1
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Cascade-amplified fluorescence polarization assay for miRNA based on aggregation strategy of Y-shaped DNA. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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2
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Yoon SA, Park SY, Cha Y, Gopala L, Lee MH. Strategies of Detecting Bacteria Using Fluorescence-Based Dyes. Front Chem 2021; 9:743923. [PMID: 34458240 PMCID: PMC8397417 DOI: 10.3389/fchem.2021.743923] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022] Open
Abstract
Identification of bacterial strains is critical for the theranostics of bacterial infections and the development of antibiotics. Many organic fluorescent probes have been developed to overcome the limitations of conventional detection methods. These probes can detect bacteria with "off-on" fluorescence change, which enables the real-time imaging and quantitative analysis of bacteria in vitro and in vivo. In this review, we outline recent advances in the development of fluorescence-based dyes capable of detecting bacteria. Detection strategies are described, including specific interactions with bacterial cell wall components, bacterial and intracellular enzyme reactions, and peptidoglycan synthesis reactions. These include theranostic probes that allow simultaneous bacterial detection and photodynamic antimicrobial effects. Some examples of other miscellaneous detections in bacteria have also been described. In addition, this review demonstrates the validation of these fluorescent probes using a variety of biological models such as gram-negative and -positive bacteria, antibiotic-resistant bacteria, infected cancer cells, tumor-bearing, and infected mice. Prospects for future research are outlined by presenting the importance of effective in vitro and in vivo detection of bacteria and development of antimicrobial agents.
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Affiliation(s)
| | | | | | | | - Min Hee Lee
- Department of Chemistry, Sookmyung Women’s University, Seoul, South Korea
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3
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Zhao L, Liu Y, Zhang Z, Wei J, Xie S, Li X. Fibrous testing papers for fluorescence trace sensing and photodynamic destruction of antibiotic-resistant bacteria. J Mater Chem B 2021; 8:2709-2718. [PMID: 32149315 DOI: 10.1039/d0tb00002g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The increasing prevalence of antibiotic-resistant bacteria needs rapid identification and efficient destruction routes. This study proposes testing paper derived from electrospun fibrous mats and aggregation-induced emission (AIE) probes for trace sensing and simultaneous destruction of antibiotic-resistant E. coli. Aptamers are conjugated on fibers for selective capture of E. coli, and the capture capability can be regenerated via rinsing with salt solution. Hydroxyl tetraphenylethene (TPE) is linked with two cephalosporin molecules to construct TPE-Cep probes, and the fluorescence emission is turned on specifically in the presence of β-lactamase, which is a critical marker for screening resistant bacteria. Fibrous mats are lit up only in the presence of antibiotic-resistant bacteria, and the fluorescence intensity changes could be statistically fitted into an equation for quantitative analysis. Fibrous strips display apparent color changes from blue to green for a visual readout of bacterial levels, and the limit of detection (LOD) is much lower than those of previous paper substrates. In addition, the TPE-Cep probes could produce reactive oxygen species (ROS) under room light illumination to kill the captured bacteria. Thus, the integration of aptamer-grafted electrospun fibers and functional AIE probes provides potential for selective capture, trace imaging and photodynamic destruction of antibiotic-resistant bacteria.
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Affiliation(s)
- Long Zhao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China. and School of Bioscience and Technology, Chengdu Medical College, Chengdu 610031, P. R. China
| | - Yuan Liu
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China.
| | - Zhanlin Zhang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China.
| | - Jiaojun Wei
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China.
| | - Songzhi Xie
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China.
| | - Xiaohong Li
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P. R. China.
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4
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Miao L, Liu W, Qiao Q, Li X, Xu Z. Fluorescent antibiotics for real-time tracking of pathogenic bacteria. J Pharm Anal 2020; 10:444-451. [PMID: 33133728 PMCID: PMC7591806 DOI: 10.1016/j.jpha.2020.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023] Open
Abstract
The harm of pathogenic bacteria to humans has promoted extensive research on physiological processes of pathogens, such as the mechanism of bacterial infection, antibiotic mode of action, and bacterial antimicrobial resistance. Most of these processes can be better investigated by timely tracking of fluorophore-derived antibiotics in living cells. In this paper, we will review the recent development of fluorescent antibiotics featuring the conjugation with various fluorophores, and focus on their applications in fluorescent imaging and real-time detection for various physiological processes of bacteria in vivo. Profiles of Fluorophores-derived Antibiotics in Development. Discussing the influence on antibiotic activity after conjugating fluorophore. Fluorescent Tracking to better understand physiological processes of Pathogenic bacteria. Live-Cell imaging to investigate bacteria in their native environment.
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Affiliation(s)
- Lu Miao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Weiwei Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaolian Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Cochrane SA, Lohans CT. Breaking down the cell wall: Strategies for antibiotic discovery targeting bacterial transpeptidases. Eur J Med Chem 2020; 194:112262. [PMID: 32248005 DOI: 10.1016/j.ejmech.2020.112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
Abstract
The enzymes involved in bacterial cell wall synthesis are established antibiotic targets, and continue to be a central focus for antibiotic development. Bacterial penicillin-binding proteins (and, in some bacteria, l,d-transpeptidases) form essential peptide cross-links in the cell wall. Although the β-lactam class of antibiotics target these enzymes, bacterial resistance threatens their clinical use, and there is an urgent unmet need for new antibiotics. However, the search for new antibiotics targeting the bacterial cell wall is hindered by a number of obstacles associated with screening the enzymes involved in peptidoglycan synthesis. This review describes recent approaches for measuring the activity and inhibition of penicillin-binding proteins and l,d-transpeptidases, highlighting strategies that are poised to serve as valuable tools for high-throughput screening of transpeptidase inhibitors, supporting the development of new antibiotics.
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Affiliation(s)
- Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of β-Lactam Target-Mediated Resistance. J Mol Biol 2019; 431:3501-3519. [PMID: 31301409 DOI: 10.1016/j.jmb.2019.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 01/26/2023]
Abstract
Even with the emergence of antibiotic resistance, penicillin and the wider family of β-lactams have remained the single most important family of antibiotics. The periplasmic/extra-cytoplasmic targets of penicillin are a family of enzymes with a highly conserved catalytic activity involved in the final stage of bacterial cell wall (peptidoglycan) biosynthesis. Named after their ability to bind penicillin, rather than their catalytic activity, these key targets are called penicillin-binding proteins (PBPs). Resistance is predominantly mediated by reducing the target drug concentration via β-lactamases; however, naturally transformable bacteria have also acquired target-mediated resistance by inter-species recombination. Here we focus on structural based interpretations of amino acid alterations associated with the emergence of resistance within clinical isolates and include new PBP3 structures along with new, and improved, PBP-β-lactam co-structures.
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7
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Shapiro AB, Comita-Prevoir J, Sylvester M. 5-Carboxytetramethylrhodamine-Ampicillin Fluorescence Anisotropy-Based Assay of Escherichia coli Penicillin-Binding Protein 2 Transpeptidase Inhibition. ACS Infect Dis 2019; 5:863-872. [PMID: 30848883 DOI: 10.1021/acsinfecdis.8b00351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The high-molecular mass penicillin-binding proteins (PBPs) are the essential targets of the β-lactam classes of antibacterial drugs. In the Gram-negative pathogen Escherichia coli, these include PBP1a, PBP1b, PBP2, and PBP3. Techniques that enable facile measurement of the potency of inhibition of these targets are valuable for understanding structure-activity relationships in programs aimed at discovering new antibiotics to combat drug-resistant infections. Continuous fluorescence anisotropy-based assays for inhibition of soluble constructs of PBP1a, PBP2, and PBP3 from the serious Gram-negative bacterial pathogens Pseudomonas aeruginosa and Acinetobacter baumannii and PBP3 from E. coli using the fluorescent phenoxypenicillin analogue BOCILLIN FL have been described previously, but this technique was not useful for PBP2 from E. coli due to a lack of change in fluorescence anisotropy or intensity upon reaction. Here, we report that a fluorescent analogue of ampicillin, 5-carboxytetramethylrhodamine-ampicillin (5-TAMRA-ampicillin), was useful as the indicator in a continuous fluorescence anisotropy-based kinetic assay for inhibition of a soluble construct of PBP2 from E. coli. The assay enables measurement of the bimolecular rate constant for inhibition kinact /Ki. This measurement was made for representative drugs from four classes of β-lactams and for the diazabicyclooctenone ETX2514. 5-TAMRA-ampicillin was also useful in a fluorescence anisotropy-based assay for P. aeruginosa PBP2 and in fluorescence intensity-based assays with PBP1a and PBP3 from P. aeruginosa and A. baumannii and PBP3 from E. coli.
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Affiliation(s)
- Adam B. Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Mark Sylvester
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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8
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Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
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9
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Fluorescence polarization assays for chemical contaminants in food and environmental analyses. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.03.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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10
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Levy N, Bruneau JM, Le Rouzic E, Bonnard D, Le Strat F, Caravano A, Chevreuil F, Barbion J, Chasset S, Ledoussal B, Moreau F, Ruff M. Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design. J Med Chem 2019; 62:4742-4754. [PMID: 30995398 DOI: 10.1021/acs.jmedchem.9b00338] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Penicillin-binding proteins (PBPs) are the targets of the β-lactams, the most successful class of antibiotics ever developed against bacterial infections. Unfortunately, the worldwide and rapid spread of large spectrum β-lactam resistance genes such as carbapenemases is detrimental to the use of antibiotics in this class. New potent PBP inhibitors are needed, especially compounds that resist β-lactamase hydrolysis. Here we describe the structure of the E. coli PBP2 in its Apo form and upon its reaction with 2 diazabicyclo derivatives, avibactam and CPD4, a new potent PBP2 inhibitor. Examination of these structures shows that unlike avibactam, CPD4 can perform a hydrophobic stacking on Trp370 in the active site of E. coli PBP2. This result, together with sequence analysis, homology modeling, and SAR, allows us to propose CPD4 as potential starting scaffold to develop molecules active against a broad range of bacterial species at the top of the WHO priority list.
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Affiliation(s)
- Nicolas Levy
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France.,IGBMC , 1 Rue Laurent Fries , 67404 Illkirch , France
| | | | - Erwann Le Rouzic
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | - Damien Bonnard
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | | | - Audrey Caravano
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | | | - Julien Barbion
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | - Sophie Chasset
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | - Benoît Ledoussal
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | - François Moreau
- Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France
| | - Marc Ruff
- IGBMC , 1 Rue Laurent Fries , 67404 Illkirch , France
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