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Tok F, Kaya M, Karaca H, Koçyiğit-Kaymakçıoğlu B. Synthesis of some novel 1,3,4-oxadiazole derivatives and evaluation of their antimicrobial activity. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2060751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fatih Tok
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Murat Kaya
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Hülya Karaca
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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Tresse C, Radigue R, Gomes Von Borowski R, Thepaut M, Hanh Le H, Demay F, Georgeault S, Dhalluin A, Trautwetter A, Ermel G, Blanco C, van de Weghe P, Jean M, Giard JC, Gillet R. Synthesis and evaluation of 1,3,4-oxadiazole derivatives for development as broad-spectrum antibiotics. Bioorg Med Chem 2019; 27:115097. [DOI: 10.1016/j.bmc.2019.115097] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
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Alumasa JN, Manzanillo PS, Peterson ND, Lundrigan T, Baughn AD, Cox JS, Keiler KC. Ribosome Rescue Inhibitors Kill Actively Growing and Nonreplicating Persister Mycobacterium tuberculosis Cells. ACS Infect Dis 2017; 3:634-644. [PMID: 28762275 PMCID: PMC5594445 DOI: 10.1021/acsinfecdis.7b00028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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The
emergence of Mycobacterium tuberculosis (MTB) strains
that are resistant to most or all available antibiotics has created
a severe problem for treating tuberculosis and has spurred a quest
for new antibiotic targets. Here, we demonstrate that trans-translation is essential for growth of MTB and is a viable target
for development of antituberculosis drugs. We also show that an inhibitor
of trans-translation, KKL-35, is bactericidal against
MTB under both aerobic and anoxic conditions. Biochemical experiments
show that this compound targets helix 89 of the 23S rRNA. In silico molecular docking predicts a binding pocket for
KKL-35 adjacent to the peptidyl-transfer center in a region not targeted
by conventional antibiotics. Computational solvent mapping suggests
that this pocket is a druggable hot spot for small molecule binding.
Collectively, our findings reveal a new target for antituberculosis
drug development and provide critical insight on the mechanism of
antibacterial action for KKL-35 and related 1,3,4-oxadiazole benzamides.
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Affiliation(s)
- John N. Alumasa
- Department of Biochemistry
and Molecular Biology, The Pennsylvania State University, 401 Althouse Laboratory, University Park, Pennsylvania 16802, United States
| | - Paolo S. Manzanillo
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Nicholas D. Peterson
- Department of Microbiology and Immunology,
Microbiology Research Facility, University of Minnesota, Rm4-115, 689 23rd Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Tricia Lundrigan
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Anthony D. Baughn
- Department of Microbiology and Immunology,
Microbiology Research Facility, University of Minnesota, Rm4-115, 689 23rd Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Jeffery S. Cox
- Department
of Molecular and Cell Biology, University of California, Berkeley, #3370, 375E Li Ka Shing Center, Berkeley, California 94720, United States
| | - Kenneth C. Keiler
- Department of Biochemistry
and Molecular Biology, The Pennsylvania State University, 401 Althouse Laboratory, University Park, Pennsylvania 16802, United States
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Huter P, Müller C, Arenz S, Beckert B, Wilson DN. Structural Basis for Ribosome Rescue in Bacteria. Trends Biochem Sci 2017. [PMID: 28629612 DOI: 10.1016/j.tibs.2017.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems.
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Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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Liu P, Chen Y, Wang D, Tang Y, Tang H, Song H, Sun Q, Zhang Y, Liu Z. Genetic Selection of Peptide Aptamers That Interact and Inhibit Both Small Protein B and Alternative Ribosome-Rescue Factor A of Aeromonas veronii C4. Front Microbiol 2016; 7:1228. [PMID: 27588015 PMCID: PMC4988972 DOI: 10.3389/fmicb.2016.01228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/22/2016] [Indexed: 12/29/2022] Open
Abstract
Aeromonas veronii is a pathogenic gram-negative bacterium, which infects a variety of animals and results in mass mortality. The stalled-ribosome rescues are reported to ensure viability and virulence under stress conditions, of which primarily include trans-translation and alternative ribosome-rescue factor A (ArfA) in A. veronii. For identification of specific peptides that interact and inhibit the stalled-ribosome rescues, peptide aptamer library (pTRG-SN-peptides) was constructed using pTRG as vector and Staphylococcus aureus nuclease (SN) as scaffold protein, in which 16 random amino acids were introduced to form an exposed surface loop. In the meantime both Small Protein B (SmpB) which acts as one of the key components in trans-translation, and ArfA were inserted to pBT to constitute pBT-SmpB and pBT-ArfA, respectively. The peptide aptamer PA-2 was selected from pTRG-SN-peptides by bacterial two-hybrid system (B2H) employing pBT-SmpB or pBT-ArfA as baits. The conserved sites G133K134 and D138K139R140 of C-terminal SmpB were identified by interacting with N-terminal SN, and concurrently the residue K62 of ArfA was recognized by interacting with the surface loop of the specific peptide aptamer PA-2. The expression plasmids pN-SN or pN-PA-2, which combined the duplication origin of pRE112 with the neokanamycin promoter expressing SN or PA-2, were created and transformed into A. veronii C4, separately. The engineered A. veronii C4 which endowing SN or PA-2 expression impaired growth capabilities under stress conditions including temperatures, sucrose, glucose, potassium chloride (KCl) and antibiotics, and the stress-related genes rpoS and nhaP were down-regulated significantly by Quantitative Real-time PCR (qRT-PCR) when treating in 2.0% KCl. Thus, the engineered A. veronii C4 conferring PA-2 expression might be potentially attenuated vaccine, and also the peptide aptamer PA-2 could develop as anti-microbial drugs targeted to the ribosome rescued factors in A. veronii.
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Affiliation(s)
- Peng Liu
- Department of Biology, College of Sciences, Shantou University Shantou, China
| | - Yong Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Dan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Yanqiong Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Hongqian Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Haichao Song
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
| | - Qun Sun
- Department of Biotechnology, College of Life Sciences, Sichuan University Chengdu, China
| | - Yueling Zhang
- Department of Biology, College of Sciences, Shantou University Shantou, China
| | - Zhu Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University Haikou, China
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