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Zhao Y, Wang Q, Meng Q, Ding D, Yang H, Gao G, Li D, Zhu W, Zhou H. Identification of Trypanosoma brucei leucyl-tRNA synthetase inhibitors by pharmacophore- and docking-based virtual screening and synthesis. Bioorg Med Chem 2012; 20:1240-50. [DOI: 10.1016/j.bmc.2011.12.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/16/2011] [Accepted: 12/17/2011] [Indexed: 10/14/2022]
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52
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Jackson KE, Pham JS, Kwek M, De Silva NS, Allen SM, Goodman CD, McFadden GI, Ribas de Pouplana L, Ralph SA. Dual targeting of aminoacyl-tRNA synthetases to the apicoplast and cytosol in Plasmodium falciparum. Int J Parasitol 2012; 42:177-86. [DOI: 10.1016/j.ijpara.2011.11.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/16/2022]
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53
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Lu X, Zhou R, Sharma I, Li X, Kumar G, Swaminathan S, Tonge PJ, Tan DS. Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis. Chembiochem 2011; 13:129-36. [PMID: 22109989 DOI: 10.1002/cbic.201100585] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 12/15/2022]
Abstract
MenE, the o-succinylbenzoate (OSB)-CoA synthetase from bacterial menaquinone biosynthesis, is a promising new antibacterial target. Sulfonyladenosine analogues of the cognate reaction intermediate, OSB-AMP, have been developed as inhibitors of the MenE enzymes from Mycobacterium tuberculosis (mtMenE), Staphylococcus aureus (saMenE) and Escherichia coli (ecMenE). Both a free carboxylate and a ketone moiety on the OSB side chain are required for potent inhibitory activity. OSB-AMS (4) is a competitive inhibitor of mtMenE with respect to ATP (K(i) =5.4±0.1 nM) and a noncompetitive inhibitor with respect to OSB (K(i) =11.2±0.9 nM). These data are consistent with a Bi Uni Uni Bi Ping-Pong kinetic mechanism for these enzymes. In addition, OSB-AMS inhibits saMenE with K(i)(app) =22±8 nM and ecMenE with K(i)(OSB) =128±5 nM. Putative active-site residues, Arg222, which may interact with the OSB aromatic carboxylate, and Ser302, which may bind the OSB ketone oxygen, have been identified through computational docking of OSB-AMP with the unliganded crystal structure of saMenE. A pH-dependent interconversion of the free keto acid and lactol forms of the inhibitors is also described, along with implications for inhibitor design.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program and Tri-Institutional Research Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Vondenhoff GHM, Van Aerschot A. Aminoacyl-tRNA synthetase inhibitors as potential antibiotics. Eur J Med Chem 2011; 46:5227-36. [PMID: 21968372 DOI: 10.1016/j.ejmech.2011.08.049] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 11/29/2022]
Abstract
Increasing resistance to antibiotics is a major problem worldwide and provides the stimulus for development of new bacterial inhibitors with preferably different modes of action. In search for new leads, several new bacterial targets are being exploited beside the use of traditional screening methods. Hereto, inhibition of bacterial protein synthesis is a long-standing validated target. Aminoacyl-tRNA synthetases (aaRSs) play an indispensable role in protein synthesis and their structures proved quite conserved in prokaryotes and eukaryotes. However, some divergence has occurred allowing the development of selective aaRS inhibitors. Following an outline on the action mechanism of aaRSs, an overview will be given of already existing aaRS inhibitors, which are largely based on mimics of the aminoacyl-adenylates, the natural reaction intermediates. This is followed by a discussion on more recent developments in the field and the bioavailability problem.
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Affiliation(s)
- Gaston H M Vondenhoff
- Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Minderbroedersstraat 10, BE-3000 Leuven, Belgium
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Andam CP, Fournier GP, Gogarten JP. Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev 2011; 35:756-67. [DOI: 10.1111/j.1574-6976.2011.00274.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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56
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Characterization of peptide chain length and constituency requirements for YejABEF-mediated uptake of microcin C analogues. J Bacteriol 2011; 193:3618-23. [PMID: 21602342 DOI: 10.1128/jb.00172-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin C (McC), a natural antibacterial compound consisting of a heptapeptide attached to a modified adenosine, is actively taken up by the YejABEF transporter, after which it is processed by cellular aminopeptidases, releasing the nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC analogues with variable length of the peptide moiety were synthesized and evaluated in order to characterize the substrate preferences of the YejABEF transporter. It was shown that a minimal peptide chain length of 6 amino acids and the presence of an N-terminal formyl-methionyl-arginyl sequence are required for transport.
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57
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Niemann M, Schneider A, Cristodero M. Mitochondrial translation in trypanosomatids: a novel target for chemotherapy? Trends Parasitol 2011; 27:429-33. [PMID: 21531629 DOI: 10.1016/j.pt.2011.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 01/31/2023]
Abstract
Trypanosomatids cause widespread disease in humans and animals. Treatment of many of these diseases is hampered by the lack of efficient and safe drugs. New strategies for drug development are therefore urgently needed. It has long been known that the single mitochondrion of trypanosomatids exhibits many unique features. Recently, the mitochondrial translation machinery of trypanosomatids has been the focus of several studies, which revealed interesting variations to the mammalian system. It is the aim of this article to review these unique features and to discuss them in the larger biological context. It is our opinion that some of these features represent promising novel targets for chemotherapeutic intervention that should be studied in more detail.
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Affiliation(s)
- Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, 3012 Bern, Switzerland.
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58
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Larson ET, Kim JE, Zucker FH, Kelley A, Mueller N, Napuli AJ, Verlinde CL, Fan E, Buckner FS, Van Voorhis WC, Merritt EA, Hol WG. Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. Biochimie 2011; 93:570-82. [PMID: 21144880 PMCID: PMC3039092 DOI: 10.1016/j.biochi.2010.11.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/29/2010] [Indexed: 01/07/2023]
Abstract
Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg(2+) ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of Escherichia coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNA(Met) complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme.
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Affiliation(s)
- Eric T. Larson
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Jessica E. Kim
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Frank H. Zucker
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Angela Kelley
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Natascha Mueller
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Alberto J. Napuli
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Christophe L.M.J. Verlinde
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Frederick S. Buckner
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Wesley C. Van Voorhis
- Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Department of Medicine, University of Washington, Seattle, WA 98195-7185, USA
| | - Ethan A. Merritt
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org
| | - Wim G.J. Hol
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA,Medical Structural Genomics of Pathogenic Protozoa (MSGPP), www.msgpp.org,Corresponding author.
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Selective inhibitors of methionyl-tRNA synthetase have potent activity against Trypanosoma brucei Infection in Mice. Antimicrob Agents Chemother 2011; 55:1982-9. [PMID: 21282428 DOI: 10.1128/aac.01796-10] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human African trypanosomiasis continues to be an important public health threat in extensive regions of sub-Saharan Africa. Treatment options for infected patients are unsatisfactory due to toxicity, difficult administration regimes, and poor efficacy of available drugs. The aminoacyl-tRNA synthetases were selected as attractive drug targets due to their essential roles in protein synthesis and cell survival. Comparative sequence analysis disclosed differences between the trypanosome and mammalian methionyl-tRNA synthetases (MetRSs) that suggested opportunities for selective inhibition using drug-like molecules. Experiments using RNA interference on the single MetRS of Trypanosoma brucei demonstrated that this gene product was essential for normal cell growth. Small molecules (diaryl diamines) similar to those shown to have potent activity on prokaryotic MetRS enzymes were synthesized and observed to have inhibitory activity on the T. brucei MetRS (50% inhibitory concentration, <50 nM) and on bloodstream forms of T. brucei cultures (50% effective concentration, as low as 4 nM). Twenty-one compounds had a close correlation between enzyme binding/inhibition and T. brucei growth inhibition, indicating that they were likely to be acting on the intended target. The compounds had minimal effects on mammalian cell growth at 20 μM, demonstrating a wide therapeutic index. The most potent compound was tested in the murine model of trypanosomiasis and demonstrated profound parasite suppression and delayed mortality. A homology model of the T. brucei MetRS based on other MetRS structures was used to model binding of the lead diaryl diamine compounds. Future studies will focus on improving the pharmacological properties of the MetRS inhibitors.
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60
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Comparative proteome analysis of Bacillus anthracis with pXO1 plasmid content. J Microbiol 2011; 48:771-7. [PMID: 21221933 DOI: 10.1007/s12275-010-0136-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 07/21/2010] [Indexed: 12/20/2022]
Abstract
Bacillus anthracis the causative agent of anthrax, is an important pathogen among the Bacillus cereus group of species because of its physiological characteristics and its importance as a biological warfare agent. Tripartite anthrax toxin proteins and a poly-D-glutamic acid capsule are produced by B. anthracis vegetative cells during mammalian hosts infection and when cultured in conditions that are thought to mimic the host environment. To identify the factors regulating virulence in B. anthracis the whole cell proteins were extracted from two B. anthracis strains and separated by narrow range immobilized pH gradient (IPG) strips (pH 4-7), followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins that were differentially expressed were identified by the peptide fingerprinting using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). A total of 23 proteins were identified as being either upregulated or downregulated in the presence or absence of the virulence plasmid pXO1. Two plasmid encoded proteins and 12 cellular proteins were identified and documented as potential virulence factors.
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61
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Baker SJ, Tomsho JW, Benkovic SJ. Boron-containing inhibitors of synthetases. Chem Soc Rev 2011; 40:4279-85. [DOI: 10.1039/c0cs00131g] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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62
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63
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Crepin T, Peterson F, Haertlein M, Jensen D, Wang C, Cusack S, Kron M. A hybrid structural model of the complete Brugia malayi cytoplasmic asparaginyl-tRNA synthetase. J Mol Biol 2010; 405:1056-69. [PMID: 21134380 DOI: 10.1016/j.jmb.2010.11.049] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 11/15/2022]
Abstract
Aminoacyl-tRNA synthetases are validated molecular targets for anti-infective drug discovery because of their essentiality in protein synthesis. Thanks to genome sequencing, it is now possible to systematically study aminoacyl-tRNA synthetases from human eukaryotic parasites as putative targets for novel drug discovery. As part of a program targeting class IIb asparaginyl-tRNA synthetases (AsnRS) from the parasitic nematode Brugia malayi for anti-filarial drugs, we report the complete structure of a eukaryotic AsnRS. Metazoan and fungal AsnRS differ from their bacterial homologues by the addition of a conserved N-terminal extension of about 110 residues whose structure we have determined by solution NMR for the B. malayi enzyme. In addition, we solved by X-ray crystallography a series of structures of the catalytically active N-terminally truncated enzyme (residues 112-548), allowing the structural basis for the mechanism of asparagine activation to be elucidated. The N-terminal domain contains a structured region with a novel fold featuring a lysine-rich helix that is shown by NMR to interact with tRNA. This is connected by an unstructured tether to the remainder of the enzyme, which is highly similar to the known structure of bacterial AsnRS. These data enable a model of the complete AsnRS-tRNA complex to be constructed.
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MESH Headings
- Amino Acid Sequence
- Animals
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/genetics
- Aspartate-tRNA Ligase/metabolism
- Base Sequence
- Brugia malayi/enzymology
- Brugia malayi/genetics
- Catalytic Domain
- Crystallography, X-Ray
- Cytoplasm/enzymology
- DNA Primers/genetics
- Enzyme Activation
- Helminth Proteins/chemistry
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Humans
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Protein Structure, Tertiary
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Homology, Amino Acid
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Affiliation(s)
- Thibaut Crepin
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38142 Grenoble Cedex 9, France
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64
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Gwynn MN, Portnoy A, Rittenhouse SF, Payne DJ. Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 2010; 1213:5-19. [PMID: 21058956 DOI: 10.1111/j.1749-6632.2010.05828.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The discovery of novel antibiotic classes has not kept pace with the growing threat of bacterial resistance. Antibiotic candidates that act at new targets or via distinct mechanisms have the greatest potential to overcome resistance; however, novel approaches are also associated with higher attrition and longer timelines. This uncertainty has contributed to the withdrawal from antibiotic programs by many pharmaceutical companies. Genomic approaches have not yielded satisfactory results, in part due to nascent knowledge about unprecedented molecular targets, the challenge of achieving antibacterial activity by lead optimization of enzyme inhibitors, and the limitations of compound screening libraries for antibacterial discovery. Enhanced diversity of compound screening banks, entry into new chemical space, and new screening technologies are currently being exploited to improve hit rates for antibacterial discovery. Antibacterial compound lead optimization faces hurdles associated with the high plasma exposures required for efficacy. Lead optimization would be enhanced by the identification of new antibiotic classes with improved tractability and by expanding the predictability of in vitro safety assays. Implementing multiple screening and target identification strategies is recommended for improving the likelihood of discovering new antibacterial compounds that address unmet needs.
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Affiliation(s)
- Michael N Gwynn
- Antibacterial Discovery Performance Unit, Infectious Diseases Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania, USA
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65
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Panwar B, Raghava GPS. Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains. BMC Genomics 2010; 11:507. [PMID: 20860794 PMCID: PMC2997003 DOI: 10.1186/1471-2164-11-507] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 09/22/2010] [Indexed: 12/02/2022] Open
Abstract
Background Aminoacyl tRNA synthetases (aaRSs) catalyse the first step of protein synthesis in all organisms. They are responsible for the precise attachment of amino acids to their cognate transfer RNAs. There are twenty different types of aaRSs, unique for each amino acid. These aaRSs have been divided into two classes, each comprising ten enzymes. It is important to predict and classify aaRSs in order to understand protein synthesis. Results In this study, all models were developed on a non-redundant dataset containing 117 aaRSs and an equal number of non-aaRSs, in which no two sequences have more than 30% similarity. First, we applied the similarity search technique, BLAST, and achieved a maximum accuracy of 67.52%. We observed that 62% of tRNA synthetases contain one or more domains from amongst the following four PROSITE domains: PS50862, PS00178, PS50860 and PS50861. An SVM-based model was developed to discriminate between aaRSs, and non-aaRSs, and achieved a maximum MCC of 0.68 with accuracy of 83.73%, using selective dipeptide composition. We developed a hybrid approach and achieved a maximum MCC of 0.72 with accuracy of 85.49%, where SVM model developed using selected dipeptide composition and information of four PROSITE domains. We further developed an SVM-based model for classifying the aaRSs into class-1 and class-2, using selective dipeptide composition and achieved an MCC of 0.79. We also observed that two domains (PS00178, PS50889) in class-1 and three domains (PS50862, PS50860, PS50861) in class-2 were preferred. A hybrid method was developed using these domains as descriptor, along with selected dipeptide composition, and achieved an MCC of 0.87 with a sensitivity of 94.55% and an accuracy of 93.19%. All models were evaluated using a five-fold cross-validation technique. Conclusions We have analyzed protein sequences of aaRSs (class-1 and class-2) and non-aaRSs and identified interesting patterns. The high accuracy achieved by our SVM models using selected dipeptide composition demonstrates that certain types of dipeptide are preferred in aaRSs. We were able to identify PROSITE domains that are preferred in aaRSs and their classes, providing interesting insights into tRNA synthetases. The method developed in this study will be useful for researchers studying aaRS enzymes and tRNA biology. The web-server based on the above study, is available at http://www.imtech.res.in/raghava/icaars/.
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Affiliation(s)
- Bharat Panwar
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India
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66
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Freilich S, Kreimer A, Borenstein E, Gophna U, Sharan R, Ruppin E. Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLoS Comput Biol 2010; 6:e1000690. [PMID: 20195496 PMCID: PMC2829043 DOI: 10.1371/journal.pcbi.1000690] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 01/26/2010] [Indexed: 11/18/2022] Open
Abstract
The evolutionary origins of genetic robustness are still under debate: it may arise as a consequence of requirements imposed by varying environmental conditions, due to intrinsic factors such as metabolic requirements, or directly due to an adaptive selection in favor of genes that allow a species to endure genetic perturbations. Stratifying the individual effects of each origin requires one to study the pertaining evolutionary forces across many species under diverse conditions. Here we conduct the first large-scale computational study charting the level of robustness of metabolic networks of hundreds of bacterial species across many simulated growth environments. We provide evidence that variations among species in their level of robustness reflect ecological adaptations. We decouple metabolic robustness into two components and quantify the extents of each: the first, environmental-dependent, is responsible for at least 20% of the non-essential reactions and its extent is associated with the species' lifestyle (specialized/generalist); the second, environmental-independent, is associated (correlation = approximately 0.6) with the intrinsic metabolic capacities of a species-higher robustness is observed in fast growers or in organisms with an extensive production of secondary metabolites. Finally, we identify reactions that are uniquely susceptible to perturbations in human pathogens, potentially serving as novel drug-targets.
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Affiliation(s)
- Shiri Freilich
- The Blavatnik School of Computer Sciences, Faculty of Life Sciences, Ramat Aviv, Israel
- Sackler School of Medicine, Faculty of Life Sciences, Ramat Aviv, Israel
- * E-mail: (SF); (ER)
| | - Anat Kreimer
- School of Mathematical Science, Faculty of Life Sciences, Ramat Aviv, Israel
- Department of Biomedical Informatics, Columbia University, New York, New York, United States of America
| | - Elhanan Borenstein
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Ramat Aviv, Israel
| | - Roded Sharan
- The Blavatnik School of Computer Sciences, Faculty of Life Sciences, Ramat Aviv, Israel
| | - Eytan Ruppin
- The Blavatnik School of Computer Sciences, Faculty of Life Sciences, Ramat Aviv, Israel
- Sackler School of Medicine, Faculty of Life Sciences, Ramat Aviv, Israel
- * E-mail: (SF); (ER)
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67
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Characterization of two seryl-tRNA synthetases in albomycin-producing Streptomyces sp. strain ATCC 700974. Antimicrob Agents Chemother 2009; 53:4619-27. [PMID: 19721072 DOI: 10.1128/aac.00782-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Trojan horse antibiotic albomycin, produced by Streptomyces sp. strain ATCC 700974, contains a thioribosyl nucleoside moiety linked to a hydroxamate siderophore through a serine residue. The seryl nucleoside structure (SB-217452) is a potent inhibitor of seryl-tRNA synthetase (SerRS) in the pathogenic bacterium Staphylococcus aureus, with a 50% inhibitory concentration (IC(50)) of approximately 8 nM. In the albomycin-producing Streptomyces sp., a bacterial SerRS homolog (Alb10) was found to be encoded in a biosynthetic gene cluster in addition to another serRS gene (serS1) at a different genetic locus. Alb10, named SerRS2 herein, is significantly divergent from SerRS1, which shows high homology to the housekeeping SerRS found in other Streptomyces species. We genetically and biochemically characterized the two genes and the proteins encoded. Both genes were able to complement a temperature-sensitive serS mutant of Escherichia coli and allowed growth at a nonpermissive temperature. serS2 was shown to confer albomycin resistance, with specific amino acid residues in the motif 2 signature sequences of SerRS2 playing key roles. SerRS1 and SerRS2 are comparably efficient in vitro, but the K(m) of serine for SerRS2 measured during tRNA aminoacylation is more than 20-fold higher than that for SerRS1. SB-217452 was also enzymatically generated and purified by two-step chromatography. Its IC(50) against SerRS1 was estimated to be 10-fold lower than that against SerRS2. In contrast, both SerRSs displayed comparable inhibition kinetics for serine hydroxamate, indicating that SerRS2 was specifically resistant to SB-217452. These data suggest that mining Streptomyces genomes for duplicated aminoacyl-tRNA synthetase genes could provide a novel approach for the identification of natural products targeting aminoacyl-tRNA synthetases.
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68
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A novel tryptophanyl-tRNA synthetase gene confers high-level resistance to indolmycin. Antimicrob Agents Chemother 2009; 53:3972-80. [PMID: 19546369 DOI: 10.1128/aac.00723-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Indolmycin, a potential antibacterial drug, competitively inhibits bacterial tryptophanyl-tRNA synthetases. An effort to identify indolmycin resistance genes led to the discovery of a gene encoding an indolmycin-resistant isoform of tryptophanyl-tRNA synthetase. Overexpression of this gene in an indolmycin-sensitive strain increased the indolmycin MIC 60-fold. Its transcription and distribution in various bacterial genera were assessed. The level of resistance conferred by this gene was compared to that of a known indolmycin resistance gene and to those of genes with resistance-conferring point mutations.
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Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MRK, Cusack S. Crystal structures of the human and fungal cytosolic Leucyl-tRNA synthetase editing domains: A structural basis for the rational design of antifungal benzoxaboroles. J Mol Biol 2009; 390:196-207. [PMID: 19426743 DOI: 10.1016/j.jmb.2009.04.073] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 04/05/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
Abstract
Leucyl-tRNA synthetase (LeuRS) specifically links leucine to the 3' end of tRNA(leu) isoacceptors. The overall accuracy of the two-step aminoacylation reaction is enhanced by an editing domain that hydrolyzes mischarged tRNAs, notably ile-tRNA(leu). We present crystal structures of the editing domain from two eukaryotic cytosolic LeuRS: human and fungal pathogen Candida albicans. In comparison with previous structures of the editing domain from bacterial and archeal kingdoms, these structures show that the LeuRS editing domain has a conserved structural core containing the active site for hydrolysis, with distinct bacterial, archeal, or eukaryotic specific peripheral insertions. It was recently shown that the benzoxaborole antifungal compound AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-1,2-benzoxaborole) inhibits LeuRS by forming a covalent adduct with the 3' adenosine of tRNA(leu) at the editing site, thus locking the enzyme in an inactive conformation. To provide a structural basis for enhancing the specificity of these benzoxaborole antifungals, we determined the structure at 2.2 A resolution of the C. albicans editing domain in complex with a related compound, AN3018 (6-(ethylamino)-5-fluorobenzo[c][1,2]oxaborol-1(3H)-ol), using AMP as a surrogate for the 3' adenosine of tRNA(leu). The interactions between the AN3018-AMP adduct and C. albicans LeuRS are similar to those previously observed for bacterial LeuRS with the AN2690 adduct, with an additional hydrogen bond to the extra ethylamine group. However, compared to bacteria, eukaryotic cytosolic LeuRS editing domains contain an extra helix that closes over the active site, largely burying the adduct and providing additional direct and water-mediated contacts. Small differences between the human domain and the fungal domain could be exploited to enhance fungal specificity.
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Affiliation(s)
- Elena Seiradake
- European Molecular Biology Laboratory, Grenoble Outstation rue Jules Horowitz, France
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70
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Guiles J, Critchley I, Sun X. New agents for Clostridium difficile-associated disease. Expert Opin Investig Drugs 2009; 17:1671-83. [PMID: 18922104 DOI: 10.1517/13543784.17.11.1671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Clostridia-derived diseases, in particular C. difficile-associated disease (CDAD), have been increasing in incidence, severity, and morbidity. The mainstay of treatment options has relied upon metronidazole and vancomycin, but these treatments routinely result in high relapse rates (20%) and, in the case of metronidazole, decreasing efficacy. OBJECTIVE Evaluate and compare the current clinical and preclinical therapies of CDAD. METHODS RESULTS/CONCLUSION The new antibiotics in development and preclinical development reflect next-generation versions of older drugs or two new mechanism-of-action class drugs (OPT-80, REP3123). Based on the current preclinical and clinical data, the next-generation drugs impart only a subtle difference from the intrinsic weaknesses of their genre. In contrast, OPT-80 and REP3123 seem to be differentiated.
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71
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Green LS, Bullard JM, Ribble W, Dean F, Ayers DF, Ochsner UA, Janjic N, Jarvis TC. Inhibition of methionyl-tRNA synthetase by REP8839 and effects of resistance mutations on enzyme activity. Antimicrob Agents Chemother 2009; 53:86-94. [PMID: 19015366 PMCID: PMC2612134 DOI: 10.1128/aac.00275-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 06/09/2008] [Accepted: 10/22/2008] [Indexed: 11/20/2022] Open
Abstract
REP8839 is a selective inhibitor of methionyl-tRNA synthetase (MetRS) with antibacterial activity against a variety of gram-positive organisms. We determined REP8839 potency against Staphylococcus aureus MetRS and assessed its selectivity for bacterial versus human orthologs of MetRS. The inhibition constant (K(i)) of REP8839 was 10 pM for Staphylococcus aureus MetRS. Inhibition of MetRS by REP8839 was competitive with methionine and uncompetitive with ATP. Thus, high physiological ATP levels would actually facilitate optimal binding of the inhibitor. While many gram-positive bacteria, such as Staphylococcus aureus, express exclusively the MetRS1 subtype, many gram-negative bacteria express an alternative homolog called MetRS2. Some gram-positive bacteria, such as Streptococcus pneumoniae and Bacillus anthracis, express both MetRS1 and MetRS2. MetRS2 orthologs were considerably less susceptible to REP8839 inhibition. REP8839 inhibition of human mitochondrial MetRS was 1,000-fold weaker than inhibition of Staphylococcus aureus MetRS; inhibition of human cytoplasmic MetRS was not detectable, corresponding to >1,000,000-fold selectivity for the bacterial target relative to its cytoplasmic counterpart. Mutations in MetRS that confer reduced susceptibility to REP8839 were examined. The mutant MetRS enzymes generally exhibited substantially impaired catalytic activity, particularly in aminoacylation turnover rates. REP8839 K(i) values ranged from 4- to 190,000-fold higher for the mutant enzymes than for wild-type MetRS. These observations provide a potential mechanistic explanation for the reduced growth fitness observed with MetRS mutant strains relative to that with wild-type Staphylococcus aureus.
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72
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Calvo J, Martínez-Martínez L. Mecanismos de acción de los antimicrobianos. Enferm Infecc Microbiol Clin 2009; 27:44-52. [DOI: 10.1016/j.eimc.2008.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 11/28/2022]
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73
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Van de Vijver P, Vondenhoff GHM, Denivelle S, Rozenski J, Verhaegen J, Van Aerschot A, Herdewijn P. Antibacterial 5'-O-(N-dipeptidyl)-sulfamoyladenosines. Bioorg Med Chem 2008; 17:260-9. [PMID: 19070499 DOI: 10.1016/j.bmc.2008.11.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 10/30/2008] [Accepted: 11/03/2008] [Indexed: 11/28/2022]
Abstract
The aminoacyl-tRNA synthetase (aaRS) class of enzymes is a validated target for antimicrobial development. Aminoacyl analogues of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines are known to be potent inhibitors of aaRS, but whole cell antibacterial activity of these compounds is very limited, and poor penetration into bacteria has been proposed as the main reason for this. Aiming to find derivatives that better penetrate bacteria, we developed a simple and short method to prepare dipeptidyl-derivatives of 5'-O-(N-L-aminoacyl)-sulfamoyladenosines, and used this method to prepare 18 5'-O-(N-dipeptidyl)-sulfamoyladenosines. The antibacterial activity of these derivatives and a number of reference compounds against S. aureus, E. faecalis and E. coli was determined. Several of the new derivatives showed improved antibacterial activity and an altered spectrum of antibacterial activity.
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Affiliation(s)
- P Van de Vijver
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroederstraat 10, B-3000 Leuven, Belgium
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74
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Critchley IA, Ochsner UA. Recent advances in the preclinical evaluation of the topical antibacterial agent REP8839. Curr Opin Chem Biol 2008; 12:409-17. [PMID: 18620074 DOI: 10.1016/j.cbpa.2008.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/09/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
REP8839 is a synthetic fluorovinylthiophene-containing diaryldiamine that inhibits bacterial methionyl tRNA synthetase (MetRS) and is a new chemical entity that represents a novel pharmacological class. The compound has potent in vitro antibacterial activity against many clinically important Gram-positive bacteria including the major skin pathogens Staphylococcus aureus and Streptococcus pyogenes. In light of the emergence of methicillin-resistant S. aureus in the community and increasing resistance to mupirocin, REP8839 is being evaluated as a topical agent for the treatment of superficial skin infections. REP8839 was active against resistant phenotypes of S. aureus and can be formulated at high concentrations to minimize the development of resistance. A formulation of REP8839 has demonstrated efficacy in a porcine partial thickness wound infection model against mupirocin-resistant S. aureus.
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Affiliation(s)
- Ian A Critchley
- Microbiology Research, Replidyne, Inc., 1450 Infinite Drive, Louisville, CO 80027, USA.
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75
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Li T, Froeyen M, Herdewijn P. Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:25-35. [DOI: 10.1007/s00249-008-0350-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 05/27/2008] [Accepted: 06/04/2008] [Indexed: 10/21/2022]
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76
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Van de Vijver P, Ostrowski T, Sproat B, Goebels J, Rutgeerts O, Van Aerschot A, Waer M, Herdewijn P. Aminoacyl-tRNA synthetase inhibitors as potent and synergistic immunosuppressants. J Med Chem 2008; 51:3020-9. [PMID: 18438987 DOI: 10.1021/jm8000746] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aminoacyl-tRNA synthetase family of enzymes is the target of many antibacterials and inhibitors of eukaryotic hyperproliferation. In screening analogues of 5'-O-(N-L-aminoacyl)-sulfamoyladenosine containing all 20 proteinogenic amino acids, we found these compounds to have potent immunosuppressive activity. Also, we found that combinations of these compounds inhibited the immune response synergistically. Based on these data, analogues with modifications at the aminoacyl and ribose moieties were designed and evaluated, and several of these showed high immunosuppressive potency, with one compound having an IC50 of 80 nM, when tested in a cellular mixed lymphocyte reaction assay. Apart from showing the potential of aminoacyl-tRNA synthetase inhibitors as immunosuppressants, the current study also provides arguments for careful evaluation of the immunosuppressive activity of developmental antibacterials that target these enzymes.
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Affiliation(s)
- Pieter Van de Vijver
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Catholic University of Leuven, Leuven, Belgium
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77
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Farrera-Sinfreu J, Español Y, Geslain R, Guitart T, Albericio F, Ribas de Pouplana L, Royo M. Solid-Phase Combinatorial Synthesis of a Lysyl-tRNA Synthetase (LysRS) Inhibitory Library. ACTA ACUST UNITED AC 2008; 10:391-400. [DOI: 10.1021/cc700157j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josep Farrera-Sinfreu
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Yaiza Español
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Renaud Geslain
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Tanit Guitart
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
| | - Miriam Royo
- Institute for Research in Biomedicine and Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, Josep Samitier 1, 08028-Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1, 08028-Barcelona, Spain, and Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010-Barcelona, Spain
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Abstract
Multiple resistant staphylococci that cause significant morbidity and mortality are the leading cause of nosocomial infections. Meanwhile, methicillin-resistant Staphylococcus aureus (MRSA) also spreads in the community, where highly virulent strains infect children and young adults who have no predisposing risk factors. Although some treatment options remain, the search for new antibacterial targets and lead compounds is urgently required to ensure that staphylococcal infections can be effectively treated in the future. Promising targets for new antibacterials are gene products that are involved in essential cell functions. In addition to antibacterials, active and passive immunization strategies are being developed that target surface components of staphylococci such as cell wall-linked adhesins, teichoic acids and capsule or immunodominant antigens.
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Affiliation(s)
- Knut Ohlsen
- University of Würzburg, Institute for Molecular Infection Biology, Röntgenring 11, 97070 Würzburg, Germany
| | - Udo Lorenz
- University of Würzburg, Centre for Operative Medicine, Department of Surgery I, Oberdürrbacher Str. 6, 97080 Würzburg, Germany
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