1
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Self-assembled H-bonded supramolecular interactions in monomeric complex [Mg(H2O)6].L2.2bipy.H2O; [LH = 2-amino-5-nitrobenzoic acid, bipy = 4,4′-bipyridine]]]]: Joint theoretical calculations and Hirshfeld surface analysis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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2
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Jia B, Ma YM, Liu B, Chen P, Hu Y, Zhang R. Synthesis, Antimicrobial Activity, Structure-Activity Relationship, and Molecular Docking Studies of Indole Diketopiperazine Alkaloids. Front Chem 2019; 7:837. [PMID: 31850323 PMCID: PMC6897290 DOI: 10.3389/fchem.2019.00837] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Strategies for the synthesis of indole diketopiperazine alkaloids (indole DKPs) have been described and involve three analogs of indole DKPs. The antimicrobial activity and structure-activity relationship (SAR) of 24 indole DKPs were explored. Compounds 3b and 3c were found to be the most active, with minimum inhibitory concentrations (MIC) values in the range of 0.94–3.87 μM (0.39–1.56 μg/mL) against the four tested bacteria (Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and Escherichia coli). Furthermore, compounds 4a and 4b displayed broad-spectrum antimicrobial activity with MIC values of 1.10–36.9 μM (0.39–12.5 μg/mL) against all tested bacteria and plant pathogenic fungi (Colletotrichum gloeosporioides, Valsa mali, Alternaria alternata and Alternaria brassicae). According to the in silico study, compounds 3c showed significant binding affinity to the FabH protein from Escherichia coli, which has been identified as the key target enzyme of fatty acid synthesis (FAS) in bacteria. Therefore, these compounds are not only promising new antibacterial agents but also potential FabH inhibitors.
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Affiliation(s)
- Bin Jia
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yang-Min Ma
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Bin Liu
- School of Pharmacy, Shaanxi Institute of International Trade and Commerce, Xi'an, China.,Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province, Xi'an, China
| | - Pu Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yan Hu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Rui Zhang
- School of Arts and Sciences, Shaanxi University of Science and Technology, Xi'an, China
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3
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Reddy AS, Mao J, Krishna LS, Badavath VN, Maji S. Synthesis, spectral investigation, molecular docking and biological evaluation of Cu(II), Ni(II) and Mn(II) complexes of (E)-2-((2-butyl-4-chloro-1H-imidazol-5-yl)methylene)-N-methylhydrazinecarbothioamide (C10H16N5ClS) and its DFT studies. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Synthesis, spectral characterization, molecular docking studies, biological activity of (E)-2-((E)-3-(3,4,5-trimethoxyphenyl)allylidene) and (E)-N-phenyl 2-((E)-3-(3,4,5-trimethoxyphenyl)allylidene)hydrazinecarbothioamides and their Cu(II) complexes. JOURNAL OF SAUDI CHEMICAL SOCIETY 2019. [DOI: 10.1016/j.jscs.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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5
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Rational design, molecular docking and synthesis of novel homopiperazine linked imidazo[1,2-a]pyrimidine derivatives as potent cytotoxic and antimicrobial agents. Bioorg Med Chem Lett 2019; 29:2248-2253. [PMID: 31239178 DOI: 10.1016/j.bmcl.2019.06.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/15/2019] [Accepted: 06/19/2019] [Indexed: 01/29/2023]
Abstract
Designed and synthesized novel homopiperazine linked imidazo[1,2-a]pyrimidine derivatives (10a-i, 11a-g, 12), and evaluated them for their in vitro cytotoxicity against HeLa cells (cervical cancer), A549 cells (lung cancer) cells, by MTT assay. Compound 12 (IC50 = 4.14 µM) and compound 10c (IC50 = 5.98 µM) were found to be 2.5 fold, and 1.74 fold more potent when compared with standard Etoposide (IC50 = 10.44 µM), against A549 (lung cancer cells). Compound 12 also found to be 1.57 and 1.13 fold potent against DU145 (IC50 = 6.24 µM) and HeLa (IC50 = 6.54 µM), respectively when compared with Etoposide (DU145, IC50 = 9.8 µM; HeLa, IC50 = 7.43 µM). Compound 10f (IC50 = 6.12 µM) was found to be 1.31 fold more potent than Etoposide (IC50 = 7.43 µM) against HeLa cell lines. Moreover compounds 10a and 11a showed cytotoxicity at low micro-molar concentrations against A549 cells. Synthesized compounds were also evaluated for their antimicrobial activity by Cup plate diffusion method. Compounds 10c, 11b, 11d and 11f displayed remarkable antimicrobial activity relating to their standard drugs Gentamycin, Amphotericin B and Ampicillin. Significantly, compound 10c showed broad spectrum activity against tested microbial strains. All the designed compounds were well occupied the binding site of the colchicine and interacted with both α- and β-tubuline interface (PDB ID: 3E22), which demonstrates that synthesized compounds are promising tubulin inhibitors. Also, the synthesized compounds occupied the catalytic triad and adenine-binding site, in the active site of β-ketoacyl-acyl carrier protein synthase III enzyme (PDB ID: 1MZS). The molecular docking results provided the useful information for the future design of more potent inhibitors. These preliminary results convinced further investigation and modifications on synthesized compounds aiming towards the development of potential cytotoxic as well as antimicrobial agents.
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6
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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7
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Hou J, Zheng H, Tzou WS, Cooper DR, Chruszcz M, Chordia MD, Kwon K, Grabowski M, Minor W. Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels. FEBS J 2018; 285:2900-2921. [PMID: 29917313 PMCID: PMC6105497 DOI: 10.1111/febs.14588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/31/2018] [Accepted: 06/15/2018] [Indexed: 01/14/2023]
Abstract
Vibrio cholerae, the causative pathogen of the life-threatening infection cholera, encodes two copies of β-ketoacyl-acyl carrier protein synthase III (vcFabH1 and vcFabH2). vcFabH1 and vcFabH2 are pathogenic proteins associated with fatty acid synthesis, lipid metabolism, and potential applications in biofuel production. Our biochemical assays characterize vcFabH1 as exhibiting specificity for acetyl-CoA and CoA thioesters with short acyl chains, similar to that observed for FabH homologs found in most gram-negative bacteria. vcFabH2 prefers medium chain-length acyl-CoA thioesters, particularly octanoyl-CoA, which is a pattern of specificity rarely seen in bacteria. Structural characterization of one vcFabH1 and six vcFabH2 structures determined in either apo form or in complex with acetyl-CoA/octanoyl-CoA indicate that the substrate-binding pockets of vcFabH1 and vcFabH2 are of different sizes, accounting for variations in substrate chain-length specificity. An unusual and unique feature of vcFabH2 is its C-terminal fragment that interacts with both the substrate-entrance loop and the dimer interface of the enzyme. Our discovery of the pattern of substrate specificity of both vcFabH1 and vcFabH2 can potentially aid the development of novel antibacterial agents against V. cholerae. Additionally, the distinctive substrate preference of FabH2 in V. cholerae and related facultative anaerobes conceivably make it an attractive component of genetically engineered bacteria used for commercial biofuel production.
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Affiliation(s)
- Jing Hou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Wen-Shyong Tzou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Taiwan
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Mahendra D. Chordia
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Keehwan Kwon
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
- Infectious Diseases, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
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8
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Lee WC, Jeong MC, Lee Y, Kwak C, Lee JY, Kim Y. Structure and substrate specificity of β-ketoacyl-acyl carrier protein synthase III from Acinetobacter baumannii. Mol Microbiol 2018. [PMID: 29528170 DOI: 10.1111/mmi.13950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Originally annotated as the initiator of fatty acid synthesis (FAS), β-ketoacyl-acyl carrier protein synthase III (KAS III) is a unique component of the bacterial FAS system. Novel variants of KAS III have been identified that promote the de novo use of additional extracellular fatty acids by FAS. These KAS III variants prefer longer acyl-groups, notably octanoyl-CoA. Acinetobacter baumannii, a clinically important nosocomial pathogen, contains such a multifunctional KAS III (AbKAS III). To characterize the structural basis of its substrate specificity, we determined the crystal structures of AbKAS III in the presence of different substrates. The acyl-group binding cavity of AbKAS III and co-crystal structure of AbKAS III and octanoyl-CoA confirmed that the cavity can accommodate acyl groups with longer alkyl chains. Interestingly, Cys264 formed a disulfide bond with residual CoA used in the crystallization, which distorted helices at the putative interface with acyl-carrier proteins. The crystal structure of KAS III in the alternate conformation can also be utilized for designing novel antibiotics.
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Affiliation(s)
- Woo Cheol Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Cheol Jeong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Yeongjoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Chulhee Kwak
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jee-Young Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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9
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Ekström AG, Kelly V, Marles-Wright J, Cockroft SL, Campopiano DJ. Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45). Org Biomol Chem 2018; 15:6310-6313. [PMID: 28715001 PMCID: PMC5708339 DOI: 10.1039/c7ob01396e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use mass spectrometry analysis and molecular modelling to show the established antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael-type addition elimination reaction mechanism.
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Affiliation(s)
- Alexander G Ekström
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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10
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Naz S, Ngo T, Farooq U, Abagyan R. Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PeerJ 2017; 5:e3765. [PMID: 28948099 PMCID: PMC5609521 DOI: 10.7717/peerj.3765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022] Open
Abstract
Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis. The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another. Methods Nine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli, two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps. Results High sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis. Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The derived pocket alignments and distance-based maps provide guidelines for drug discovery and repurposing. In addition they also provide recommendations for the relevant model bacteria that may be used for initial drug testing. Discussion Comparing ligand binding sites through sequence identity calculation could be an effective approach to identify conserved orthologs as drug binding pockets have shown higher level of conservation among various species. By using this approach we could avoid the problems associated with full sequence comparison. We identified essential metabolic enzymes among ESKAPE pathogens that share high sequence identity in their putative drug binding pockets (up to 100%), of which known inhibitors can potentially antagonize these identical pockets in the various species in a similar manner.
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Affiliation(s)
- Sadia Naz
- Department of Chemistry, COMSATS Intitute of Information Technology, Abbottabad, Pakistan.,Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, CA, United States of America
| | - Tony Ngo
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, CA, United States of America.,Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Umar Farooq
- Department of Chemistry, COMSATS Intitute of Information Technology, Abbottabad, Pakistan
| | - Ruben Abagyan
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, CA, United States of America
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11
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Segretti ND, Serafim RA, Segretti MC, Miyata M, Coelho FR, Augusto O, Ferreira EI. New antibacterial agents: Hybrid bioisoster derivatives as potential E. coli FabH inhibitors. Bioorg Med Chem Lett 2016; 26:3988-93. [DOI: 10.1016/j.bmcl.2016.06.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/30/2022]
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12
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McKinney DC, Eyermann CJ, Gu RF, Hu J, Kazmirski SL, Lahiri SD, McKenzie AR, Shapiro AB, Breault G. Antibacterial FabH Inhibitors with Mode of Action Validated in Haemophilus influenzae by in Vitro Resistance Mutation Mapping. ACS Infect Dis 2016; 2:456-64. [PMID: 27626097 DOI: 10.1021/acsinfecdis.6b00053] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fatty acid biosynthesis is essential to bacterial growth in Gram-negative pathogens. Several small molecules identified through a combination of high-throughput and fragment screening were cocrystallized with FabH (β-ketoacyl-acyl carrier protein synthase III) from Escherichia coli and Streptococcus pneumoniae. Structure-based drug design was used to merge several scaffolds to provide a new class of inhibitors. After optimization for Gram-negative enzyme inhibitory potency, several compounds demonstrated antimicrobial activity against an efflux-negative strain of Haemophilus influenzae. Mutants resistant to these compounds had mutations in the FabH gene near the catalytic triad, validating FabH as a target for antimicrobial drug discovery.
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Affiliation(s)
- David C. McKinney
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Charles J. Eyermann
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rong-Fang Gu
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jun Hu
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sushmita D. Lahiri
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Andrew R. McKenzie
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Adam B. Shapiro
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gloria Breault
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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13
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Zhou Y, Luo Y, Yang YS, Lu L, Zhu HL. Study of acylhydrazone derivatives with deoxygenated seven-membered rings as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00263c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yin Luo
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Liang Lu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
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14
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Composing compound libraries for hit discovery--rationality-driven preselection or random choice by structural diversity? Future Med Chem 2015; 6:2057-72. [PMID: 25531968 DOI: 10.4155/fmc.14.142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
AIMS In order to identify new scaffolds for drug discovery, surface plasmon resonance is frequently used to screen structurally diverse libraries. Usually, hit rates are low and identification processes are time consuming. Hence, approaches which improve hit rates and, thus, reduce the library size are required. METHODS In this work, we studied three often used strategies for their applicability to identify inhibitors of PqsD. In two of them, target-specific aspects like inhibition of a homologous protein or predicted binding determined by virtual screening were used for compound preselection. Finally, a fragment library, covering a large chemical space, was screened and served as comparison. RESULTS & CONCLUSION Indeed, higher hit rates were observed for methods employing preselected libraries indicating that target-oriented compound selection provides a time-effective alternative.
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15
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Mittal A, Johnson ME. Conformational diversity of bacterial FabH: implications for molecular recognition specificity. J Mol Graph Model 2014; 55:115-22. [PMID: 25437098 DOI: 10.1016/j.jmgm.2014.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 09/22/2014] [Accepted: 11/07/2014] [Indexed: 11/25/2022]
Abstract
The molecular basis of variable substrate and inhibitor specificity of the highly conserved bacterial fatty acid synthase enzyme, FabH, across different bacterial species remains poorly understood. In the current work, we explored the conformational diversity of FabH enzymes to understand the determinants of diverse interaction specificity across Gram-positive and Gram-negative bacteria. Atomistic molecular dynamics simulations reveal that FabH from E. coli and E. faecalis exhibit distinct native state conformational ensembles and dynamic behaviors. Despite strikingly similar substrate binding pockets, hot spot assessment using computational solvent mapping identified quite different favorable binding interactions between the two homologs. Our data suggest that FabH utilizes protein dynamics and seemingly minor sequence and structural differences to modulate its molecular recognition and substrate specificity across bacterial species. These insights will potentially facilitate the rational design and development of antibacterial inhibitors against FabH enzymes.
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Affiliation(s)
- Anuradha Mittal
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave-m/c 870, Chicago, IL 60607-7173, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave-m/c 870, Chicago, IL 60607-7173, USA.
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16
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Qin YJ, Wang PF, Makawana JA, Wang ZC, Wang ZN, Yan-Gu, Jiang AQ, Zhu HL. Design, synthesis and biological evaluation of metronidazole-thiazole derivatives as antibacterial inhibitors. Bioorg Med Chem Lett 2014; 24:S0960-894X(14)01007-5. [PMID: 25318998 DOI: 10.1016/j.bmcl.2014.09.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 09/11/2014] [Accepted: 09/18/2014] [Indexed: 10/24/2022]
Abstract
A series of metronidazole-thiazole derivatives has been designed, synthesized and evaluated as potential antibacterial inhibitors. All the synthesized compounds were determined by elemental analysis, 1H NMR and MS. They were also tested for antibacterial activity against Escherichia coli, Bacillus thuringiensis, Bacillus subtilis and Pseudomonas aeruginosa as well as for the inhibition to FabH. The results showed that compound 5e exhibited the most potent inhibitory activity against E. coli FabH with IC50 of 4.9μM. Molecular modeling simulation studies were performed in order to predict the biological activity of proposed compounds. Toxicity assay of compounds 5a, 5b, 5d, 5e, 5g and 5i showed that they were noncytotoxic against human macrophage. The results revealed that these compounds offered remarkable viability.
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Affiliation(s)
- Ya-Juan Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Peng-Fei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Jigar A Makawana
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Zhong-Chang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Ze-Nan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Yan-Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Ai-Qin Jiang
- School of Medicine, Nanjing University, Nanjing 210093, People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China.
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Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance? Mol Divers 2014; 18:637-54. [PMID: 24671521 DOI: 10.1007/s11030-014-9513-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the β-ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.
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Song H, Ao GZ, Li HQ. Novel FabH inhibitors: an updated article literature review (July 2012 to June 2013). Expert Opin Ther Pat 2013; 24:19-27. [DOI: 10.1517/13543776.2014.847091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Wang Y, Ma S. Recent Advances in Inhibitors of Bacterial Fatty Acid Synthesis Type II (FASII) System Enzymes as Potential Antibacterial Agents. ChemMedChem 2013; 8:1589-608. [DOI: 10.1002/cmdc.201300209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/30/2013] [Indexed: 12/25/2022]
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20
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Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
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Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
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Ramamoorthy D, Turos E, Guida WC. Identification of a New Binding Site in E. coli FabH using Molecular Dynamics Simulations: Validation by Computational Alanine Mutagenesis and Docking Studies. J Chem Inf Model 2013; 53:1138-56. [DOI: 10.1021/ci3003528] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Divya Ramamoorthy
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue,
Tampa, Florida 33620, United States
| | - Edward Turos
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue,
Tampa, Florida 33620, United States
- Center for Molecular Diversity in Drug Design, Discovery and Delivery, 4202
E. Fowler Avenue, Tampa, Florida 33620, United States
- Center for Drug Discovery and Innovation, 4202 E. Fowler Avenue, Tampa,
Florida 33620, United States
| | - Wayne C. Guida
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue,
Tampa, Florida 33620, United States
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa,
Florida 33612, United States
- Center for Molecular Diversity in Drug Design, Discovery and Delivery, 4202
E. Fowler Avenue, Tampa, Florida 33620, United States
- Center for Drug Discovery and Innovation, 4202 E. Fowler Avenue, Tampa,
Florida 33620, United States
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Zhou Y, Du QR, Sun J, Li JR, Fang F, Li DD, Qian Y, Gong HB, Zhao J, Zhu HL. Novel Schiff-base-derived FabH inhibitors with dioxygenated rings as antibiotic agents. ChemMedChem 2013; 8:433-41. [PMID: 23401291 DOI: 10.1002/cmdc.201200587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Indexed: 11/10/2022]
Abstract
Fatty acid biosynthesis plays a vital role in bacterial survival and several key enzymes involved in this biosynthetic pathway have been identified as attractive targets for the development of new antibacterial agents. Of these promising targets, β-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) is the most attractive target that could trigger the initiation of fatty acid biosynthesis and is highly conserved among Gram-positive and -negative bacteria. Designing small molecules with FabH inhibitory activity displays great significance for developing antibiotic agents, which should be highly selective, nontoxic and broad-spectrum. In this manuscript, a series of novel Schiff base compounds were designed and synthesized, and their biological activities were evaluated as potential inhibitors. Among these 21 new compounds, (E)-N-((3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)methylene)hexadecan-1-amine (10) showed the most potent antibacterial activity with a MIC value of 3.89-7.81 μM(-1) against the tested bacterial strains and exhibited the most potent E. coli FabH inhibitory activity with an IC(50) value of 1.6 μM. Docking simulation was performed to position compound 10 into the E. coli FabH active site to determine the probable binding conformation.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Hankou Road, Nanjing 210093, PR China
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Luo Y, Yang YS, Fu J, Zhu HL. Novel FabH inhibitors: a patent and article literature review (2000--2012). Expert Opin Ther Pat 2012; 22:1325-36. [PMID: 22998551 DOI: 10.1517/13543776.2012.727798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The traditional antimicrobial chemotherapy drugs play their effects mostly via bacterial interference with in vivo amino acids, nucleotides, amino sugars and other small molecule synthesis, or interfering the biochemical processes of these small molecules to synthesize nucleic acids, peptidoglycan and other biological macromolecules. In recent years, enzymes with single function in bacterial fatty acid synthetase system have become the genome-driven novel antibacterial drug targets. Among inhibitors of these targets, FabH inhibitors are distinguished, for their target is different from that of existing antibiotics. Therefore, discovery of FabH inhibitors might be a potential orientation to overcome bacterial resistance. AREAS COVERED This review summarized new patents and articles published on FabH inhibitors from 2000 to 2012. EXPERT OPINION The review gives a brief understanding about the background and development in the area of FabH inhibitors that aims to solve the bacterial resistance problem. This review puts emphasis on some typical small molecules, which participate in the process of FabH inhibition. Overall, the research scopes of antibacterial agents are getting broad. Fatty acid synthase (FAS) pathway has been proved to be a promising target for the therapy. However, claim of novel antibacterial agents with more active and higher specificity is still continued.
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Affiliation(s)
- Yin Luo
- Nanjing University, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing 210093, People's Republic of China
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Luo Y, Zhang LR, Hu Y, Zhang S, Fu J, Wang XM, Zhu HL. Synthesis and Antimicrobial Activities of Oximes Derived from O-Benzylhydroxylamine as FabH Inhibitors. ChemMedChem 2012; 7:1587-93. [DOI: 10.1002/cmdc.201200225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/12/2012] [Indexed: 11/07/2022]
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25
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Yang YS, Zhang F, Gao C, Zhang YB, Wang XL, Tang JF, Sun J, Gong HB, Zhu HL. Discovery and modification of sulfur-containing heterocyclic pyrazoline derivatives as potential novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Bioorg Med Chem Lett 2012; 22:4619-24. [DOI: 10.1016/j.bmcl.2012.05.091] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/14/2012] [Accepted: 05/28/2012] [Indexed: 01/18/2023]
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Synthesis of potent inhibitors of β-ketoacyl-acyl carrier protein synthase III as potential antimicrobial agents. Molecules 2012; 17:4770-81. [PMID: 22534662 PMCID: PMC6268549 DOI: 10.3390/molecules17054770] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 04/11/2012] [Accepted: 04/16/2012] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis FabH, an essential enzyme in the mycolic acid biosynthetic pathway, is an attractive target for novel anti-tubercolosis agents. Structure-based design and synthesis of 1-(4-carboxybutyl)-4-(4-(substituted benzyloxy)phenyl)-1H-pyrrole-2-carboxylic acid derivatives 7a–h, a subset of eight potential FabH inhibitors, is described in this paper. The Vilsmeier-Haack reaction was employed as a key step. The structures of all the newly synthesized compounds were identified by IR, 1H-NMR, 13C-NMR, ESI-MS and HRMS. The alamarBlue™ microassay was employed to evaluate the compounds 7a–h against Mycobacterium tuberculosis H37Rv. The results demonstrate that the compound 7d possesses good in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv (Minimum Inhibitory Concentration value [MIC], 12.5 µg/mL).These compounds may prove useful in the discovery and development of new anti-tuberculosis drugs.
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Ozawa T, Takahata S, Kitagawa H. Search for the Dual Inhibitors of Bacterial Enoyl-acyl Carrier Protein (ACP) Reductases (FabI and FabK) as Antibacterial Agents. J SYN ORG CHEM JPN 2012. [DOI: 10.5059/yukigoseikyokaishi.70.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Discovery of novel selective inhibitors of Staphylococcus aureus β-ketoacyl acyl carrier protein synthase III. Eur J Med Chem 2011; 47:261-9. [PMID: 22104972 DOI: 10.1016/j.ejmech.2011.10.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/22/2011] [Accepted: 10/28/2011] [Indexed: 11/22/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase III (KAS III) is a condensing enzyme in bacterial fatty acid synthesis and a potential target while designing novel antibiotics. In our previous report, we discovered the lead compound YKAs3003, which serves as an inhibitor of Escherichia coli KAS III (ecKAS III), and determined a reliable pharmacophore map from in silico screening. In this study, we determined two pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the x-ray structure of Staphylococcus aureus KAS III (saKAS III) to identify potent saKAS III inhibitors. We discovered a new potential inhibitor (6) with broad-spectrum antimicrobial activity and 0.8 nM binding affinity for saKAS III, proving the reliability of our pharmacophore map. Using optimization procedures, we identified three new antimicrobial saKAS III inhibitors: 6c (2,4-dichloro-benzoic acid (2,3,4-trihydroxy-benzylidene)-hydrazide), 6e (4-[(3-chloro-pyrazin-2-yl)-hydrazonomethyl]-benzene-1,3-diol), and 6 (4-[(5-trifluoromethyl-pyridin-2-yl)-hydrazonomethyl]-benzene-1,3-diol). All three inhibitors have a novel 4-hydrazonomethyl-benzene-1,3-diol core structure. These inhibitors exhibited high binding affinity to saKAS III and highly selective antimicrobial activities against S. aureus and methicillin-resistant S. aureus, with minimal inhibitory concentration values of 1-2 μg/mL.
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Zhang HJ, Qin X, Liu K, Zhu DD, Wang XM, Zhu HL. Synthesis, antibacterial activities and molecular docking studies of Schiff bases derived from N-(2/4-benzaldehyde-amino) phenyl-N′-phenyl-thiourea. Bioorg Med Chem 2011; 19:5708-15. [DOI: 10.1016/j.bmc.2011.06.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/24/2011] [Accepted: 06/25/2011] [Indexed: 10/17/2022]
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30
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Lu X, Wan B, Franzblau SG, You Q. Design, synthesis and anti-tubercular evaluation of new 2-acylated and 2-alkylated amino-5-(4-(benzyloxy)phenyl)thiophene-3-carboxylic acid derivatives. Part 1. Eur J Med Chem 2011; 46:3551-63. [DOI: 10.1016/j.ejmech.2011.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/03/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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31
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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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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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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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34
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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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35
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Structure-based design, synthesis of novel inhibitors of Mycobacterium tuberculosis FabH as potential anti-tuberculosis agents. CHINESE CHEM LETT 2009. [DOI: 10.1016/j.cclet.2009.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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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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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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Functional expression of Francisella tularensis FabH and FabI, potential antibacterial targets. Protein Expr Purif 2009; 65:83-91. [DOI: 10.1016/j.pep.2008.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 11/19/2022]
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39
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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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40
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Novel E. coli beta-ketoacyl-acyl carrier protein synthase III inhibitors as targeted antibiotics. Bioorg Med Chem 2009; 17:1506-13. [PMID: 19185501 DOI: 10.1016/j.bmc.2009.01.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 01/07/2009] [Accepted: 01/08/2009] [Indexed: 11/21/2022]
Abstract
Beta-ketoacyl-acyl carrier protein synthase (KAS) III is a condensing enzyme that initiates fatty acid biosynthesis in most bacteria. We determined three pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the X-ray structure of Escherichia coli KAS III (ecKAS III) and choose 16 compounds as candidate ecKAS III inhibitors. Binding inhibitors were characterized using saturation-transfer difference NMR spectroscopy (STD-NMR), and binding constants were determined with fluorescence quenching experiments. Based on the results, we propose that the antimicrobial compound, 4-cyclohexyliminomethyl-benzene-1,3-diol (YKAs3003), is a potent inhibitor of pathogenic KAS III, displaying minimal inhibitory concentration (MIC) values in the range 128-256 microg/mL against various bacteria.
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Turos E, Revell KD, Ramaraju P, Gergeres DA, Greenhalgh K, Young A, Sathyanarayan N, Dickey S, Lim D, Alhamadsheh MM, Reynolds K. Unsymmetric aryl-alkyl disulfide growth inhibitors of methicillin-resistant Staphylococcus aureus and Bacillus anthracis. Bioorg Med Chem 2008; 16:6501-8. [PMID: 18524602 PMCID: PMC2526022 DOI: 10.1016/j.bmc.2008.05.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 05/08/2008] [Accepted: 05/14/2008] [Indexed: 11/29/2022]
Abstract
This study describes the antibacterial properties of synthetically produced mixed aryl-alkyl disulfide compounds as a means to control the growth of Staphylococcus aureus and Bacillus anthracis. Some of these compounds exerted strong in vitro bioactivity. Our results indicate that among the 12 different aryl substituents examined, nitrophenyl derivatives provide the strongest antibiotic activities. This may be the result of electronic activation of the arylthio moiety as a leaving group for nucleophilic attack on the disulfide bond. Small alkyl residues on the other sulfur provide the best activity as well, which for different bacteria appears to be somewhat dependent on the nature of the alkyl moiety. The mechanism of action of these lipophilic disulfides is likely similar to that of previously reported N-thiolated beta-lactams, which have been shown to produce alkyl-CoA disulfides through a thiol-disulfide exchange within the cytoplasm, ultimately inhibiting type II fatty acid synthesis. However, the mixed alkyl-CoA disulfides themselves show no antibacterial activity, presumably due to the inability of the highly polar compounds to cross the bacterial cell membrane. These structurally simple disulfides have been found to inhibit beta-ketoacyl-acyl carrier protein synthase III, or FabH, a key enzyme in type II fatty acid biosynthesis, and thus may serve as new leads to the development of effective antibacterials for MRSA and anthrax infections.
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Affiliation(s)
- Edward Turos
- Center for Molecular Diversity in Drug Design, Discovery, and Delivery, Department of Chemistry, 4202 East Fowler Avenue, CHE 205, University of South Florida, Tampa, FL 33620, USA.
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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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43
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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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44
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Wang J, Kodali S, Lee SH, Galgoci A, Painter R, Dorso K, Racine F, Motyl M, Hernandez L, Tinney E, Colletti SL, Herath K, Cummings R, Salazar O, González I, Basilio A, Vicente F, Genilloud O, Pelaez F, Jayasuriya H, Young K, Cully DF, Singh SB. Discovery of platencin, a dual FabF and FabH inhibitor with in vivo antibiotic properties. Proc Natl Acad Sci U S A 2007; 104:7612-6. [PMID: 17456595 PMCID: PMC1863502 DOI: 10.1073/pnas.0700746104] [Citation(s) in RCA: 297] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Indexed: 11/18/2022] Open
Abstract
Emergence of bacterial resistance is a major issue for all classes of antibiotics; therefore, the identification of new classes is critically needed. Recently we reported the discovery of platensimycin by screening natural product extracts using a target-based whole-cell strategy with antisense silencing technology in concert with cell free biochemical validations. Continued screening efforts led to the discovery of platencin, a novel natural product that is chemically and biologically related but different from platensimycin. Platencin exhibits a broad-spectrum Gram-positive antibacterial activity through inhibition of fatty acid biosynthesis. It does not exhibit cross-resistance to key antibiotic resistant strains tested, including methicillin-resistant Staphylococcus aureus, vancomycin-intermediate S. aureus, and vancomycin-resistant Enterococci. Platencin shows potent in vivo efficacy without any observed toxicity. It targets two essential proteins, beta-ketoacyl-[acyl carrier protein (ACP)] synthase II (FabF) and III (FabH) with IC50 values of 1.95 and 3.91 microg/ml, respectively, whereas platensimycin targets only FabF (IC50 = 0.13 microg/ml) in S. aureus, emphasizing the fact that more antibiotics with novel structures and new modes of action can be discovered by using this antisense differential sensitivity whole-cell screening paradigm.
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Affiliation(s)
- Jun Wang
- *Merck Research Laboratories, Rahway, NJ 07065; and
| | | | - Sang Ho Lee
- *Merck Research Laboratories, Rahway, NJ 07065; and
| | | | | | - Karen Dorso
- *Merck Research Laboratories, Rahway, NJ 07065; and
| | - Fred Racine
- *Merck Research Laboratories, Rahway, NJ 07065; and
| | - Mary Motyl
- *Merck Research Laboratories, Rahway, NJ 07065; and
| | | | | | | | | | | | - Oscar Salazar
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
| | - Ignacio González
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
| | - Angela Basilio
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
| | - Francisca Vicente
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
| | - Olga Genilloud
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
| | - Fernando Pelaez
- Centro de Investigación Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcárcel 38, Madrid 28027, Spain
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45
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Thomaides HB, Davison EJ, Burston L, Johnson H, Brown DR, Hunt AC, Errington J, Czaplewski L. Essential bacterial functions encoded by gene pairs. J Bacteriol 2006; 189:591-602. [PMID: 17114254 PMCID: PMC1797375 DOI: 10.1128/jb.01381-06] [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] [Indexed: 11/20/2022] Open
Abstract
To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.
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Affiliation(s)
- Helena B Thomaides
- Prolysis Ltd., Begbroke Science Park, Sandy Lane, Yarnton OX5 1PF, Oxfordshire, UK.
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46
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Srinivas K, Srinivas U, Bhanuprakash K, Harakishore K, Murthy USN, Rao VJ. Synthesis and antibacterial activity of various substituted s-triazines. Eur J Med Chem 2006; 41:1240-6. [PMID: 16815597 DOI: 10.1016/j.ejmech.2006.05.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/25/2006] [Accepted: 05/25/2006] [Indexed: 11/29/2022]
Abstract
Series of substituted-s-triazines (1-22) were synthesized and evaluated for their in vitro antibacterial activity against six representative Gram-positive and Gram-negative bacterial strains. Many compounds have displayed comparable antibacterial activity against Bacillus sphaericus and significantly active against other tested organisms with reference to streptomycin.
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Affiliation(s)
- K Srinivas
- Organic Chemistry Division II, Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad, India
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47
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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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48
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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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49
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Singh SB, Barrett JF. Empirical antibacterial drug discovery—Foundation in natural products. Biochem Pharmacol 2006; 71:1006-15. [PMID: 16412984 DOI: 10.1016/j.bcp.2005.12.016] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Revised: 12/09/2005] [Accepted: 12/09/2005] [Indexed: 11/21/2022]
Abstract
Natural products have been a rich source in providing leads for the development of drugs for the treatment of bacterial infections. However, beyond the discovery of the natural product, thienamycin and the synthetic lead, oxazolidinone in the 1970s, there has been a dearth of new compounds. This commentary provides an overview of current antibiotic leads and their mechanism of action, and highlights tools that can be applied to the discovery of new antibiotics.
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Affiliation(s)
- Sheo B Singh
- Natural Products Chemistry, RY80Y-350, Merck Research Laboratories, P.O. 2000, Rahway, NJ 07065, USA.
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50
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Young K, Jayasuriya H, Ondeyka JG, Herath K, Zhang C, Kodali S, Galgoci A, Painter R, Brown-Driver V, Yamamoto R, Silver LL, Zheng Y, Ventura JI, Sigmund J, Ha S, Basilio A, Vicente F, Tormo JR, Pelaez F, Youngman P, Cully D, Barrett JF, Schmatz D, Singh SB, Wang J. Discovery of FabH/FabF inhibitors from natural products. Antimicrob Agents Chemother 2006; 50:519-26. [PMID: 16436705 PMCID: PMC1366929 DOI: 10.1128/aac.50.2.519-526.2006] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/02/2005] [Accepted: 11/30/2005] [Indexed: 11/20/2022] Open
Abstract
Condensing enzymes are essential in type II fatty acid synthesis and are promising targets for antibacterial drug discovery. Recently, a new approach using a xylose-inducible plasmid to express antisense RNA in Staphylococcus aureus has been described; however, the actual mechanism was not delineated. In this paper, the mechanism of decreased target protein production by expression of antisense RNA was investigated using Northern blotting. This revealed that the antisense RNA acts posttranscriptionally by targeting mRNA, leading to 5' mRNA degradation. Using this technology, a two-plate assay was developed in order to identify FabF/FabH target-specific cell-permeable inhibitors by screening of natural product extracts. Over 250,000 natural product fermentation broths were screened and then confirmed in biochemical assays, yielding a hit rate of 0.1%. All known natural product FabH and FabF inhibitors, including cerulenin, thiolactomycin, thiotetromycin, and Tü3010, were discovered using this whole-cell mechanism-based screening approach. Phomallenic acids, which are new inhibitors of FabF, were also discovered. These new inhibitors exhibited target selectivity in the gel elongation assay and in the whole-cell-based two-plate assay. Phomallenic acid C showed good antibacterial activity, about 20-fold better than that of thiolactomycin and cerulenin, against S. aureus. It exhibited a spectrum of antibacterial activity against clinically important pathogens including methicillin-resistant Staphylococcus aureus, Bacillus subtilis, and Haemophilus influenzae.
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