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Monobe K, Taniguchi H, Aoki S. In silico Identification of Potential Inhibitors against Staphylococcus aureus Tyrosyl-tRNA Synthetase. Curr Comput Aided Drug Des 2024; 20:452-462. [PMID: 37309761 DOI: 10.2174/1573409919666230612120819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/28/2023] [Accepted: 05/16/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Drug-resistant Staphylococcus aureus (S. aureus) has spread from nosocomial to community-acquired infections. Novel antimicrobial drugs that are effective against resistant strains should be developed. S. aureus tyrosyl-tRNA synthetase (saTyrRS) is considered essential for bacterial survival and is an attractive target for drug screening. OBJECTIVES The purpose of this study was to identify potential new inhibitors of saTyrRS by screening compounds in silico and evaluating them using molecular dynamics (MD) simulations. METHODS A 3D structural library of 154,118 compounds was screened using the DOCK and GOLD docking simulations and short-time MD simulations. The selected compounds were subjected to MD simulations of a 75-ns time frame using GROMACS. RESULTS Thirty compounds were selected by hierarchical docking simulations. The binding of these compounds to saTyrRS was assessed by short-time MD simulations. Two compounds with an average value of less than 0.15 nm for the ligand RMSD were ultimately selected. The longtime (75 ns) MD simulation results demonstrated that two novel compounds bound stably to saTyrRS in silico. CONCLUSION Two novel potential saTyrRS inhibitors with different skeletons were identified by in silico drug screening using MD simulations. The in vitro validation of the inhibitory effect of these compounds on enzyme activity and their antibacterial effect on drug-resistant S. aureus would be useful for developing novel antibiotics.
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Affiliation(s)
- Kohei Monobe
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
| | - Hinata Taniguchi
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
| | - Shunsuke Aoki
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Japan
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Abstract
Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.
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Affiliation(s)
- Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.
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Farshadfar C, Mollica A, Rafii F, Noorbakhsh A, Nikzad M, Seyedi SH, Abdi F, Verki SA, Mirzaie S. Novel potential inhibitor discovery against tyrosyl-tRNA synthetase from Staphylococcus aureus by virtual screening, molecular dynamics, MMPBSA and QMMM simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1726911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Adriano Mollica
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Chieti, Italy
| | - Fatemeh Rafii
- Division of Microbiology, National Center for Toxicological Research Jefferson, Jefferson, AR, USA
| | - Akbar Noorbakhsh
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Mozhgan Nikzad
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Seyed Hamid Seyedi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Fatemeh Abdi
- Department of Medicine and Paramedical, Qazvin Branch, Islamic Azad University, Qazvin, Iran
| | | | - Sako Mirzaie
- Department of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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4
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Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for protein synthesis with evolutionarily conserved enzymatic mechanisms. Despite their similarity across organisms, scientists have been able to generate effective anti-infective agents based on the structural differences in the catalytic clefts of ARSs from pathogens and humans. However, recent genomic, proteomic and functionomic advances have unveiled unexpected disease-associated mutations and altered expression, secretion and interactions in human ARSs, revealing hidden biological functions beyond their catalytic roles in protein synthesis. These studies have also brought to light their potential as a rich and unexplored source for new therapeutic targets and agents through multiple avenues, including direct targeting of the catalytic sites, controlling disease-associated protein-protein interactions and developing novel biologics from the secreted ARS proteins or their parts. This Review addresses the emerging biology and therapeutic applications of human ARSs in diseases including autoimmune and rare diseases, and cancer.
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5
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Barros-Álvarez X, Kerchner KM, Koh CY, Turley S, Pardon E, Steyaert J, Ranade RM, Gillespie JR, Zhang Z, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ. Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts. Biochimie 2017; 138:124-136. [PMID: 28427904 PMCID: PMC5484532 DOI: 10.1016/j.biochi.2017.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023]
Abstract
The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 Å resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains. Comparing the two independent chains in the asymmetric unit reveals that the two pseudo-monomers of LdTyrRS can bend with respect to each other essentially as rigid bodies. This flexibility might be useful in the positioning of tRNA for catalysis since both pseudo-monomers in the LdTyrRS chain are needed for charging tRNATyr. An "extra pocket" (EP) appears to be present near the adenine binding region of LdTyrRS. Since this pocket is absent in the two human homologous enzymes, the EP provides interesting opportunities for obtaining selective drugs for treating infections caused by L. donovani, a unicellular parasite causing visceral leishmaniasis, or kala azar, which claims 20,000 to 30,000 deaths per year. Sequence and structural comparisons indicate that the EP is a characteristic which also occurs in the active site of several other important pathogenic protozoa. Therefore, the structure of LdTyrRS could inspire the design of compounds useful for treating several different parasitic diseases.
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Affiliation(s)
- Ximena Barros-Álvarez
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Keshia M Kerchner
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Stewart Turley
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Ranae M Ranade
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - J Robert Gillespie
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Frederick S Buckner
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - Wim G J Hol
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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6
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Affiliation(s)
- Juan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- School of Life Sciences, Shandong University of Technology, Zibo, PR China
| | - Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
- School of Life Sciences, Shandong University of Technology, Zibo, PR China
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Ramakrishna B, Sudharani C, Sridhar PR. Synthesis of β- C
-Glycosyl Amino Acids by Ring Opening of Donor-Acceptor Spiro-cyclopropanecarboxylated Sugars. Isr J Chem 2016. [DOI: 10.1002/ijch.201500087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bandi Ramakrishna
- School of Chemistry; University of Hyderabad, Gachibowli; Hyderabad- 500046 Telangana India
| | - Chalapala Sudharani
- School of Chemistry; University of Hyderabad, Gachibowli; Hyderabad- 500046 Telangana India
| | - Perali Ramu Sridhar
- School of Chemistry; University of Hyderabad, Gachibowli; Hyderabad- 500046 Telangana India
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9
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Chandrasekaran SN, Yardimci GG, Erdogan O, Roach J, Carter CW. Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases. Mol Biol Evol 2013; 30:1588-604. [PMID: 23576570 PMCID: PMC3684856 DOI: 10.1093/molbev/mst070] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We tested the idea that ancestral class I and II aminoacyl-tRNA synthetases arose on opposite strands of the same gene. We assembled excerpted 94-residue Urgenes for class I tryptophanyl-tRNA synthetase (TrpRS) and class II Histidyl-tRNA synthetase (HisRS) from a diverse group of species, by identifying and catenating three blocks coding for secondary structures that position the most highly conserved, active-site residues. The codon middle-base pairing frequency was 0.35 ± 0.0002 in all-by-all sense/antisense alignments for 211 TrpRS and 207 HisRS sequences, compared with frequencies between 0.22 ± 0.0009 and 0.27 ± 0.0005 for eight different representations of the null hypothesis. Clustering algorithms demonstrate further that profiles of middle-base pairing in the synthetase antisense alignments are correlated along the sequences from one species-pair to another, whereas this is not the case for similar operations on sets representing the null hypothesis. Most probable reconstructed sequences for ancestral nodes of maximum likelihood trees show that middle-base pairing frequency increases to approximately 0.42 ± 0.002 as bacterial trees approach their roots; ancestral nodes from trees including archaeal sequences show a less pronounced increase. Thus, contemporary and reconstructed sequences all validate important bioinformatic predictions based on descent from opposite strands of the same ancestral gene. They further provide novel evidence for the hypothesis that bacteria lie closer than archaea to the origin of translation. Moreover, the inverse polarity of genetic coding, together with a priori α-helix propensities suggest that in-frame coding on opposite strands leads to similar secondary structures with opposite polarity, as observed in TrpRS and HisRS crystal structures.
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Simmons KJ, Chopra I, Fishwick CWG. Structure-based discovery of antibacterial drugs. Nat Rev Microbiol 2011; 8:501-10. [PMID: 20551974 DOI: 10.1038/nrmicro2349] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The modern era of antibacterial chemotherapy began in the 1930s, and the next four decades saw the discovery of almost all the major classes of antibacterial agents that are currently in use. However, bacterial resistance to many of these drugs is becoming an increasing problem. As such, the discovery of drugs with novel modes of action will be vital to meet the threats created by the emergence of resistance. Success in discovering inhibitors using high-throughput screening of chemical libraries is rare. In this Review we explore the exciting opportunities for antibacterial-drug discovery arising from structure-based drug design.
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Affiliation(s)
- Katie J Simmons
- Antimicrobial Research Centre, University of Leeds, Leeds, UK
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11
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Preparation and conformational analysis of C-glycosyl β2- and β/β2-peptides. Carbohydr Res 2009; 344:613-26. [DOI: 10.1016/j.carres.2009.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 01/13/2009] [Accepted: 01/20/2009] [Indexed: 11/20/2022]
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12
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Inaba Y, Yano S, Mikata Y. Preparation ofC-Glycoside Pendant β2- and β2,2-Amino Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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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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Ochsner UA, Sun X, Jarvis T, Critchley I, Janjic N. Aminoacyl-tRNA synthetases: essential and still promising targets for new anti-infective agents. Expert Opin Investig Drugs 2007; 16:573-93. [PMID: 17461733 DOI: 10.1517/13543784.16.5.573] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The emergence of resistance to existing antibiotics demands the development of novel antimicrobial agents directed against novel targets. Historically, bacterial cell wall synthesis, protein, and DNA and RNA synthesis have been major targets of very successful classes of antibiotics such as beta-lactams, glycopeptides, macrolides, aminoglycosides, tetracyclines, rifampicins and quinolones. Recently, efforts have been made to develop novel agents against validated targets in these pathways but also against new, previously unexploited targets. The era of genomics has provided insights into novel targets in microbial pathogens. Among the less exploited--but still promising--targets is the family of 20 aminoacyl-tRNA synthetases (aaRSs), which are essential for protein synthesis. These targets have been validated in nature as aaRS inhibition has been shown as the specific mode of action for many natural antimicrobial agents synthesized by bacteria and fungi. Therefore, aaRSs have the potential to be targeted by novel agents either from synthetic or natural sources to yield specific and selective anti-infectives. Numerous high-throughput screening programs aimed at identifying aaRS inhibitors have been performed over the last 20 years. A large number of promising lead compounds have been identified but only a few agents have moved forward into clinical development. This review provides an update on the present strategies to develop novel aaRS inhibitors as anti-infective drugs.
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Affiliation(s)
- Urs A Ochsner
- Replidyne, Inc., 1450 Infinite Dr, Louisville, CO 80027, USA.
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15
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Inaba Y, Yano S, Mikata Y. Facile synthesis of 2-(β-C-glucopyranosyl)-β-amino acid: a new class of glycopeptide building block. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2006.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Janin YL. Antituberculosis drugs: ten years of research. Bioorg Med Chem 2007; 15:2479-513. [PMID: 17291770 DOI: 10.1016/j.bmc.2007.01.030] [Citation(s) in RCA: 335] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 12/26/2006] [Accepted: 01/17/2007] [Indexed: 02/03/2023]
Abstract
Tuberculosis is today amongst the worldwide health threats. As resistant strains of Mycobacterium tuberculosis have slowly emerged, treatment failure is too often a fact, especially in countries lacking the necessary health care organisation to provide the long and costly treatment adapted to patients. Because of lack of treatment or lack of adapted treatment, at least two million people will die of tuberculosis this year. Due to this concern, this infectious disease was the focus of renewed scientific interest in the last decade. Regimens were optimized and much was learnt on the mechanisms of action of the antituberculosis drugs used. Moreover, the quest for original drugs overcoming some of the problems of current regimens also became the focus of research programmes and many new series of M. tuberculosis growth inhibitors were reported. This review presents the drugs currently used in antituberculosis treatments and the most advanced compounds undergoing clinical trials. We then provide a description of their mechanism of action along with other series of inhibitors known to act on related biochemical targets. This is followed by other inhibitors of M. tuberculosis growth, including recently reported compounds devoid of a reported mechanism of action.
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Affiliation(s)
- Yves L Janin
- URA 2128 CNRS-Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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17
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Kim S, Lee SW, Choi EC, Choi SY. Aminoacyl-tRNA synthetases and their inhibitors as a novel family of antibiotics. Appl Microbiol Biotechnol 2003; 61:278-88. [PMID: 12743756 DOI: 10.1007/s00253-003-1243-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2002] [Revised: 01/02/2003] [Accepted: 01/03/2003] [Indexed: 10/25/2022]
Abstract
The emergence of multidrug-resistant strains of pathogenic microorganisms and the slow progress in new antibiotic development has led in recent years to a resurgence of infectious diseases that threaten the well-being of humans. The result of many microorganisms becoming immune to major antibiotics means that fighting off infection by these pathogens is more difficult. The best strategy to get around drug resistance is to discover new drug targets, taking advantage of the abundant information that was recently obtained from genomic and proteomic research, and explore them for drug development. In this regard, aminoacyl-tRNA synthetases (ARSs) provide a promising platform to develop novel antibiotics that show no cross-resistance to other classical antibiotics. During the last few years there has been a comprehensive attempt to find the compounds that can specifically target ARSs and inhibit bacterial growth. In this review, the current status in the development of ARS inhibitors will be briefly summarized, based on their chemical structures and working mechanisms.
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Affiliation(s)
- S Kim
- National Creative Research Initiatives Center for ARS Network, College of Pharmacy, Seoul National University, San 56-1, 151-742 Shillim-dong, Kwanak-gu, Seoul, Korea.
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18
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Austin J, First EA. Catalysis of tyrosyl-adenylate formation by the human tyrosyl-tRNA synthetase. J Biol Chem 2002; 277:14812-20. [PMID: 11856731 DOI: 10.1074/jbc.m103396200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the active site residues in the Bacillus stearothermophilus and human tyrosyl-tRNA synthetases are largely conserved, several differences exist between the two enzymes. In particular, three amino acids that stabilize the transition state for the activation of tyrosine in B. stearothermophilus tyrosyl-tRNA synthetase (Cys-35, His-48, and Lys-233) are not present in the human enzyme. This raises the question of whether the activation energy for the tyrosine activation step is higher for the human tyrosyl-tRNA synthetase than for the B. stearothermophilus enzyme. In this paper, we demonstrate that intrinsic fluorescence changes can be used to monitor the pre-steady state kinetics of human tyrosyl-tRNA synthetase. In contrast to the B. stearothermophilus enzyme, catalysis of the tyrosine activation step is potassium-dependent in the human tyrosyl-tRNA synthetase. Specifically, potassium increases the forward rate constant for tyrosine activation 260-fold in the human tyrosyl-tRNA synthetase. Comparison of the forward rate constants for catalysis of tyrosine activation by the human and B. stearothermophilus enzymes indicates that despite differences in their active sites and the potassium requirement of the human enzyme, the activation energies for tyrosine activation are identical for the two enzymes. The results of these investigations suggest that differences exist between the active sites of the bacterial and human tyrosyl-tRNA synthetases that could be exploited to design antimicrobials that target the bacterial enzyme.
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Affiliation(s)
- Joseph Austin
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, Shreveport, Louisiana 71130, USA
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Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL. Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors. Protein Sci 2001; 10:2008-16. [PMID: 11567092 PMCID: PMC2374228 DOI: 10.1110/ps.18001] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2001] [Revised: 07/05/2001] [Accepted: 07/12/2001] [Indexed: 10/17/2022]
Abstract
SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.
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Affiliation(s)
- X Qiu
- GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA.
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20
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Jarvest RL, Berge JM, Houge-Frydrych CS, Mensah LM, O'Hanlon PJ, Pope AJ. Inhibitors of bacterial tyrosyl tRNA synthetase: synthesis of carbocyclic analogues of the natural product SB-219383. Bioorg Med Chem Lett 2001; 11:2499-502. [PMID: 11549455 DOI: 10.1016/s0960-894x(01)00475-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Carbocyclic analogues of the microbial metabolite SB-219383 have been synthesised and evaluated as inhibitors of bacterial tyrosyl tRNA synthetase. One compound showed highly potent and selective nanomolar inhibition.
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Affiliation(s)
- R L Jarvest
- GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park, Third Avenue, Harlow, CM19 5AW, Essex, UK
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