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Schäfer AB, Wenzel M. A How-To Guide for Mode of Action Analysis of Antimicrobial Peptides. Front Cell Infect Microbiol 2020; 10:540898. [PMID: 33194788 PMCID: PMC7604286 DOI: 10.3389/fcimb.2020.540898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to classical antibiotics in the fight against multi-resistant bacteria. They are produced by organisms from all domains of life and constitute a nearly universal defense mechanism against infectious agents. No drug can be approved without information about its mechanism of action. In order to use them in a clinical setting, it is pivotal to understand how AMPs work. While many pore-forming AMPs are well-characterized in model membrane systems, non-pore-forming peptides are often poorly understood. Moreover, there is evidence that pore formation may not happen or not play a role in vivo. It is therefore imperative to study how AMPs interact with their targets in vivo and consequently kill microorganisms. This has been difficult in the past, since established methods did not provide much mechanistic detail. Especially, methods to study membrane-active compounds have been scarce. Recent advances, in particular in microscopy technology and cell biological labeling techniques, now allow studying mechanisms of AMPs in unprecedented detail. This review gives an overview of available in vivo methods to investigate the antibacterial mechanisms of AMPs. In addition to classical mode of action classification assays, we discuss global profiling techniques, such as genomic and proteomic approaches, as well as bacterial cytological profiling and other cell biological assays. We cover approaches to determine the effects of AMPs on cell morphology, outer membrane, cell wall, and inner membrane properties, cellular macromolecules, and protein targets. We particularly expand on methods to examine cytoplasmic membrane parameters, such as composition, thickness, organization, fluidity, potential, and the functionality of membrane-associated processes. This review aims to provide a guide for researchers, who seek a broad overview of the available methodology to study the mechanisms of AMPs in living bacteria.
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Affiliation(s)
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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2
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Awuni E. Status of Targeting MreB for the Development of Antibiotics. Front Chem 2020; 7:884. [PMID: 31998684 PMCID: PMC6965359 DOI: 10.3389/fchem.2019.00884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Although many prospective antibiotic targets are known, bacterial infections and resistance to antibiotics remain a threat to public health partly because the druggable potentials of most of these targets have yet to be fully tapped for the development of a new generation of therapeutics. The prokaryotic actin homolog MreB is one of the important antibiotic targets that are yet to be significantly exploited. MreB is a bacterial cytoskeleton protein that has been widely studied and is associated with the determination of rod shape as well as important subcellular processes including cell division, chromosome segregation, cell wall morphogenesis, and cell polarity. Notwithstanding that MreB is vital and conserved in most rod-shaped bacteria, no approved antibiotics targeting it are presently available. Here, the status of targeting MreB for the development of antibiotics is concisely summarized. Expressly, the known therapeutic targets and inhibitors of MreB are presented, and the way forward in the search for a new generation of potent inhibitors of MreB briefly discussed.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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3
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Effects of EGTA on cell surface structures of Corynebacterium glutamicum. Arch Microbiol 2017; 200:281-289. [DOI: 10.1007/s00203-017-1445-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/28/2017] [Accepted: 10/19/2017] [Indexed: 11/25/2022]
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4
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Santiago-Morales J, Amariei G, Letón P, Rosal R. Antimicrobial activity of poly(vinyl alcohol)-poly(acrylic acid) electrospun nanofibers. Colloids Surf B Biointerfaces 2016; 146:144-51. [DOI: 10.1016/j.colsurfb.2016.04.052] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/05/2016] [Accepted: 04/30/2016] [Indexed: 11/28/2022]
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5
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Ito H, Ura A, Oyamada Y, Yoshida H, Yamagishi JI, Narita SI, Matsuyama SI, Tokuda H. A New Screening Method to Identify Inhibitors of the Lol (Localization of lipoproteins) System, a Novel Antibacterial Target. Microbiol Immunol 2013; 51:263-70. [PMID: 17380045 DOI: 10.1111/j.1348-0421.2007.tb03906.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the Lol system, which is involved in localization of lipoproteins, is essential for Escherichia coli growth and widely conserved among gram-negative bacteria, it is considered to be a promising target for the development of anti-gram-negative bacterial agents. However, no high-throughput screening method has so far been developed to screen for Lol system inhibitors. By combining three assay systems (anucleate cell blue assay, Lpp assay, and LolA-dependent release inhibition assay) and a drug susceptibility test, we have successfully developed a new screening method for identification of compounds that inhibit the Lol system. Using this new screening method, we screened 23,600 in-house chemical compounds and found 2 Lol system inhibitors. We therefore conclude that our new screening method can efficiently identify new antibacterial agents that target the Lol system.
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Affiliation(s)
- Hideaki Ito
- Pharmacology Research Laboratories, Dainippon Sumitomo Pharma Co Ltd, Suita, Osaka, Japan.
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6
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Oyamada Y, Yamagishi JI, Kihara T, Yoshida H, Wachi M, Ito H. Mechanism of Inhibition of DNA Gyrase by ES-1273, a Novel DNA Gyrase Inhibitor. Microbiol Immunol 2013; 51:977-84. [DOI: 10.1111/j.1348-0421.2007.tb03994.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Yoshihiro Oyamada
- Pharmacology Research Laboratories; Dainippon Sumitomo Pharma Co., Ltd.; Suita Osaka 564-0053 Japan
| | - Jun-ichi Yamagishi
- Technology Research & Development Center; Dainippon Sumitomo Pharma Co., Ltd.; Osaka Osaka 553-0001 Japan
| | - Takahiro Kihara
- Genomic Science Laboratories; Dainippon Sumitomo Pharma Co., Ltd.; Osaka Osaka 554-0022 Japan
| | - Hiroaki Yoshida
- Pharmacology Research Laboratories; Dainippon Sumitomo Pharma Co., Ltd.; Suita Osaka 564-0053 Japan
| | - Masaaki Wachi
- Department of Bioengineering; Tokyo Institute of Technology; Yokohama Kanagawa 226-8501 Japan
| | - Hideaki Ito
- Pharmacology Research Laboratories; Dainippon Sumitomo Pharma Co., Ltd.; Suita Osaka 564-0053 Japan
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7
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Wachi M, Iwai N. [Bacterial actin-like cytoskeletal protein as a new target of antibacterial agents]. Nihon Saikingaku Zasshi 2008; 62:397-404. [PMID: 18186290 DOI: 10.3412/jsb.62.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Masaaki Wachi
- Department of Bioengineering, Tokyo Institute of Technology
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8
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Ito H, Ura A, Oyamada Y, Tanitame A, Yoshida H, Yamada S, Wachi M, Yamagishi JI. A 4-aminofurazan derivative-A189-inhibits assembly of bacterial cell division protein FtsZ in vitro and in vivo. Microbiol Immunol 2007; 50:759-64. [PMID: 17053311 DOI: 10.1111/j.1348-0421.2006.tb03851.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Out of 95,000 commercially available chemical compounds screened by the anucleate cell blue assay, 138 selected hit compounds were further screened. As a result, A189, a 4-aminofurazan derivative was found to inhibit FtsZ GTPase with an IC(50) of 80 mug/ml and to exhibit antibacterial activity against Staphylococcus aureus and Escherichia coli. Light scattering demonstrated that A189 inhibited FtsZ assembly in vitro, and microscopic observation of A189-treated E. coli indicated that A189 perturbed FtsZ ring formation and made bacterial cells filamentous. However, nucleoids staining with DAPI revealed that A189 did not affect DNA replication and chromosome segregation in bacterial filamentous cells. Furthermore, A189 made sulA-deleted E. coli cells filamentous. Taken together, these findings suggest that A189 inhibits FtsZ GTPase activity, resulting in perturbation of FtsZ ring formation, which leads to bacterial cell death.
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Affiliation(s)
- Hideaki Ito
- Pharmacology Research Laboratories, Dainippon Sumitomo Pharma Co. Ltd., 2-6-8 Doshomachi, Chuo-ku, Osaka, Osaka 541-0045, Japan.
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9
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Iwai N, Fujii T, Nagura H, Wachi M, Kitazume T. Structure-activity relationship study of the bacterial actin-like protein MreB inhibitors: effects of substitution of benzyl group in S-benzylisothiourea. Biosci Biotechnol Biochem 2007; 71:246-8. [PMID: 17213642 DOI: 10.1271/bbb.60443] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We comprehensively investigated the effects of substitution of the benzyl group in S-benzylisothiourea derivatives on antibacterial activity, because we found previously that some substitutions enhanced it. A 2,4-Cl2-derivative was found to be the most effective compound, it was stronger than the original one in Gram-negative rod shaped-bacteria such as Escherichia coli and Salmonella typhimurium.
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Affiliation(s)
- Noritaka Iwai
- Department of Bioengineering, Tokyo Institute of Technology, Japan.
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10
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Oyamada Y, Ito H, Fujimoto-Nakamura M, Tanitame A, Iwai N, Nagai K, Yamagishi JI, Wachi M. Anucleate cell blue assay: a useful tool for identifying novel type II topoisomerase inhibitors. Antimicrob Agents Chemother 2006; 50:348-50. [PMID: 16377708 PMCID: PMC1346804 DOI: 10.1128/aac.50.1.348-350.2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About 95,000 compounds were screened by the anucleate cell blue assay. Fifty-one of the hit compounds had various structures and showed inhibitory activity against DNA gyrase and/or topoisomerase IV. Moreover, the compounds exhibited antibacterial activity against a fluoroquinolone- and novobiocin-resistant strain of Staphylococcus aureus. The anucleate cell blue assay is therefore a useful tool for finding novel type II topoisomerase inhibitors.
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Affiliation(s)
- Yoshihiro Oyamada
- Pharmacology & Microbiology Research Laboratories, Dainippon Pharmaceutical Co., Ltd., Enoki 33-94, Suita, Osaka 564-0053, Japan
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11
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Kruse T, Blagoev B, Løbner-Olesen A, Wachi M, Sasaki K, Iwai N, Mann M, Gerdes K. Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli. Genes Dev 2006; 20:113-24. [PMID: 16391237 PMCID: PMC1356105 DOI: 10.1101/gad.366606] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The actin-like MreB cytoskeletal protein and RNA polymerase (RNAP) have both been suggested to provide the force for chromosome segregation. Here, we identify MreB and RNAP as in vivo interaction partners. The interaction was confirmed using in vitro purified components. We also present convincing evidence that MreB and RNAP are both required for chromosome segregation in Escherichia coli. MreB is required for origin and bulk DNA segregation, whereas RNAP is required for bulk DNA, terminus, and possibly also for origin segregation. Furthermore, flow cytometric analyses show that MreB depletion and inactivation of RNAP confer virtually identical and highly unusual chromosome segregation defects. Thus, our results raise the possibility that the MreB-RNAP interaction is functionally important for chromosome segregation.
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Affiliation(s)
- Thomas Kruse
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK-5230 Odense M, Denmark
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12
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Tanitame A, Oyamada Y, Ofuji K, Terauchi H, Kawasaki M, Wachi M, Yamagishi JI. Synthesis and antibacterial activity of a novel series of DNA gyrase inhibitors: 5-[(E)-2-arylvinyl]pyrazoles. Bioorg Med Chem Lett 2005; 15:4299-303. [PMID: 16087337 DOI: 10.1016/j.bmcl.2005.06.103] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 06/15/2005] [Accepted: 06/17/2005] [Indexed: 10/25/2022]
Abstract
The 2-arylvinyl moiety in 1-(3-chlorophenyl)-3-(4-piperidyl)-5-[(E)-2-(5-chloro-1H-indol-3-yl)vinyl]pyrazole 2, which has previously shown improved DNA gyrase inhibition and target-related antibacterial activity, was transformed to other groups and the in vitro antibacterial activity of the synthesized compounds was evaluated. Many of the 5-[(E)-2-arylvinyl]pyrazoles synthesized in this study exhibited potent antibacterial activity against quinolone-resistant clinical isolates of gram-positive bacteria with minimal inhibitory concentration values equivalent to those against susceptible strains.
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Affiliation(s)
- Akihiko Tanitame
- Chemistry Research Laboratories, Dainippon Pharmaceutical Co., Ltd, 33-94, Enoki, Suita, Osaka 564-0053, Japan.
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13
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Tanitame A, Oyamada Y, Ofuji K, Fujimoto M, Suzuki K, Ueda T, Terauchi H, Kawasaki M, Nagai K, Wachi M, Yamagishi JI. Synthesis and antibacterial activity of novel and potent DNA gyrase inhibitors with azole ring. Bioorg Med Chem 2005; 12:5515-24. [PMID: 15465328 DOI: 10.1016/j.bmc.2004.08.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 08/10/2004] [Indexed: 11/17/2022]
Abstract
The 4-piperidyl moiety and the pyrazole ring in 1-(3-chlorophenyl)-5-(4-phenoxyphenyl)-3-(4-piperidyl)pyrazole 2, which has previously shown improved DNA gyrase inhibition and target-related antibacterial activity, were transformed to other groups and the in vitro antibacterial activity of the synthesized compounds was evaluated. The selected pyrazole, oxazole and imidazole derivatives showed moderate inhibition against DNA gyrase and topoisomerase IV with similar IC(50) values (IC(50)=9.4-25 microg/mL). In addition, many of the pyrazole, oxazole and imidazole derivatives synthesized in this study exhibited potent antibacterial activity against quinolone-resistant clinical isolates and coumarin-resistant laboratory isolates of Gram-positive bacteria with minimal inhibitory concentration values equivalent to those against susceptible strains.
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Affiliation(s)
- Akihiko Tanitame
- Chemistry Research Laboratories, Dainippon Pharmaceutical Co. Ltd, 33-94 Enoki, Suita, Osaka 564-0053, Japan.
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14
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Tanitame A, Oyamada Y, Ofuji K, Fujimoto M, Iwai N, Hiyama Y, Suzuki K, Ito H, Terauchi H, Kawasaki M, Nagai K, Wachi M, Yamagishi JI. Synthesis and Antibacterial Activity of a Novel Series of Potent DNA Gyrase Inhibitors. Pyrazole Derivatives. J Med Chem 2004; 47:3693-6. [PMID: 15214796 DOI: 10.1021/jm030394f] [Citation(s) in RCA: 229] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have previously found that a pyrazole derivative 1 possesses antibacterial activity and inhibitory activity against DNA gyrase and topoisomerase IV. Here, we synthesized new pyrazole derivatives and found that 5-[(E)-2-(5-chloroindol-3-yl)vinyl]pyrazole 16 possesses potent antibacterial activity and selective inhibitory activity against bacterial topoisomerases. Many of the synthesized pyrazole derivatives were potent against clinically isolated quinolone- or coumarin-resistant Gram-positive strains and had minimal inhibitory concentration values against these strains equivalent to those against susceptible strains.
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Affiliation(s)
- Akihiko Tanitame
- Chemistry Research Laboratories, Pharmacology and Microbiology Research Laboratories, Dainippon Pharmaceutical Co. Ltd., 33-94 Enoki, Suita, Osaka 564-0053, Japan.
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15
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Tanitame A, Oyamada Y, Ofuji K, Kyoya Y, Suzuki K, Ito H, Kawasaki M, Nagai K, Wachi M, Yamagishi JI. Design, synthesis and structure–activity relationship studies of novel indazole analogues as DNA gyrase inhibitors with Gram-positive antibacterial activity. Bioorg Med Chem Lett 2004; 14:2857-62. [PMID: 15125947 DOI: 10.1016/j.bmcl.2004.03.044] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 03/15/2004] [Indexed: 11/23/2022]
Abstract
In this study, we report the design, synthesis and structure-activity relationships of novel indazole derivatives as DNA gyrase inhibitors with Gram-positive antibacterial activity. Our results show that selected compounds from this series exhibit potent antibacterial activity against Gram-positive bacteria including multi-drug resistant strains that is methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE).
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Affiliation(s)
- Akihiko Tanitame
- Chemistry Research Laboratories, Dainippon Pharmaceutical Co., Ltd, 33-94, Enoki, Suita, Osaka 564-0053, Japan.
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16
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Tanitame A, Oyamada Y, Ofuji K, Suzuki K, Ito H, Kawasaki M, Wachi M, Yamagishi JI. Potent DNA gyrase inhibitors; novel 5-vinylpyrazole analogues with Gram-positive antibacterial activity. Bioorg Med Chem Lett 2004; 14:2863-6. [PMID: 15125948 DOI: 10.1016/j.bmcl.2004.03.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Accepted: 03/15/2004] [Indexed: 11/24/2022]
Abstract
In this study, we designed and synthesized novel 5-vinylpyrazole analogues by decreasing the lipophilicity of the parent compounds 1a,b; 3-[(3-methoxycarbonyl)cyclohexylaminomethyl]indazoles while keeping the van der Waals interaction with the lipophilic area of DNA gyrase B. The selected compound 8bb exhibited good antibacterial activity against staphylococci and enterococci, including multi-drug resistant strains.
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Affiliation(s)
- Akihiko Tanitame
- Chemistry Research Laboratories, Dainippon Pharmaceutical Co., Ltd, 33-94, Enoki, Suita, Osaka 564-0053, Japan.
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Iwai N, Nagai K, Wachi M. Novel S-benzylisothiourea compound that induces spherical cells in Escherichia coli probably by acting on a rod-shape-determining protein(s) other than penicillin-binding protein 2. Biosci Biotechnol Biochem 2002; 66:2658-62. [PMID: 12596863 DOI: 10.1271/bbb.66.2658] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Random screening for inhibitors of chromosome partitioning in Escherichia coli was done by the anucleate cell blue assay. A novel S-benzylisothiourea derivative, S-(3,4-dichlorobenzyl)isothiourea, tentatively named A22, was found to induce spherical cells and spherical anucleate cells in E. coli. Mecillinam, a specific inhibitor of penicillin-binding protein 2, which induces spherical cells in E. coli, also caused anucleate cell production. Spherical cells induced by treatment with either A22 or mecillinam varied in size, and anucleate cells seemed to be more frequent among the smaller cells. These results suggest that loss of the rod shape in E. coli leads to asymmetric cell division that results in production of anucleate cells. No competition was observed even in the presence of a 10-fold excess A22 in an in vitro assay of 14C-penicillin G binding, but mecillinam specifically inhibited binding of 14C-penicillin G to penicillin-binding protein 2. Simultaneous treatment with mecillinam and cephalexin, a specific inhibitor of penicillin-binding protein 3, induced lysis of E. coli cells, but a combination of A22 and cephalexin did not. These results suggest that the target molecule(s) of A22 was not penicillin-binding protein 2. A22 may act on a rod-shape-determining protein(s) other than penicillin-binding protein 2, such as RodA or MreB.
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Affiliation(s)
- Noritaka Iwai
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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