51
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Pérez-Castillo Y, Froeyen M, Cabrera-Pérez MÁ, Nowé A. Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling. J Comput Aided Mol Des 2011; 25:371-93. [DOI: 10.1007/s10822-011-9427-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 04/09/2011] [Indexed: 10/18/2022]
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52
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Pistorius D, Ullrich A, Lucas S, Hartmann RW, Kazmaier U, Müller R. Biosynthesis of 2-Alkyl-4(1H)-Quinolones in Pseudomonas aeruginosa: Potential for Therapeutic Interference with Pathogenicity. Chembiochem 2011; 12:850-3. [DOI: 10.1002/cbic.201100014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Indexed: 11/07/2022]
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53
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Huang HR, Du ZY, Lu YJ, Fang YX, Zhang K. Methyl 4-bromo-3-hydroxybenzoate. Acta Crystallogr Sect E Struct Rep Online 2011; 67:o115. [PMID: 21522626 PMCID: PMC3050187 DOI: 10.1107/s1600536810051445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 12/08/2010] [Indexed: 11/10/2022]
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54
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Lv PC, Sun J, Luo Y, Yang Y, Zhu HL. Design, synthesis, and structure-activity relationships of pyrazole derivatives as potential FabH inhibitors. Bioorg Med Chem Lett 2010; 20:4657-60. [PMID: 20594840 DOI: 10.1016/j.bmcl.2010.05.105] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/24/2010] [Accepted: 05/29/2010] [Indexed: 10/19/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival. FabH, beta-ketoacyl-acyl carrier protein (ACP) synthase III, is a particularly attractive target, since it is central to the initiation of fatty acid biosynthesis and is highly conserved among Gram-positive and -negative bacteria. Fifty-six 1-acetyl-3,5-diphenyl-4,5-dihydro-(1H)-pyrazole derivatives were synthesized and developed as potent inhibitors of FabH. This inhibitor class demonstrates strong antibacterial activity. Escherichia coli FabH inhibitory assay and docking simulation indicated that the compounds 1-(5-(4-fluorophenyl)-3-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)ethanone (12) and 1-(5-(4-chlorophenyl)-3-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)ethanone (13) were potent inhibitors of E. coli FabH.
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Affiliation(s)
- Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People's Republic of China
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55
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Recent Advances in the Inhibition of Bacterial Fatty Acid Biosynthesis. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45018-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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56
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Lv PC, Wang KR, Yang Y, Mao WJ, Chen J, Xiong J, Zhu HL. Design, synthesis and biological evaluation of novel thiazole derivatives as potent FabH inhibitors. Bioorg Med Chem Lett 2009; 19:6750-4. [DOI: 10.1016/j.bmcl.2009.09.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/23/2009] [Accepted: 09/26/2009] [Indexed: 10/20/2022]
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57
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Gajiwala KS, Margosiak S, Lu J, Cortez J, Su Y, Nie Z, Appelt K. Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme. FEBS Lett 2009; 583:2939-46. [PMID: 19665020 DOI: 10.1016/j.febslet.2009.08.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/17/2009] [Accepted: 08/02/2009] [Indexed: 11/27/2022]
Abstract
FabH (beta-ketoacyl-acyl carrier protein synthase III) is unique in that it initiates fatty acid biosynthesis, is inhibited by long-chain fatty acids providing means for feedback control of the process, and dictates the fatty acid profile of the organism by virtue of its substrate specificity. We report the crystal structures of bacterial FabH enzymes from four different pathogenic species: Enterococcus faecalis, Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Structural data on the enzyme from different species show important differences in the architecture of the substrate-binding sites that parallel the inter-species diversity in the substrate specificities of these enzymes.
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58
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Lee PJ, Bhonsle JB, Gaona HW, Huddler DP, Heady TN, Kreishman-Deitrick M, Bhattacharjee A, McCalmont WF, Gerena L, Lopez-Sanchez M, Roncal NE, Hudson TH, Johnson JD, Prigge ST, Waters NC. Targeting the fatty acid biosynthesis enzyme, beta-ketoacyl-acyl carrier protein synthase III (PfKASIII), in the identification of novel antimalarial agents. J Med Chem 2009; 52:952-63. [PMID: 19191586 DOI: 10.1021/jm8008103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of fatty acids to the human malaria parasite, Plasmodium falciparum, and differences due to a type I fatty acid synthesis (FAS) pathway in the parasite, make it an attractive drug target. In the present study, we developed and a utilized a pharmacophore to select compounds for testing against PfKASIII, the initiating enzyme of FAS. This effort identified several PfKASIII inhibitors that grouped into various chemical classes of sulfides, sulfonamides, and sulfonyls. Approximately 60% of the submicromolar inhibitors of PfKASIII inhibited in vitro growth of the malaria parasite. These compounds inhibited both drug sensitive and resistant parasites and testing against a mammalian cell line revealed an encouraging in vitro therapeutic index for the most active compounds. Docking studies into the active site of PfKASIII suggest a potential binding mode that exploits amino acid residues at the mouth of the substrate tunnel.
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Affiliation(s)
- Patricia J Lee
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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59
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A synthesis of sulfonamide analogs of platensimycin employing a palladium-mediated carbonylation strategy. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.04.105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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60
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Johnson SL, Chen LH, Barille E, Emdadi A, Sabet M, Yuan H, Wei J, Guiney D, Pellecchia M. Structure-activity relationship studies of a novel series of anthrax lethal factor inhibitors. Bioorg Med Chem 2009; 17:3352-68. [PMID: 19359184 PMCID: PMC2730741 DOI: 10.1016/j.bmc.2009.03.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 03/13/2009] [Accepted: 03/20/2009] [Indexed: 10/21/2022]
Abstract
We report on the identification of a novel small molecule inhibitor of anthrax lethal factor using a high-throughput screening approach. Guided by molecular docking studies, we carried out structure-activity relationship (SAR) studies and evaluated activity and selectivity of most promising compounds in in vitro enzyme inhibition assays and cellular assays. Selected compounds were further analyzed for their in vitro ADME properties, which allowed us to select two compounds for further preliminary in vivo efficacy studies. The data provided represents the basis for further pharmacology and medicinal chemistry optimizations that could result in novel anti-anthrax therapies.
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Affiliation(s)
- Sherida L. Johnson
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Li-Hsing Chen
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Elisa Barille
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Aras Emdadi
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Mojgan Sabet
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Hongbin Yuan
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Jun Wei
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
| | - Donald Guiney
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maurizio Pellecchia
- Burnham Institute for Medical Research, Cancer Research Center and Infectious and Inflammatory Disease Center, 10901 North Torrey Pines Rd, La Jolla, CA 92037
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61
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Jeong KW, Lee JY, Kang DI, Lee JU, Shin SY, Kim Y. Screening of flavonoids as candidate antibiotics against Enterococcus faecalis. JOURNAL OF NATURAL PRODUCTS 2009; 72:719-724. [PMID: 19236029 DOI: 10.1021/np800698d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
beta-Ketoacyl acyl carrier protein synthase (KAS) III, the most divergent member of the condensing enzyme family, is a key catalyst in bacterial fatty acid biosynthesis and, thus, an attractive target for novel antibiotics. Here, we perform docking studies between Enterococcus faecalis KAS III (efKAS III) and one flavanone and 11 hydroxyflavanones with hydroxy groups at various positions. The MIC values of these flavanones for E. faecalis and vancomycin-resistant E. faecalis (VREF) were measured, and binding affinities to efKAS III were determined. Naringenin (9), eriodictyol (10), and taxifolin (12), with high-scoring functions and good binding affinities, docked well with efKAS III, resulting in MIC values in the range 128-512 microg/mL. Our results indicate that hydrogen bonds between the 5- and 4'-hydroxy groups and the side-chain of Arg38 and the backbone carbonyl of Phe308 are the key interactions for efKAS III inhibition. These flavanones are good candidate KAS III inhibitors and may be utilized as effective antimicrobials.
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Affiliation(s)
- Ki-Woong Jeong
- Department of Bioscience and Biotechnology, and Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
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62
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He L, Zhang L, Liu X, Li X, Zheng M, Li H, Yu K, Chen K, Shen X, Jiang H, Liu H. Discovering Potent Inhibitors Against the β-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) of Helicobacter pylori: Structure-Based Design, Synthesis, Bioassay, and Crystal Structure Determination. J Med Chem 2009; 52:2465-81. [DOI: 10.1021/jm8015602] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Lingyan He
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liang Zhang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaofeng Liu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xianghua Li
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Mingyue Zheng
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Kunqian Yu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Kaixian Chen
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Shen
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hualiang Jiang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hong Liu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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63
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Ashek A, San Juan AA, Cho SJ. HQSAR study of β-ketoacyl‐acyl carrier protein synthase III (FabH) inhibitors. J Enzyme Inhib Med Chem 2008; 22:7-14. [PMID: 17373541 DOI: 10.1080/14756360600920149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The enzyme FabH catalyzes the initial step of fatty acid biosynthesis via a type II fatty acid synthase. The pivotal role of this essential enzyme combined with its unique structural features and ubiquitous occurrence in bacteria has made it an attractive new target for the development of antibacterial and antiparasitic compounds. Predictive hologram quantitative structure activity relationship (HQSAR) model was developed for a series of benzoylamino benzoic acid derivatives acting as FabH inhibitor. The best HQSAR model was generated using atoms and bond types as fragment distinction and 4-7 as fragment size showing cross-validated q2 value of 0.678 and conventional r2 value of 0.920. The predictive ability of the model was validated by an external test set of 6 compounds giving satisfactory predictive r2 value of 0.82. The contribution maps obtained from this model were used to explain the individual atomic contributions to the overall activity. It was confirmed from the contribution map that both ring A and ring C play a vital role for activity. Moreover hydroxyl substitution in the ortho position of ring A is favorable for better inhibitory activity. Therefore the information derived from the contribution map can be used to design potent FabH inhibitors.
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Affiliation(s)
- Ali Ashek
- Korea Institute of Science and Technology, Biochemicals Research Center, Cheongryang, Seoul 130-650, South Korea
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64
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Mycobacterium tuberculosis β-Ketoacyl Acyl Carrier Protein Synthase III (mtFabH) Assay: Principles and Method. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-59745-246-5_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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65
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Pappenberger G, Schulz-Gasch T, Kusznir E, Müller F, Hennig M. Structure-assisted discovery of an aminothiazole derivative as a lead molecule for inhibition of bacterial fatty-acid synthesis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:1208-16. [PMID: 18084068 PMCID: PMC2483479 DOI: 10.1107/s0907444907049852] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 10/10/2007] [Indexed: 12/05/2022]
Abstract
Fatty-acid synthesis in bacteria is of great interest as a target for the discovery of antibacterial compounds. The addition of a new acetyl moiety to the growing fatty-acid chain, an essential step in this process, is catalyzed by beta-ketoacyl-ACP synthase (KAS). It is inhibited by natural antibiotics such as cerulenin and thiolactomycin; however, these lack the requirements for optimal drug development. Structure-based biophysical screening revealed a novel synthetic small molecule, 2-phenylamino-4-methyl-5-acetylthiazole, that binds to Escherichia coli KAS I with a binding constant of 25 microM as determined by fluorescence titration. A 1.35 A crystal structure of its complex with its target reveals noncovalent interactions with the active-site Cys163 and hydrophobic residues of the fatty-acid binding pocket. The active site is accessible through an open conformation of the Phe392 side chain and no conformational changes are induced at the active site upon ligand binding. This represents a novel binding mode that differs from thiolactomycin or cerulenin interaction. The structural information on the protein-ligand interaction offers strategies for further optimization of this low-molecular-weight compound.
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Affiliation(s)
- Günter Pappenberger
- F. Hoffmann–La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland
| | - Tanja Schulz-Gasch
- F. Hoffmann–La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland
| | - Eric Kusznir
- F. Hoffmann–La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland
| | - Francis Müller
- F. Hoffmann–La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland
| | - Michael Hennig
- F. Hoffmann–La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland
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66
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Homology Modeling and Docking Study of β-Ketoacyl Acyl Carrier Protein Synthase Ⅲ from Enterococcus Faecalis. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.8.1335] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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67
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Wright HT, Reynolds KA. Antibacterial targets in fatty acid biosynthesis. Curr Opin Microbiol 2007; 10:447-53. [PMID: 17707686 PMCID: PMC2271077 DOI: 10.1016/j.mib.2007.07.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Accepted: 07/02/2007] [Indexed: 11/28/2022]
Abstract
The fatty acid biosynthesis pathway is an attractive but still largely unexploited target for the development of new antibacterial agents. The extended use of the antituberculosis drug isoniazid and the antiseptic triclosan, which are inhibitors of fatty acid biosynthesis, validates this pathway as a target for antibacterial development. Differences in subcellular organization of the bacterial and eukaryotic multienzyme fatty acid synthase systems offer the prospect of inhibitors with host versus target specificity. Platensimycin, platencin, and phomallenic acids, newly discovered natural product inhibitors of the condensation steps in fatty acid biosynthesis, represent new classes of compounds with antibiotic potential. An almost complete catalog of crystal structures for the enzymes of the type II fatty acid biosynthesis pathway can now be exploited in the rational design of new inhibitors, as well as the recently published crystal structures of type I FAS complexes.
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Affiliation(s)
- H Tonie Wright
- Department of Biochemistry and Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh St. Suite 212, Richmond, VA 23219-1540, USA.
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68
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Alhamadsheh MM, Musayev F, Komissarov AA, Sachdeva S, Wright HT, Scarsdale N, Florova G, Reynolds KA. Alkyl-CoA Disulfides as Inhibitors and Mechanistic Probes for FabH Enzymes. ACTA ACUST UNITED AC 2007; 14:513-24. [PMID: 17524982 DOI: 10.1016/j.chembiol.2007.03.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 02/26/2007] [Accepted: 03/16/2007] [Indexed: 11/22/2022]
Abstract
The first step of the reaction catalyzed by the homodimeric FabH from a dissociated fatty acid synthase is acyl transfer from acyl-CoA to an active site cysteine. We report that C1 to C10 alkyl-CoA disulfides irreversibly inhibit Escherichia coli FabH (ecFabH) and Mycobacterium tuberculosis FabH with relative efficiencies that reflect these enzymes' differential acyl-group specificity. Crystallographic and kinetic studies with MeSSCoA show rapid inhibition of one monomer of ecFabH through formation of a methyl disulfide conjugate with this cysteine. Reaction of the second subunit with either MeSSCoA or acetyl-CoA is much slower. In the presence of malonyl-ACP, the acylation rate of the second subunit is restored to that of the native ecFabH. These observations suggest a catalytic model in which a structurally disordered apo-ecFabH dimer orders on binding either the first substrate, acetyl-CoA, or the inhibitor MeSSCoA, and is restored to a disordered state on binding of malonyl-ACP.
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69
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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: 360] [Impact Index Per Article: 21.2] [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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70
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Abstract
The availability of microbial genome sequences has ushered in the genomics era and has led to numerous technical advancements over the past decade. These advances have been both in the bioinformatics field that has integrated computer-based approaches with biology and in research methods in the laboratory. The advances have assisted scientists in their study of bacterial gene complements and the roles of their gene products in the bacterial life cycle. Assignment of genes as essential to the bacterial cell nominated them as potential targets for antibacterial drugs and spurred attempts to exploit this information and convert it into drugs. At present, these efforts have met with minimal success. There are several possible reasons for these disappointing results including choice of targets and screen designs, compound libraries chosen for screens, and decreased commitment to antibacterial drug discovery by many large pharmaceutical companies. Structure-based approaches could become very effective in the future as methodologies continue to improve.
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71
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Abstract
The type II fatty acid synthase consists of a series of individual enzymes, each encoded by a separate gene, that catalyze discrete steps in chain elongation. The formation of fatty acids is vital to bacteria, and each of the essential enzymes and their acyl group carriers represent a potential target for the development of novel antibacterial therapeutics. High resolution x-ray and/or NMR structures of representative members of every enzyme in the type II pathway are now available, and these structures are a valuable resource to guide antibacterial drug discovery. The role of each enzyme in regulating pathway activity and the diversity in the components of the pathway in the major human pathogens are important considerations in deciding the most suitable targets for future drug development.
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Affiliation(s)
- Yong-Mei Zhang
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105-2794, USA
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72
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Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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73
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Ashek A, Cho SJ. A combined approach of docking and 3D QSAR study of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Bioorg Med Chem 2006; 14:1474-82. [PMID: 16275103 DOI: 10.1016/j.bmc.2005.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 09/30/2005] [Accepted: 10/01/2005] [Indexed: 11/27/2022]
Abstract
The enzyme FabH catalyzes the initial step of fatty acid biosynthesis via a type II fatty acid synthase. The pivotal role of this essential enzyme combined with its unique structural features and ubiquitous occurrence in bacteria has made it an attractive new target for the development of antibacterial and antiparasitic compounds. Three-dimensional quantitative structure-activity relationship (3D QSAR) studies such as comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) and docking simulations were conducted on a series of potent benzoylaminobenzoic acids. Docking studies were employed to position the inhibitors into the FabH active site to determine the probable binding conformation. A reasonable correlation between the predicated binding free energy and the inhibitory activity was found. CoMFA and CoMSIA were performed based on the docking conformations, giving q(2) of 0.637 and 0.697 for CoMFA and CoMSIA models, respectively. The predictive ability of the models was validated using a set of compounds that were not included in the training set and progressive scrambling test. Mapping the 3D QSAR models to the active site of FabH related that some important amino acid residues are responsible for protein-inhibitor interaction. These results should be applicable to the prediction of the activities of new FabH inhibitors, as well as providing structural understanding.
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Affiliation(s)
- Ali Ashek
- Biochemicals Research Center, Korea Institute of Science and Technology, Cheongryang, Seoul, Republic of Korea
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Schmid MB. Crystallizing new approaches for antimicrobial drug discovery. Biochem Pharmacol 2006; 71:1048-56. [PMID: 16458857 DOI: 10.1016/j.bcp.2005.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 12/07/2005] [Accepted: 12/09/2005] [Indexed: 11/29/2022]
Abstract
Over the past decade, the sequences of microbial genomes have accumulated, changing the strategies for the discovery of novel anti-infective agents. Targets have become plentiful, yet new antimicrobial agents have been slow to emerge from this effort. In part, this reflects the long discovery and development times needed to bring new drugs to market. In addition, bottlenecks have been revealed in the antimicrobial drug discovery process at the steps of identifying good leads, and optimizing those leads into drug candidates. The fruit of structural genomics may provide opportunities to overcome these bottlenecks and fill the antimicrobial pipeline, by using the tools of structure guided drug discovery (SGDD).
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Affiliation(s)
- Molly B Schmid
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
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Mills SD. When will the genomics investment pay off for antibacterial discovery? Biochem Pharmacol 2006; 71:1096-102. [PMID: 16387281 DOI: 10.1016/j.bcp.2005.11.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 11/17/2005] [Accepted: 11/28/2005] [Indexed: 12/11/2022]
Abstract
Effective solutions to antibacterial resistance are among the key unmet medical needs driving the antibacterial industry. A major thrust in a number of companies is the development of agents with new modes of action in order to bypass the increasing emergence of antibacterial resistance. However, few antibacterials marketed in the last 30 years have novel modes of action. Most recently, genomics and target-based screening technologies have been emphasized as a means to facilitate this and expedite the antibacterial discovery process. And although no new antibacterials have yet been marketed as result of these technologies, genomics has delivered well-validated novel bacterial targets as well as a host of genetic approaches to support the antibacterial discovery process. Likewise, high throughput screening technologies have delivered the capacity to perform robust screenings of large compound collections to identify target inhibitors for lead generation. One of the principal challenges still facing antibacterial discovery is to become proficient at optimizing target inhibitors into broad-spectrum antibacterials with appropriate in vivo properties. Genomics-based technologies clearly have the potential for additional application throughout the discovery process especially in the areas of structural biology and safety assessment.
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Affiliation(s)
- Scott D Mills
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451 USA.
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