-3-one (1), (5R)-trans-1,7-diphenyl-5-hydroxyhept-6-en-3-one (2), (3S,5S)-trans-1,7-diphenylhept-1-ene-3,5-diol (3) and the flavonoid pinocembrin (4), from Alpinia katsumadai, Zingiberaceae, were examined for their antimycobacterial activity and their synergistic effects with different antibiotics against M. smegmatis mc(2) 155. Furthermore, these compounds were evaluated as potential EtBr efflux inhibitors. Although they showed weak antimycobacterial activities (MIC ≥ 64 mg/L), especially compound 1 revealed a significant activity on the EtBr accumulation and efflux as well as a synergistic effect in combination with rifampicin.
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Goemaere E, Melet A, Larue V, Lieutaud A, Alves de Sousa R, Chevalier J, Yimga-Djapa L, Giglione C, Huguet F, Alimi M, Meinnel T, Dardel F, Artaud I, Pagès JM. New peptide deformylase inhibitors and cooperative interaction: a combination to improve antibacterial activity. J Antimicrob Chemother 2012; 67:1392-400. [PMID: 22378679 DOI: 10.1093/jac/dks058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES Bacterial drug resistance is a worrying public health problem and there is an urgent need for research and development to provide new antibacterial molecules. Peptide deformylase (PDF) is now a well-described intracellular target selected for the design of a new antibiotic group, PDF inhibitors (PDFIs). The initial bacterial susceptibility to an inhibitor of a cytoplasmic target is directly associated with the diffusion of the compound through the membrane barrier of Gram-negative bacteria and with its cytosolic accumulation at the required concentration. METHODS We have recently demonstrated that the activity of different PDFIs is strongly dependent on the accumulation of the active molecules by using permeabilizing agents, efflux inhibitors or efflux-mutated strains. In this work we assessed various combination protocols using different putative inhibitors (PDFIs, methionine aminopeptidase inhibitors etc.) to improve antibacterial activity against various resistant Gram-negative bacteria. RESULTS The maximum effect was observed when combining actinonin with a dual inhibitor of methionine aminopeptidase and PDF, this molecule being also able to interact with the target while actinonin is bound to the PDF active site. CONCLUSIONS Such a combination of inhibitors acting on two tightly associated metabolic steps results in a cooperative effect on bacterial cells and opens an original way to combat multidrug-resistant bacteria.
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Affiliation(s)
- Emilie Goemaere
- UMR-MD1, Transporteurs Membranaires, Chimiorésistance et Drug-Design, Aix-Marseille Université, IRBA, Marseille, France
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Tan C, Phillip Smith R, Srimani JK, Riccione KA, Prasada S, Kuehn M, You L. The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. Mol Syst Biol 2012; 8:617. [PMID: 23047527 PMCID: PMC3472685 DOI: 10.1038/msb.2012.49] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/29/2012] [Indexed: 12/25/2022] Open
Abstract
The inoculum effect (IE) refers to the decreasing efficacy of an antibiotic with increasing bacterial density. It represents a unique strategy of antibiotic tolerance and it can complicate design of effective antibiotic treatment of bacterial infections. To gain insight into this phenomenon, we have analyzed responses of a lab strain of Escherichia coli to antibiotics that target the ribosome. We show that the IE can be explained by bistable inhibition of bacterial growth. A critical requirement for this bistability is sufficiently fast degradation of ribosomes, which can result from antibiotic-induced heat-shock response. Furthermore, antibiotics that elicit the IE can lead to 'band-pass' response of bacterial growth to periodic antibiotic treatment: the treatment efficacy drastically diminishes at intermediate frequencies of treatment. Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes.
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Affiliation(s)
- Cheemeng Tan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Jaydeep K Srimani
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Sameer Prasada
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Meta Kuehn
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
- Center for Systems Biology, Duke University, Durham, NC, USA
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Kirst HA. Recent derivatives from smaller classes of fermentation-derived antibacterials. Expert Opin Ther Pat 2011; 22:15-35. [DOI: 10.1517/13543776.2012.642370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet 2011; 7:e1002377. [PMID: 22125496 PMCID: PMC3219608 DOI: 10.1371/journal.pgen.1002377] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/24/2011] [Indexed: 12/28/2022] Open
Abstract
As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. Proper assembly of the cell envelope is essential for bacterial growth, environmental adaptation, and drug resistance. Yet, while the biological roles of the many genes and pathways involved in biosynthesis of the cell envelope have been studied extensively in isolation, how the myriad components intersect functionally to maintain envelope integrity under different growth conditions has not been explored systematically. Genome-scale genetic interaction screens have increasingly been performed to great impact in yeast; no analogous comprehensive studies have yet been reported for bacteria despite their prominence in human health and disease. We addressed this by using a synthetic genetic array technology to generate quantitative maps of genetic interactions encompassing virtually all the components of the cell envelope biosynthetic machinery of the classic model bacterium E. coli in two common laboratory growth conditions (rich and minimal medium). From the resulting networks of high-confidence genetic interactions, we identify condition-specific functional dependencies underlying envelope assembly and global remodeling of genetic backup mechanisms that ensure envelope integrity under environmental challenge.
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Moradpour Z, Ghasemian A. Modified phages: Novel antimicrobial agents to combat infectious diseases. Biotechnol Adv 2011; 29:732-8. [DOI: 10.1016/j.biotechadv.2011.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 05/25/2011] [Accepted: 06/06/2011] [Indexed: 12/12/2022]
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Gao J, Cheng Y, Cui W, Chen Q, Zhang F, Du Y, Ji M. 3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9672-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Robinson JA. Protein epitope mimetics as anti-infectives. Curr Opin Chem Biol 2011; 15:379-86. [PMID: 21419690 DOI: 10.1016/j.cbpa.2011.02.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/17/2011] [Indexed: 01/09/2023]
Abstract
There is growing interest in the design of synthetic molecules that mimic the structures and functions of epitopes found on the surface of peptides and proteins. Epitope mimetics can provide valuable tools to probe complex biological processes, as well as interesting leads for drug and vaccine discovery. One application of epitope mimetics is reviewed here, focusing on mimetics of the cationic antimicrobial peptides that form part of the innate immune response to microbial and viral infection in many organisms. Mimetics of these naturally occurring peptides and proteins may be useful to explore mechanisms of antimicrobial and immunomodulatory action, and as a potential source of new antibiotics to address one of the most pressing current threats to human health.
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Affiliation(s)
- John A Robinson
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Wörmann ME, Corrigan RM, Simpson PJ, Matthews SJ, Gründling A. Enzymatic activities and functional interdependencies of Bacillus subtilis lipoteichoic acid synthesis enzymes. Mol Microbiol 2010; 79:566-83. [PMID: 21255105 PMCID: PMC3089822 DOI: 10.1111/j.1365-2958.2010.07472.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Lipoteichoic acid (LTA) is an important cell wall polymer in Gram-positive bacteria. The enzyme responsible for polyglycerolphosphate LTA synthesis is LtaS, first described in Staphylococcus aureus. Four LtaS orthologues, LtaSBS, YfnI, YqgS and YvgJ, are present in Bacillus subtilis. Using an in vitro enzyme assay, we determined that all four proteins are Mn2+-dependent metal enzymes that use phosphatidylglycerol as a substrate. We show that LtaSBS, YfnI and YqgS can produce polymers, suggesting that these three proteins are bona-fide LTA synthases while YvgJ functions as an LTA primase, as indicated by the accumulation of a GroP-Glc2-DAG glycolipid. Western blot analysis of LTA produced by ltaSBS, yfnI, yqgS and yvgJ single, triple and the quadruple mutant, showed that LTA production was only abolished in the quadruple and the YvgJ-only expressing mutant. B. subtilis strains expressing YfnI in the absence of LtaSBS produced LTA of retarded mobility, presumably caused by an increase in chain length as suggested by a structural analysis of purified LTA. Taken together, the presented results indicate that the mere presence or absence of LTA cannot account for cell division and sporulation defects observed in the absence of individual enzymes and revealed an unexpected enzymatic interdependency of LtaS-type proteins in B. subtilis.
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Affiliation(s)
- Mirka E Wörmann
- Section of Microbiology Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Sutcliffe IC. Priming and elongation: dissection of the lipoteichoic acid biosynthetic pathway in Gram-positive bacteria. Mol Microbiol 2010; 79:553-6. [PMID: 21255102 DOI: 10.1111/j.1365-2958.2010.07480.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The biosynthesis of lipoteichoic acids is a potential target for the development of novel antimicrobials against significant Firmicute pathogens. Excellent progress has been made in recent years towards understanding the biochemistry and genetics of polyglycerophosphate lipoteichoic acid biosynthesis but it has remained unclear whether this pathway requires an initial 'priming' reaction to initiate synthesis on the glycolipid anchor. Recent work from the laboratory of Angelika Gründling, including a new study by Wörmann et al. in this issue of Molecular Microbiology, provides confirmation of the priming step and further insights into the functional redundancy of lipoteichoic acid biosynthesis enzymes in Bacillus subtilis.
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Affiliation(s)
- Iain C Sutcliffe
- Biomolecular and Biomedical Research Centre, School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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Mendoza N, Tyring SK. Emerging drugs for complicated skin and skin-structure infections. Expert Opin Emerg Drugs 2010; 15:509-20. [PMID: 20557269 DOI: 10.1517/14728214.2010.497486] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
UNLABELLED IMPORTANCE OF THE FILED: With the worldwide surge of MRSA, skin and skin-structure infection (SSTI) treatment has become a challenge for physicians. Cultures and antibiotic susceptibility tests for SSTIs are the rule due to the implication in morbidity and mortality rates associated with MRSA infections. The need for new antibiotics is evident and the effort to decrease antibiotic resistance is a world priority. AREAS COVERED IN THIS REVIEW This manuscript accesses the actual treatments and the developing of antibiotics for MRSA SSTIs. WHAT THE READER WILL GAIN This is a review of the data on the available and emerging treatments for MRSA SSTIs. TAKE HOME MESSAGE There is an unmet medical need for new antibiotics in the new millennium. As physicians, we must assure all appropriate procedures are completed in order to reduce the bacterial resistance, especially for MRSA.
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Affiliation(s)
- Natalia Mendoza
- Center for Clinical Studies, 6655 Travis Suite 120, Houston, TX 77030, USA.
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Rossolini GM, Thaller MC. Coping with antibiotic resistance: contributions from genomics. Genome Med 2010; 2:15. [PMID: 20236502 PMCID: PMC2847706 DOI: 10.1186/gm136] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Antibiotic resistance is a public health issue of global dimensions with a significant impact on morbidity, mortality and healthcare-associated costs. The problem has recently been worsened by the steady increase in multiresistant strains and by the restriction of antibiotic discovery and development programs. Recent advances in the field of bacterial genomics will further current knowledge on antibiotic resistance and help to tackle the problem. Bacterial genomics and transcriptomics can inform our understanding of resistance mechanisms, and comparative genomic analysis can provide relevant information on the evolution of resistant strains and on resistance genes and cognate genetic elements. Moreover, bacterial genomics, including functional and structural genomics, is also proving to be instrumental in the identification of new targets, which is a crucial step in new antibiotic discovery programs.
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Affiliation(s)
- Gian Maria Rossolini
- Department of Molecular Biology, Section of Microbiology, University of Siena, and Clinical Microbiology Unit, Siena University Hospital, Policlinico Santa Maria alle Scotte, Viale Bracci, 53100 Siena, Italy.
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