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Höger B, Peifer C, Beitz E. Cell-free production of fluorescent proteins for the discovery of novel ribosome-targeting antibiotics. J Microbiol Methods 2023; 213:106814. [PMID: 37652138 DOI: 10.1016/j.mimet.2023.106814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023]
Abstract
Various issues including the overuse of antibiotics has led to the development of threatening multidrug-resistant bacterial strains urging development of novel anti-infectives. One quarter of current clinical phase III antibiotic drug candidates address ribosomal protein translation as a target. Here, we describe an effective cell-free in vitro screening system for inhibitors of bacterial ribosome activity with direct fluorescence read-out. Using ribosomal S30 extracts from Escherichia coli, Salmonella enterica, and Pseudomonas putida, the validity of this system is demonstrated by concentration-dependent inhibition of translation by a set of different classes of translation-targeting drugs. The single-compartment cell-free translation reaction is compatible with multi-well formats. Fluorophore formation of green fluorescent protein or monomeric NeonGreen occurs in an hour time frame without the need of adding reagents for secondary enzymatic detection saving handling time, and prohibiting false positives. As label-free readout, the dose response further allows for IC50 determination in the same setup. Together, we show that cell-free production of fluorescent proteins for the discovery of ribosome-targeting antibiotics is feasible and amenable to high-throughput applications.
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Affiliation(s)
- Bastian Höger
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany.
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2
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Liu W, Zhu Y, Stellacci F. Recycling of Polymerase Chain Reaction (PCR) Kits. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:5524-5536. [PMID: 37041891 PMCID: PMC10081572 DOI: 10.1021/acssuschemeng.2c07309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/07/2023] [Indexed: 06/19/2023]
Abstract
Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginning of the pandemic, there was a shortage of PCR kits. So far, the ecosystem of a PCR kit is linear use; that is, kits are produced, used once, and disposed of as biolab waste. Here, we show that to mitigate the risk of future shortages, it is possible to envision recyclable PCR kits based on a more sustainable use of nucleic acid resources. A PCR kit is mainly composed of primers, nucleotides, and enzymes. In the case of a positive test, the free nucleotides are polymerized onto the primers to form longer DNA strands. Our approach depolymerizes such strands, keeping the primers and regenerating the nucleotides, i.e., returning the nucleic acid materials to the original state. The polymerized long DNA strands are hydrolyzed into nucleotide monophosphates that are then phosphorylated into triphosphates using a method that is developed from a recent publication. We used oligonucleotides with a 3'-terminal phosphorothioate (PS) backbone modification as nonhydrolyzable PCR primers, which are able to undergo the recycling process unchanged. The nuclease resistance of oligonucleotides with a ribose sugar modification was also evaluated, which showed worse recycling efficiency than PS-modified oligonucleotides. We successfully recycled both PCR primers and nucleotide monomers (∼75% yield). We demonstrate that the method allows for the direct reuse of PCR kits. We also show that the recycled primers can be isolated and then added to endpoint or quantitative PCR. This recycling approach provides a new path for circularly reusing nucleic acid materials in PCR kits.
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Affiliation(s)
- Weina Liu
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
| | - Yong Zhu
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
| | - Francesco Stellacci
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
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3
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Singh M, Sykes EME, Li Y, Kumar A. MexXY RND pump of Pseudomonas aeruginosa PA7 effluxes bi-anionic β-lactams carbenicillin and sulbenicillin when it partners with the outer membrane factor OprA but not with OprM. MICROBIOLOGY-SGM 2020; 166:1095-1106. [PMID: 32909933 DOI: 10.1099/mic.0.000971] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antibiotic resistance in Pseudomonas aeruginosa is a serious concern in healthcare systems. Among the determinants of antibiotic resistance in P. aeruginosa, efflux pumps belonging to the resistance-nodulation-division (RND) family confer resistance to a broad range of antibacterial compounds. The MexXY efflux system is widely overexpressed in P. aeruginosa isolates from cystic fibrosis (CF) patients. MexXY can form functional complexes with two different outer membrane factors (OMFs), OprA and OprM. In this study, using state-of-the-art genetic tools, the substrate specificities of MexXY-OprA and MexXY-OprM complexes were determined. Our results show, for the first time, that the substrate profile of the MexXY system from P. aeruginosa PA7 can vary depending on which OM factor (OprM or OprA) it complexes with. While both MexXY-OprA and MexXY-OprM complexes are capable of effluxing aminoglycosides, the bi-anionic β-lactam molecules carbenicillin and sulbenicillin were found to only be the substrate of MexXY-OprA. Our study therefore shows that by partnering with different OMF proteins MexY can expand its substrate profile.
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Affiliation(s)
- Manu Singh
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Yanqi Li
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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4
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Loza E, Sarciaux M, Ikaunieks M, Katkevics M, Kukosha T, Trufilkina N, Ryabova V, Shubin K, Pantel L, Serri M, Huseby DL, Cao S, Yadav K, Hjort K, Hughes D, Gualtieri M, Suna E, Racine E. Structure-activity relationship studies on the inhibition of the bacterial translation of novel Odilorhabdins analogues. Bioorg Med Chem 2020; 28:115469. [PMID: 32279921 DOI: 10.1016/j.bmc.2020.115469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
Abstract
A structure-activity relationship (SAR) study of NOSO-95179, a nonapeptide from the Odilorhabdin class of antibacterials, was performed by systematic variations of amino acids in positions 2 and 5 of the peptide. A series of non-proteinogenic amino acids was synthesized in high enantiomeric purity from Williams' chiral diphenyloxazinone by highly diastereoselective alkylation or by aldol-type reaction. NOSO-95179 analogues for SAR studies were prepared using solid-phase peptide synthesis. Inhibition of bacterial translation by each of the synthesized Odilorhabdin analogues was measured using an in vitro test. For the most efficient analogues, antibacterial efficacy was measured against two wild-type Enterobacteriaceae (Escherichia coli and Klebsiella pneumoniae) and against an efflux defective E. coli strain (ΔtolC) to evaluate the impact of efflux on the antibacterial activity.
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Affiliation(s)
- Einars Loza
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Matthieu Sarciaux
- Nosopharm, 110 allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France
| | - Martins Ikaunieks
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Tatyana Kukosha
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Nadezhda Trufilkina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Victoria Ryabova
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Kirill Shubin
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Lucile Pantel
- Nosopharm, 110 allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France
| | - Marine Serri
- Nosopharm, 110 allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Kavita Yadav
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Maxime Gualtieri
- Nosopharm, 110 allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia.
| | - Emilie Racine
- Nosopharm, 110 allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France.
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5
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Sun C, Hunt DK, Chen CL, Deng Y, He M, Clark RB, Fyfe C, Grossman TH, Sutcliffe JA, Xiao XY. Design, Synthesis, and Biological Evaluation of Hexacyclic Tetracyclines as Potent, Broad Spectrum Antibacterial Agents. J Med Chem 2015; 58:4703-12. [DOI: 10.1021/acs.jmedchem.5b00262] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cuixiang Sun
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Diana K. Hunt
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Chi-Li Chen
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Yonghong Deng
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Minsheng He
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Roger B. Clark
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Corey Fyfe
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Trudy H. Grossman
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Joyce A. Sutcliffe
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
| | - Xiao-Yi Xiao
- Discovery Chemistry, ‡Microbiology, Tetraphase Pharmaceuticals, 480
Arsenal Street, Watertown, Massachusetts 02472, United States
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Heidary DK, Glazer EC. A Light-Activated Metal Complex Targets both DNA and RNA in a Fluorescent in Vitro Transcription and Translation Assay. Chembiochem 2014; 15:507-11. [DOI: 10.1002/cbic.201300681] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Indexed: 12/22/2022]
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