1
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Canabal R, González-Bello C. Chemical sensors for the early diagnosis of bacterial resistance to β-lactam antibiotics. Bioorg Chem 2024; 150:107528. [PMID: 38852309 DOI: 10.1016/j.bioorg.2024.107528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
β-Lactamases are bacterial enzymes that inactivate β-lactam antibiotics and, as such, are the most prevalent cause of antibiotic resistance in Gram-negative bacteria. The ever-increasing production and worldwide dissemination of bacterial strains producing carbapenemases is currently a global health concern. These enzymes catalyze the hydrolysis of carbapenems - the β-lactam antibiotics with the broadest spectrum of activity that are often considered as drugs of last resort. The incidence of carbapenem-resistant pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and carbapenemase or extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, which are frequent in clinical settings, is worrisome since, in some cases, no therapies are available. These include all metallo-β-lactamases (VIM, IMP, NDM, SMP, and L1), and serine-carbapenemases of classes A (KPC, SME, IMI, and GES), and of classes D (OXA-23, OXA-24/40, OXA-48 and OXA-58). Consequently, the early diagnosis of bacterial strains harboring carbapenemases is a pivotal task in clinical microbiology in order to track antibiotic bacterial resistance and to improve the worldwide management of infectious diseases. Recent research efforts on the development of chromogenic and fluorescent chemical sensors for the specific and sensitive detection and quantification of β-lactamase production in multidrug-resistant pathogens are summarized herein. Studies to circumvent the main limitations of the phenotypic and molecular methods are discussed. Recently reported chromogenic and fluorogenic cephalosporin- and carbapenem-based β-lactamase substrates will be reviewed as alternative options to the currently available nitrocefin and related compounds, a chromogenic cephalosporin-based reagent widely used in clinical microbiology laboratories. The scope of these new chemical sensors, along with the synthetic approaches to synthesize them, is also summarized.
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Affiliation(s)
- Rafael Canabal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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2
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Stavropoulou K, Papanastasiou IP. Overview of Small Molecules as Fluorescent Probes of Mycobacterium tuberculosis. ACS OMEGA 2024; 9:31220-31227. [PMID: 39072060 PMCID: PMC11270572 DOI: 10.1021/acsomega.4c01992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
Tuberculosis (TB) remains one of the leading infectious causes of death worldwide. Detecting and precisely quantifying viable Mycobacterium tuberculosis (M. tuberculosis) is crucial for comprehending mycobacterial pathogenicity; the progression and outcomes of tuberculosis; and the action, efficacy, and resistance of drugs. Fluorescent probes have emerged as indispensable tools for studying the intricate structure and dynamic interactions of M. tuberculosis with its host environment. This minireview underscores the significance of small molecules as fluorescent probes in advancing our understanding of mycobacterial biology and highlights their potential for guiding the development of novel therapeutic interventions against tuberculosis.
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Affiliation(s)
- Konstantina Stavropoulou
- Division of Pharmaceutical
Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupoli-Zografou, 157 71 Athens, Greece
| | - Ioannis P. Papanastasiou
- Division of Pharmaceutical
Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupoli-Zografou, 157 71 Athens, Greece
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3
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Ma Z, Liu R, Wang J, Yu T, Zou Y, Chen F, Cui C, Yang H, Xie H. Rapid Detection of Bacterial Resistance to β-Lactam Antibiotics with a Relay-Response Chemiluminescence Assay. ACS Infect Dis 2024; 10:1970-1979. [PMID: 38819944 DOI: 10.1021/acsinfecdis.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Bacterial resistance caused by β-lactamases has been a major threat to public health around the world, seriously weakening the efficacy of β-lactam antibiotics, the most widely used therapeutic agents against infectious diseases. To detect the bacterial resistance to β-lactam antibiotics, particularly specific type of β-lactam antibiotics, in a rapid manner, we report herein a relay-response chemiluminescence assay. This assay mainly consists of two reagents: a β-lactam-caged thiophenol and a thiophenol-sensitive chemiluminescence reporter, both of which are synthetically feasible. The selective hydrolysis of β-lactam by β-lactamase leads to the releasing of free thiophenol, which then triggers the emission of a chemiluminescence signal in a relay manner. Three thiophenol-caged β-lactams, structural analogues of cephalothin, cefotaxime, and meropenem, respectively, have been synthesized. And the application of this assay with these analogues of β-lactam antibiotics allows fast detection of β-lactamase-expressing resistant bacteria and, more impressively, provides detailed information on the resistant scope of bacteria.
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Affiliation(s)
- Zheng Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Runqiu Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tao Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yingqiu Zou
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Fangfang Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Cui Cui
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huixin Yang
- Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian 362000, China
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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4
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Hong X, Geng P, Tian N, Li X, Gao M, Nie L, Sun Z, Liu G. From Bench to Clinic: A Nitroreductase Rv3368c-Responsive Cyanine-Based Probe for the Specific Detection of Live Mycobacterium tuberculosis. Anal Chem 2024; 96:1576-1586. [PMID: 38190499 DOI: 10.1021/acs.analchem.3c04293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Tuberculosis (TB), characterized by high mortality and low diagnosis, is caused by a single pathogen, Mycobacterium tuberculosis (Mtb). Imaging tools that can be used to track Mtb without pre-labeling and to diagnose live Mtb in clinical samples can shorten the gap between bench and clinic, fuel the development of novel anti-TB drugs, strengthen TB prevention, and improve patient treatment. In this study, we report an unprecedented novel nitroreductase-responsive cyanine-based fluorescent probe (Cy3-NO2-tre) that rapidly and specifically labels Mtb and detects it in clinical samples. Cy3-NO2-tre generated fluorescence after activation by a specific nitroreductase, Rv3368c, which is conserved in the Mycobacteriaceae. Cy3-NO2-tre effectively imaged mycobacteria within infected host cells, tracked the infection process, and visualized Mycobacterium smegmatis being endocytosed by macrophages. Cy3-NO2-tre also detected Mtb in the sputum of patients with TB and exhibited excellent photostability. Furthermore, the Cy3-NO2-tre/auramine O percentage change within 7 ± 2 days post drug treatment in the sputum of inpatients was closely correlated with the reexamination results of the chest computed tomography, strongly demonstrating the clinical application of Cy3-NO2-tre as a prognostic indicator in monitoring the therapeutic efficacy of anti-TB drugs in the early patient care stage.
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Affiliation(s)
- Xiaoqiao Hong
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, China
| | - Pengfei Geng
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, China
| | - Na Tian
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xueyuan Li
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, China
| | - Mengqiu Gao
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lihui Nie
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zhaogang Sun
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, China
| | - Gang Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, China
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5
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Dutta A, Mukherjee S, Haldar J, Maitra U. Augmenting Antimicrobial Resistance Surveillance: Rapid Detection of β-Lactamase-Expressing Drug-Resistant Bacteria through Sensitized Luminescence on a Paper-Supported Hydrogel. ACS Sens 2024; 9:351-360. [PMID: 38156608 DOI: 10.1021/acssensors.3c02065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The emergence of antimicrobial resistance (AMR) in pathogenic bacteria, expedited by the overuse and misuse of antibiotics, necessitates the development of a rapid and pan-territorially accessible diagnostic protocol for resistant bacterial infections, which would not only enable judicious prescription of drugs, leading to infection control but also augment AMR surveillance. In this study, we introduce for the first time a "turn-on" terbium (Tb3+) photoluminescence assay supported on a paper-based platform for rapid point-of-care (POC) detection of β-lactamase (BL)-producing bacteria. We strategically conjugated biphenyl-4-carboxylic acid (BCA), a potent Tb3+ sensitizer, with cephalosporin to engineer a BL substrate CCS, where the energy transfer to terbium is arrested. However, BL, a major resistance element produced by bacteria resistant to β-lactam antibiotics, triggers a spontaneous release of BCA, empowering terbium sensitization within a supramolecular scaffold supported on paper. The remarkable optical response facilitates quick assessment with a binary answer, and the time-gated signal acquisition ensues improved sensitivity with a detection limit as low as 0.1 mU/mL. Furthermore, to ensure accessibility, particularly in resource-limited areas, we have developed an in loco imaging device as an affordable alternative to high-end instruments. The integration of the assay with the device readily identified the BL-associated drug-resistant strains in the mimic urinary tract infection samples within 2 h, demonstrating its excellent potential for in-field translation. We believe that this rapid paper-based POC assay, coupled with the in loco device, can be deployed anywhere, especially in developing regions, and will enable extensive surveillance on antibiotic-resistant infections.
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Affiliation(s)
- Arnab Dutta
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sudip Mukherjee
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Jayanta Haldar
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Uday Maitra
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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6
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Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
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Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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7
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Dai T, Xiao Z, Shan D, Moreno A, Li H, Prakash M, Banaei N, Rao J. Culture-Independent Multiplexed Detection of Drug-Resistant Bacteria Using Surface-Enhanced Raman Scattering. ACS Sens 2023; 8:3264-3271. [PMID: 37506677 DOI: 10.1021/acssensors.3c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The rapid and accurate detection of bacteria resistance to β-lactam antibiotics is critical to inform optimal treatment and prevent overprescription of potent antibiotics. Here, we present a fast, culture-independent method for the detection of extended-spectrum β-lactamases (ESBLs) using surface-enhanced Raman scattering (SERS). The method uses Raman probes that release sulfur-based Raman active molecules in the presence of β-lactamases. The released thiol molecules can be captured by gold nanoparticles, leading to amplified Raman signals. A broad-spectrum cephalosporin probe R1G and an ESBL-specific probe R3G are designed to enable duplex detection of bacteria expressing broad-spectrum β-lactamases or ESBLs with a detection limit of 103 cfu/mL in 1 h incubation. Combined with a portable Raman microscope, our culturing-free SERS assay has reduced screening time to 1.5 h without compromising sensitivity and specificity.
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Affiliation(s)
- Tingting Dai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Zhen Xiao
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Dingying Shan
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Hongquan Li
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, California 94304, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Jianghong Rao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
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8
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Nath P, Mahtaba KR, Ray A. Fluorescence-Based Portable Assays for Detection of Biological and Chemical Analytes. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23115053. [PMID: 37299780 DOI: 10.3390/s23115053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Fluorescence-based detection techniques are part of an ever-expanding field and are widely used in biomedical and environmental research as a biosensing tool. These techniques have high sensitivity, selectivity, and a short response time, making them a valuable tool for developing bio-chemical assays. The endpoint of these assays is defined by changes in fluorescence signal, in terms of its intensity, lifetime, and/or shift in spectrum, which is monitored using readout devices such as microscopes, fluorometers, and cytometers. However, these devices are often bulky, expensive, and require supervision to operate, which makes them inaccessible in resource-limited settings. To address these issues, significant effort has been directed towards integrating fluorescence-based assays into miniature platforms based on papers, hydrogels, and microfluidic devices, and to couple these assays with portable readout devices like smartphones and wearable optical sensors, thereby enabling point-of-care detection of bio-chemical analytes. This review highlights some of the recently developed portable fluorescence-based assays by discussing the design of fluorescent sensor molecules, their sensing strategy, and the fabrication of point-of-care devices.
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Affiliation(s)
- Peuli Nath
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
| | - Kazi Ridita Mahtaba
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
| | - Aniruddha Ray
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
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9
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Velema WA. Exploring antibiotic resistance with chemical tools. Chem Commun (Camb) 2023; 59:6148-6158. [PMID: 37039397 PMCID: PMC10194278 DOI: 10.1039/d3cc00759f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Antibiotic resistance is an enormous problem that is accountable for over a million deaths annually, with numbers expected to significantly increase over the coming decades. Although some of the underlying causes leading up to antibiotic resistance are well understood, many of the molecular processes involved remain elusive. To better appreciate at a molecular level how resistance emerges, customized chemical biology tools can offer a solution. This Feature Article attempts to provide an overview of the wide variety of tools that have been developed over the last decade, by highlighting some of the more illustrative examples. These include the use of fluorescent, photoaffinity and activatable antibiotics and bacterial components to start to unravel the molecular mechanisms involved in resistance. The antibiotic crisis is an eminent global threat and requires the continuous development of creative chemical tools to dissect and ultimately counteract resistance.
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Affiliation(s)
- Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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10
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Finin P, Khan RMN, Oh S, Boshoff HIM, Barry CE. Chemical approaches to unraveling the biology of mycobacteria. Cell Chem Biol 2023; 30:420-435. [PMID: 37207631 PMCID: PMC10201459 DOI: 10.1016/j.chembiol.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Mycobacterium tuberculosis (Mtb), perhaps more than any other organism, is intrinsically appealing to chemical biologists. Not only does the cell envelope feature one of the most complex heteropolymers found in nature1 but many of the interactions between Mtb and its primary host (we humans) rely on lipid and not protein mediators.2,3 Many of the complex lipids, glycolipids, and carbohydrates biosynthesized by the bacterium still have unknown functions, and the complexity of the pathological processes by which tuberculosis (TB) disease progress offers many opportunities for these molecules to influence the human response. Because of the importance of TB in global public health, chemical biologists have applied a wide-ranging array of techniques to better understand the disease and improve interventions.
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Affiliation(s)
- Peter Finin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - R M Naseer Khan
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA.
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11
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Dai T, Xie J, Buonomo JA, Moreno A, Banaei N, Bertozzi CR, Rao J. Bioluminogenic Probe for Rapid, Ultrasensitive Detection of β-Lactam-Resistant Bacteria. Anal Chem 2023; 95:7329-7335. [PMID: 37083185 PMCID: PMC10175212 DOI: 10.1021/acs.analchem.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Increasingly difficult-to-treat infections by antibiotic-resistant bacteria have become a major public health challenge. Rapid detection of common resistance mechanisms before empiric antibiotic usage is essential for optimizing therapeutic outcomes and containing further spread of resistance to antibiotics among other bacteria. Herein, we present a bioluminogenic probe, D-Bluco, for rapid detection of β-lactamase activity in viable pathogenic bacteria. D-Bluco is a pro-luciferin caged by a β-lactamase-responsive cephalosporin structure and further conjugated with a dabcyl quencher. The caging and quenching significantly decreased the initial background emission and increased the signal-to-background ratio by more than 1200-fold. D-Bluco was shown to detect a broad range of β-lactamases at the femtomolar level. An ultrasensitive RAPID bioluminescence assay using D-Bluco can detect 102 to 103 colony forming unit per milliliter (cfu/mL) of β-lactamase-producing Enterobacterales in urine samples within 30 min. The high sensitivity and rapid detection make the assay attractive for the use of point-of-care diagnostics for lactam-resistant pathogens.
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Affiliation(s)
- Tingting Dai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jinghang Xie
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Joseph A Buonomo
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, California 94304, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jianghong Rao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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12
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Liyanage S, Raviranga NGH, Ryan JG, Shell SS, Ramström O, Kalscheuer R, Yan M. Azide-Masked Fluorescence Turn-On Probe for Imaging Mycobacteria. JACS AU 2023; 3:1017-1028. [PMID: 37124305 PMCID: PMC10131213 DOI: 10.1021/jacsau.2c00449] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
A fluorescence turn-on probe, an azide-masked and trehalose-derivatized carbazole (Tre-Cz), was developed to image mycobacteria. The fluorescence turn-on is achieved by photoactivation of the azide, which generates a fluorescent product through an efficient intramolecular C-H insertion reaction. The probe is highly specific for mycobacteria and could image mycobacteria in the presence of other Gram-positive and Gram-negative bacteria. Both the photoactivation and detection can be accomplished using a handheld UV lamp, giving a limit of detection of 103 CFU/mL, which can be visualized by the naked eye. The probe was also able to image mycobacteria spiked in sputum samples, although the detection sensitivity was lower. Studies using heat-killed, stationary-phase, and isoniazid-treated mycobacteria showed that metabolically active bacteria are required for the uptake of Tre-Cz. The uptake decreased in the presence of trehalose in a concentration-dependent manner, indicating that Tre-Cz hijacked the trehalose uptake pathway. Mechanistic studies demonstrated that the trehalose transporter LpqY-SugABC was the primary pathway for the uptake of Tre-Cz. The uptake decreased in the LpqY-SugABC deletion mutants ΔlpqY, ΔsugA, ΔsugB, and ΔsugC and fully recovered in the complemented strain of ΔsugC. For the mycolyl transferase antigen 85 complex (Ag85), however, only a slight reduction of uptake was observed in the Ag85 deletion mutant ΔAg85C, and no incorporation of Tre-Cz into the outer membrane was observed. The unique intracellular incorporation mechanism of Tre-Cz through the LpqY-SugABC transporter, which differs from other trehalose-based fluorescence probes, unlocks potential opportunities to bring molecular cargoes to mycobacteria for both fundamental studies and theranostic applications.
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Affiliation(s)
- Sajani
H. Liyanage
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - N. G. Hasitha Raviranga
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Julia G. Ryan
- Department
of Biology and Biotechnology, Worcester
Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Scarlet S. Shell
- Department
of Biology and Biotechnology, Worcester
Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Olof Ramström
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
- Department
of Chemistry and Biomedical Sciences, Linnaeus
University, SE-39182 Kalmar, Sweden
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Mingdi Yan
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
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13
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Schmidt M, Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia J, Mariani V, Pandey S, Poudyal I, Sierra R, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman H, Stojković E, Batyuk A, Boutet S, Phillips G, Pollack L. Heterogeneity in the M. tuberculosis β-Lactamase Inhibition by Sulbactam. RESEARCH SQUARE 2023:rs.3.rs-2334665. [PMID: 36712138 PMCID: PMC9882615 DOI: 10.21203/rs.3.rs-2334665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC) 1-5 at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals 6 . Here, we report in atomic detail and with millisecond time-resolution how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating 7-9 , cooperativity, induced fit 10,11 and conformational selection 11-13 all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme non-covalently before reacting to a trans- enamine. This was made possible in part by the application of the singular value decomposition 14 to the MISC data using a newly developed program that remains functional even if unit cell parameters change during the reaction.
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14
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Banahene N, Gepford DM, Biegas KJ, Swanson DH, Hsu YP, Murphy BA, Taylor ZE, Lepori I, Siegrist MS, Obregón-Henao A, Van Nieuwenhze MS, Swarts BM. A Far-Red Molecular Rotor Fluorogenic Trehalose Probe for Live Mycobacteria Detection and Drug-Susceptibility Testing. Angew Chem Int Ed Engl 2023; 62:e202213563. [PMID: 36346622 PMCID: PMC9812908 DOI: 10.1002/anie.202213563] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 11/11/2022]
Abstract
Increasing the speed, specificity, sensitivity, and accessibility of mycobacteria detection tools are important challenges for tuberculosis (TB) research and diagnosis. In this regard, previously reported fluorogenic trehalose analogues have shown potential, but their green-emitting dyes may limit sensitivity and applications in complex settings. Here, we describe a trehalose-based fluorogenic probe featuring a molecular rotor turn-on fluorophore with bright far-red emission (RMR-Tre). RMR-Tre, which exploits the unique biosynthetic enzymes and environment of the mycobacterial outer membrane to achieve fluorescence activation, enables fast, no-wash, low-background fluorescence detection of live mycobacteria. Aided by the red-shifted molecular rotor fluorophore, RMR-Tre exhibited up to a 100-fold enhancement in M. tuberculosis labeling compared to existing fluorogenic trehalose probes. We show that RMR-Tre reports on M. tuberculosis drug resistance in a facile assay, demonstrating its potential as a TB diagnostic tool.
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Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
- Biochemistry, Cellular, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, USA
| | - Dana M Gepford
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
| | - Kyle J Biegas
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
- Biochemistry, Cellular, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, USA
| | - Daniel H Swanson
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
| | - Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Brennan A Murphy
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Zachary E Taylor
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Irene Lepori
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | | | - Michael S Van Nieuwenhze
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
- Biochemistry, Cellular, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, USA
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15
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Ma Y, Liang Y, Guo M, Min D, Zheng L, Tang Y, Sun X. Strategic design of lysine-targeted irreversible covalent NDM-1 inhibitors. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Cole MS, Hegde PV, Aldrich CC. β-Lactamase-Mediated Fragmentation: Historical Perspectives and Recent Advances in Diagnostics, Imaging, and Antibacterial Design. ACS Infect Dis 2022; 8:1992-2018. [PMID: 36048623 DOI: 10.1021/acsinfecdis.2c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The discovery of β-lactam (BL) antibiotics in the early 20th century represented a remarkable advancement in human medicine, allowing for the widespread treatment of infectious diseases that had plagued humanity throughout history. Yet, this triumph was followed closely by the emergence of β-lactamase (BLase), a bacterial weapon to destroy BLs. BLase production is a primary mechanism of resistance to BL antibiotics, and the spread of new homologues with expanded hydrolytic activity represents a pressing threat to global health. Nonetheless, researchers have developed strategies that take advantage of this defense mechanism, exploiting BLase activity in the creation of probes, diagnostic tools, and even novel antibiotics selective for resistant organisms. Early discoveries in the 1960s and 1970s demonstrating that certain BLs expel a leaving group upon BLase cleavage have spawned an entire field dedicated to employing this selective release mechanism, termed BLase-mediated fragmentation. Chemical probes have been developed for imaging and studying BLase-expressing organisms in the laboratory and diagnosing BL-resistant infections in the clinic. Perhaps most promising, new antibiotics have been developed that use BLase-mediated fragmentation to selectively release cytotoxic chemical "warheads" at the site of infection, reducing off-target effects and allowing for the repurposing of putative antibiotics against resistant organisms. This Review will provide some historical background to the emergence of this field and highlight some exciting recent reports that demonstrate the promise of this unique release mechanism.
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Affiliation(s)
- Malcolm S Cole
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Pooja V Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
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17
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Cole MS, Howe MD, Buonomo JA, Sharma S, Lamont EA, Brody SI, Mishra NK, Minato Y, Thiede JM, Baughn AD, Aldrich CC. Cephem-Pyrazinoic Acid Conjugates: Circumventing Resistance in Mycobacterium tuberculosis. Chemistry 2022; 28:e202200995. [PMID: 35697660 PMCID: PMC9474573 DOI: 10.1002/chem.202200995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 01/14/2023]
Abstract
Tuberculosis (TB) is a leading source of infectious disease mortality globally. Antibiotic-resistant strains comprise an estimated 10 % of new TB cases and present an urgent need for novel therapeutics. β-lactam antibiotics have traditionally been ineffective against M. tuberculosis (Mtb), the causative agent of TB, due to the organism's inherent expression of β-lactamases that destroy the electrophilic β-lactam warhead. We have developed novel β-lactam conjugates, which exploit this inherent β-lactamase activity to achieve selective release of pyrazinoic acid (POA), the active form of a first-line TB drug. These conjugates are selectively active against M. tuberculosis and related mycobacteria, and activity is retained or even potentiated in multiple resistant strains and models. Preliminary mechanistic investigations suggest that both the POA "warhead" as well as the β-lactam "promoiety" contribute to the observed activity, demonstrating a codrug strategy with important implications for future TB therapy.
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Affiliation(s)
- Malcolm S. Cole
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
| | - Michael D. Howe
- Department of Microbiology, ImmunologyUniversity of Minnesota Medical School689 23 Ave SEMinneapolisMinnesota 55455USA
| | - Joseph A. Buonomo
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
| | - Sachin Sharma
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
| | - Elise A. Lamont
- Department of Microbiology, ImmunologyUniversity of Minnesota Medical School689 23 Ave SEMinneapolisMinnesota 55455USA
| | - Scott I. Brody
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
| | - Neeraj K. Mishra
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
- Department of BiotechnologyGandhi Institute of Technology and Management (GITAM) School of ScienceDeemed to be UniversityGandhi nagarRushikonda, Visakhapatnam-530045Andhra PradeshIndia
| | - Yusuke Minato
- Department of Microbiology, ImmunologyUniversity of Minnesota Medical School689 23 Ave SEMinneapolisMinnesota 55455USA
- Department of MicrobiologyFujita Health University School of Medicine1-98 Dengakugakubo, Kutsukake-choToyoakeAichi 470-1192Japan
| | - Joshua M. Thiede
- Department of Microbiology, ImmunologyUniversity of Minnesota Medical School689 23 Ave SEMinneapolisMinnesota 55455USA
| | - Anthony D. Baughn
- Department of Microbiology, ImmunologyUniversity of Minnesota Medical School689 23 Ave SEMinneapolisMinnesota 55455USA
| | - Courtney C. Aldrich
- Department of Medicinal ChemistryUniversity of Minnesota308 Harvard St SEMinneapolisMinnesota 55455USA
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18
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Selective inhibition of resistant bacterial pathogens using a β-lactamase-activatable antimicrobial peptide with significantly reduced cytotoxicity. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Alebouyeh S, Weinrick B, Achkar JM, García MJ, Prados-Rosales R. Feasibility of novel approaches to detect viable Mycobacterium tuberculosis within the spectrum of the tuberculosis disease. Front Med (Lausanne) 2022; 9:965359. [PMID: 36072954 PMCID: PMC9441758 DOI: 10.3389/fmed.2022.965359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is a global disease caused by Mycobacterium tuberculosis (Mtb) and is manifested as a continuum spectrum of infectious states. Both, the most common and clinically asymptomatic latent tuberculosis infection (LTBI), and the symptomatic disease, active tuberculosis (TB), are at opposite ends of the spectrum. Such binary classification is insufficient to describe the existing clinical heterogeneity, which includes incipient and subclinical TB. The absence of clinically TB-related symptoms and the extremely low bacterial burden are features shared by LTBI, incipient and subclinical TB states. In addition, diagnosis relies on cytokine release after antigenic T cell stimulation, yet several studies have shown that a high proportion of individuals with immunoreactivity never developed disease, suggesting that they were no longer infected. LTBI is estimated to affect to approximately one fourth of the human population and, according to WHO data, reactivation of LTBI is the main responsible of TB cases in developed countries. Assuming the drawbacks associated to the current diagnostic tests at this part of the disease spectrum, properly assessing individuals at real risk of developing TB is a major need. Further, it would help to efficiently design preventive treatment. This quest would be achievable if information about bacterial viability during human silent Mtb infection could be determined. Here, we have evaluated the feasibility of new approaches to detect viable bacilli across the full spectrum of TB disease. We focused on methods that specifically can measure host-independent parameters relying on the viability of Mtb either by its direct or indirect detection.
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Affiliation(s)
- Sogol Alebouyeh
- Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
| | | | - Jacqueline M. Achkar
- Departments of Medicine, Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Maria J. García
- Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
- *Correspondence: Maria J. García,
| | - Rafael Prados-Rosales
- Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, Madrid, Spain
- Rafael Prados-Rosales,
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20
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Yan F, He S, Han X, Wang J, Tian X, Wang C, James TD, Cui J, Ma X, Feng L. High-throughput fluorescent screening of β-lactamase inhibitors to improve antibiotic treatment strategies for tuberculosis. Biosens Bioelectron 2022; 216:114606. [DOI: 10.1016/j.bios.2022.114606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
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21
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Stabilization of Tuberculosis Reporter Enzyme Fluorescence (REFtb) Diagnostic Reagents for Use at the Point of Care. Diagnostics (Basel) 2022; 12:diagnostics12071745. [PMID: 35885648 PMCID: PMC9324015 DOI: 10.3390/diagnostics12071745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is one of the most frequent causes of death in humans worldwide. One of the primary reasons tuberculosis remains a public health threat is that diagnosis can take weeks to months, is often not very sensitive and cannot be accomplished in many remote environments. A rapid, sensitive and inexpensive point-of-care (POC) diagnostic would have a major impact on tuberculosis eradication efforts. The tuberculosis diagnostic system REFtb is based on specific detection of the constitutively expressed β-lactamase (BlaC) in Mycobacterium tuberculosis using a custom fluorogenic substrate designated as CDG-3. REFtb has potential as a diagnostic for tuberculosis that could be very inexpensive (<USD 2.00/test), used at the POC and could provide definitive diagnosis within 10 min. However, the reagents for REFtb are currently in liquid form, making them more susceptible to degradation and difficult to transport. We evaluated the improvement in the stability of REFtb reagents by lyophilization under a variety of conditions through their effects on the performance of REFtb. We found that lyophilization of REFtb components produces an easily reconstituted powder that displays similar performance to the liquid system and that lactose represents one of the most promising excipients for use in a final POC REFtb diagnostic system. These studies provide the foundation for the production of a stable POC REFtb system that could be easily distributed worldwide with minimal or no requirement for refrigeration.
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22
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Discovery of environment-sensitive fluorescent probes for detecting and inhibiting metallo-β-lactamase. Bioorg Chem 2022; 128:106048. [DOI: 10.1016/j.bioorg.2022.106048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 11/23/2022]
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23
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Alkekhia D, LaRose C, Shukla A. β-Lactamase-Responsive Hydrogel Drug Delivery Platform for Bacteria-Triggered Cargo Release. ACS APPLIED MATERIALS & INTERFACES 2022; 14:27538-27550. [PMID: 35675049 DOI: 10.1021/acsami.2c02614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a growing public health threat that complicates the treatment of infections. β-Lactamase enzymes, which hydrolyze the β-lactam ring present in many common antibiotics, are a major cause of this resistance and are produced by a broad range of bacterial pathogens. Here, we developed hydrogels that degrade specifically in the presence of β-lactamases and β-lactamase-producing bacteria as a platform for bacteria-triggered drug delivery. A maleimide-functionalized β-lactamase-cleavable cephalosporin was used as a crosslinker in the fabrication of hydrogels through end-crosslinked polymerization with multiarm thiol-terminated poly(ethylene glycol) macromers via Michael-type addition. We demonstrated that only hydrogels containing the responsive crosslinker were degraded by β-lactamases and β-lactamase-producing bacteria in vitro and in an ex vivo porcine skin infection model. Fluorescent polystyrene nanoparticles, encapsulated in the hydrogels as model cargo, were released at rates that closely tracked hydrogel wet mass loss, confirming β-lactamase-triggered controlled cargo release. Nonresponsive hydrogels, lacking the β-lactam crosslinker, remained stable in the presence of β-lactamases and β-lactamase-producing bacteria and exhibited no change in mass or nanoparticle release. Furthermore, the responsive hydrogels remained stable in non-β-lactamase enzymes, including collagenases and lipases. These hydrogels have the potential to be used as a bacteria-triggered drug delivery system to control unnecessary exposure to encapsulated antimicrobials, which can provide effective infection treatment without exacerbating resistance.
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Affiliation(s)
- Dahlia Alkekhia
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Cassi LaRose
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Anita Shukla
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
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24
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Dong B, He Z, Li Y, Xu X, Wang C, Zeng J. Improved Conventional and New Approaches in the Diagnosis of Tuberculosis. Front Microbiol 2022; 13:924410. [PMID: 35711765 PMCID: PMC9195135 DOI: 10.3389/fmicb.2022.924410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). Timely diagnosis and effective treatment are essential in the control of TB. Conventional smear microscopy still has low sensitivity and is unable to reveal the drug resistance of this bacterium. The traditional culture-based diagnosis is time-consuming, since usually the results are available after 3–4 weeks. Molecular biology methods fail to differentiate live from dead M. tuberculosis, while diagnostic immunology methods fail to distinguish active from latent TB. In view of these limitations of the existing detection techniques, in addition to the continuous emergence of multidrug-resistant and extensively drug-resistant TB, in recent years there has been an increase in the demand for simple, rapid, accurate and economical point-of-care approaches. This review describes the development, evaluation, and implementation of conventional diagnostic methods for TB and the rapid new approaches for the detection of M. tuberculosis.
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Affiliation(s)
- Baoyu Dong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyue Xu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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25
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Xu Y, Chen H, Xu S, Liu J, Chen Y, Gui L, Li H, Li R, Yuan Z, Li B. β-Lactamase-Responsive Probe for Efficient Photodynamic Therapy of Drug-Resistant Bacterial Infection. ACS Sens 2022; 7:1361-1371. [PMID: 35442628 DOI: 10.1021/acssensors.1c02485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several photosensitizers have recently been proposed as novel approaches against β-lactamase-producing drug-resistant bacteria. However, these reported photosensitizers are rarely used for accurate recognition of drug-resistant bacteria. To tackle this challenge, the structurally modified photosensitizer CySG-2 based on a lipophilic cationic heptamethine indocyanine near-infrared (NIR) dye (IR-780) and an important synthesis intermediate of cephalosporin antibiotic (GCLE) not only achieved the accurate recognition of TEM-1 methicillin-resistant Staphylococcus aureus (MRSA) successfully but also achieved antimicrobial photodynamic therapy (aPDT) in animal models infected by drug-resistant bacteria. Accurate enzyme recognition and efficient photodynamic therapy capabilities allow CySG-2 to achieve one stone with two birds. In addition, CySG-2 could also promote the eradication of internalized MRSA by facilitating the autophagy process, which is synergistic with its capacity of inducing reactive oxygen species generation under NIR laser irradiation for aPDT. Collectively, it is an effective multifunctional photosensitizer with the potential ability to guide the optimal use of different antibiotics and apply them in clinical treatment.
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Affiliation(s)
- Yue Xu
- Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Haiyan Chen
- Cancer Systems Imaging Department, The University of Texas MD Anderson Cancer Center, 1881 East Road, 3SCR4.3600, Houston, Texas 77054, United States
| | - Shufen Xu
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Ji Liu
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Yang Chen
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Lijuan Gui
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Hua Li
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Ruixi Li
- Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
| | - Zhenwei Yuan
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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26
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Stereochemically altered cephalosporins as potent inhibitors of New Delhi metallo-β-lactamases. Eur J Med Chem 2022; 232:114174. [DOI: 10.1016/j.ejmech.2022.114174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/12/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
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27
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Wang Z, Xing B. Small-molecule fluorescent probes: big future for specific bacterial labeling and infection detection. Chem Commun (Camb) 2021; 58:155-170. [PMID: 34882159 DOI: 10.1039/d1cc05531c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial infections remain a global healthcare problem that is particularly attributed to the spread of antibiotic resistance and the evolving pathogenicity. Accurate and swift approaches for infection diagnosis are urgently needed to facilitate antibiotic stewardship and effective medical treatment. Direct optical imaging for specific bacterial labeling and infection detection offers an attractive prospect of precisely monitoring the infectious disease status and therapeutic response in real time. This feature article focuses on the recent advances of small-molecule probes developed for fluorescent imaging of bacteria and infection, which covers the probe design, responsive mechanisms and representative applications. In addition, the perspective and challenges to advance small-molecule fluorescent probes in the field of rapid drug-resistant bacterial detection and clinical diagnosis of bacterial infections are discussed. We envision that the continuous advancement and clinical translations of such a technique will have a strong impact on future anti-infective medicine.
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Affiliation(s)
- Zhimin Wang
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Bengang Xing
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 637371, Singapore. .,School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
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28
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Hu L, Liu R, Ma Z, Yu T, Li Z, Zou Y, Yuan C, Chen F, Xie H. Specific detection of IMP-1 β-lactamase activity using a trans cephalosporin-based fluorogenic probe. Chem Commun (Camb) 2021; 57:13586-13589. [PMID: 34847209 DOI: 10.1039/d1cc05955f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A fluorogenic probe for the specific detection of IMP-1 β-lactamase activity has been developed. This imaging reagent features a unique trans-acetylamino cephalosporin as an enzymatic recognition moiety, exhibiting excellent selectivity to IMP-1 β-lactamase over other β-lactamases, including serine- and metallo-β-lactamases. The selective activation of the probe by IMP-1 β-lactamase leads to over 30-fold enhancement in the fluorescence intensity, which allows enzyme activity to be reported with high sensitivity.
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Affiliation(s)
- Liqiang Hu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Runqiu Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Zheng Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Tao Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Ziyao Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Yingqiu Zou
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Chang Yuan
- Shanghai Soong Ching Ling School, Shanghai 201703, China
| | - Fangfang Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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29
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Chan LW. Advances in activity-based diagnostics for infectious disease and microbiome health. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19:100296. [PMID: 34179594 PMCID: PMC8224833 DOI: 10.1016/j.cobme.2021.100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In the human body, pathogens and the endogenous microbiome produce enzymes that aid in replication and survival. The activity from these enzymes as well as energy-dependent transport processes can be used as functional biomarkers for pathogen identification, antimicrobial treatment monitoring, and surveillance of microbiome health. To produce visual and/or quantifiable readouts from this activity, concepts from chemical biology and nanomedicine have been utilized to develop signal-producing probes for patient samples or for direct administration in vivo. In the context of infection, activity-based diagnostics offer several potential advantages over current diagnostics including the ability to differentiate between active infection and sterile inflammation, which is made possible by targeting microbial enzymes with orthogonal activity to that of the host. In this review, we discuss new developments in the making of activity-based infection diagnostics and the beginnings of microbiome activity-based diagnostics.
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Affiliation(s)
- Leslie W. Chan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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30
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Xie J, Mu R, Fang M, Cheng Y, Senchyna F, Moreno A, Banaei N, Rao J. A dual-caged resorufin probe for rapid screening of infections resistant to lactam antibiotics. Chem Sci 2021; 12:9153-9161. [PMID: 34276945 PMCID: PMC8261730 DOI: 10.1039/d1sc01471d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/19/2021] [Indexed: 12/04/2022] Open
Abstract
The alarming increase of antimicrobial resistance urges rapid diagnosis and pathogen specific infection management. This work reports a rapid screening assay for pathogenic bacteria resistant to lactam antibiotics. We designed a fluorogenic N-cephalosporin caged 3,7-diesterphenoxazine probe CDA that requires sequential activations to become fluorescent resorufin. A series of studies with recombinant β-lactamases and clinically prevalent pathogens including Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae and Serratia marcescens demonstrated that CDA possessed superior sensitivity in reporting the activity of β-lactamases including cephalosporinases and carbapenemases. After a simple filtration, lactam-resistant bacteria in urine samples could be detected at 103 colony-forming units per milliliter within 2 hours.
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Affiliation(s)
- Jinghang Xie
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine Stanford CA 94305 USA
| | - Ran Mu
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine Stanford CA 94305 USA
| | - Mingxi Fang
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine Stanford CA 94305 USA
| | - Yunfeng Cheng
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine Stanford CA 94305 USA
| | - Fiona Senchyna
- Department of Pathology, Stanford University School of Medicine Stanford CA 94305 USA
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine Stanford CA 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine Stanford CA 94305 USA
- Clinical Microbiology Laboratory, Stanford University Medical Center Palo Alto CA 94304 USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine Stanford CA 94305 USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine Stanford CA 94305 USA
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31
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Babin B, Fernandez-Cuervo G, Sheng J, Green O, Ordonez AA, Turner ML, Keller LJ, Jain SK, Shabat D, Bogyo M. Chemiluminescent Protease Probe for Rapid, Sensitive, and Inexpensive Detection of Live Mycobacterium tuberculosis. ACS CENTRAL SCIENCE 2021; 7:803-814. [PMID: 34079897 PMCID: PMC8161474 DOI: 10.1021/acscentsci.0c01345] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 05/05/2023]
Abstract
Tuberculosis (TB) is a top-ten cause of death worldwide. Successful treatment is often limited by insufficient diagnostic capabilities, especially at the point of care in low-resource settings. The ideal diagnostic must be fast, be cheap, and require minimal clinical resources while providing high sensitivity, selectivity, and the ability to differentiate live from dead bacteria. We describe here the development of a fast, luminescent, and affordable sensor of Hip1 (FLASH) for detecting and monitoring drug susceptibility of Mycobacterium tuberculosis (Mtb). FLASH is a selective chemiluminescent substrate for the Mtb protease Hip1 that, when processed, produces visible light that can be measured with a high signal-to-noise ratio using inexpensive sensors. FLASH is sensitive to fmol of recombinant Hip1 enzyme in vitro and can detect as few as thousands of Mtb cells in culture or in human sputum samples within minutes. The probe is highly selective for Mtb compared to other nontuberculous mycobacteria and can distinguish live from dead cells. Importantly, FLASH can be used to measure antibiotic killing of Mtb in culture with greatly accelerated timelines compared to traditional protocols. Overall, FLASH has the potential to enhance both TB diagnostics and drug resistance monitoring in resource-limited settings.
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Affiliation(s)
- Brett
M. Babin
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Gabriela Fernandez-Cuervo
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Jessica Sheng
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
| | - Ori Green
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alvaro A. Ordonez
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Mitchell L. Turner
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Laura J. Keller
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Sanjay K. Jain
- Center
for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Center
for Tuberculosis Research, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21287, United States
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21205, United States
| | - Doron Shabat
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, Stanford, California 94305, United States
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, Stanford, California 94305, United States
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32
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Huang Y, Chen W, Chung J, Yin J, Yoon J. Recent progress in fluorescent probes for bacteria. Chem Soc Rev 2021; 50:7725-7744. [PMID: 34013918 DOI: 10.1039/d0cs01340d] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.
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Affiliation(s)
- Yurou Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Weijie Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Jeewon Chung
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
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33
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Lentz CS. What you see is what you get: activity-based probes in single-cell analysis of enzymatic activities. Biol Chem 2021; 401:233-248. [PMID: 31939273 DOI: 10.1515/hsz-2019-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/25/2019] [Indexed: 11/15/2022]
Abstract
Molecular imaging methods can provide spatio-temporal information about the distribution of biomolecules or biological processes, such as certain enzymatic activities, in single cells. Within a cell, it is possible to define the subcellular location of a target, its trafficking through the cell, colocalization with other biomolecules of interest and involvement in certain cell biological processes. On the other hand, single-cell imaging promises to distinguish cells that are phenotypically different from each other. The corresponding cellular diversity comprises the presence of functionally distinct cells in a population ('phenotypic heterogeneity'), as well as dynamic cellular responses to external stimuli ('phenotypic plasticity'), which is highly relevant, e.g. during cell differentiation, activation (of immune cells), or cell death. This review focuses on applications of a certain class of chemical probes, the so-called activity-based probes (ABPs), for visualization of enzymatic activities in the single-cell context. It discusses the structure of ABPs and other chemical probes, exemplary applications of ABPs in single-cell studies in human, mouse and bacterial systems and considerations to be made with regard to data interpretation.
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Affiliation(s)
- Christian S Lentz
- Department of Chemical Biology (CBIO), Helmholtz-Centre for Infection Research, Inhoffenstr. 7, D-38102 Braunschweig, Germany
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34
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Huang J, Zhong Y, Li W, Wang W, Li C, Wang A, Yan H, Wan Y, Li J. Fluorescent and Opt-Electric Recording Bacterial Identification Device for Ultrasensitive and Specific Detection of Microbials. ACS Sens 2021; 6:443-449. [PMID: 33369433 DOI: 10.1021/acssensors.0c02007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since microbial detection is an important aspect for the prevention and control of foodborne diseases, an ideal detection system with high sensitivity, strong specificity, and timeliness is needed. Here, we proposed a fluorescent and opt-electric recording bacterial identification device (FORBID) for fully automatic real-time photoelectric sensing analysis of microbials by integrating the metabolic characteristics of microbial and selective substrate catalysis. It simplifies the testing process (one-step) and decreases the need of professional technicians. Besides, the system exhibits ultrasensitive (1 CFU/mL) and specific detection (99%) in both microbials, Escherichia coli and Pseudomonas aeruginosa. More importantly, the timeliness of this system is even better than that of the traditional culture methods. It is believed that this system can be extended to the detection of other microorganisms and provide a potential alternative for the detection of pathogens.
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Affiliation(s)
- Jiaomei Huang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yongjie Zhong
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wenxing Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wenxia Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Chaoyang Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Hong Yan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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35
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Kumar G, Narayan R, Kapoor S. Chemical Tools for Illumination of Tuberculosis Biology, Virulence Mechanisms, and Diagnosis. J Med Chem 2020; 63:15308-15332. [PMID: 33307693 DOI: 10.1021/acs.jmedchem.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases and begs the scientific community to up the ante for research and exploration of completely novel therapeutic avenues. Chemical biology-inspired design of tunable chemical tools has aided in clinical diagnosis, facilitated discovery of therapeutics, and begun to enable investigation of virulence mechanisms at the host-pathogen interface of Mycobacterium tuberculosis. This Perspective highlights chemical tools specific to mycobacterial proteins and the cell lipid envelope that have furnished rapid and selective diagnostic strategies and provided unprecedented insights into the function of the mycobacterial proteome and lipidome. We discuss chemical tools that have enabled elucidating otherwise intractable biological processes by leveraging the unique lipid and metabolite repertoire of mycobacterial species. Some of these probes represent exciting starting points with the potential to illuminate poorly understood aspects of mycobacterial pathogenesis, particularly the host membrane-pathogen interactions.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda 403 401, Goa, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
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36
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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37
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Yu F, Chen J, Wang Z, Yang H, Li H, Jia W, Xue S, Xie H, Xu D. Screening aptamers for serine β-lactamase-expressing bacteria with Precision-SELEX. Talanta 2020; 224:121750. [PMID: 33379005 DOI: 10.1016/j.talanta.2020.121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/24/2022]
Abstract
Klebsiella pneumoniae carbapenemase 2 (KPC-2) is a serine β-lactamase that can hydrolyze almost all β-lactam antibiotics. The drug resistant problem of bacteria expressing carbapenemases is currently a global problem, therefore, rapid and specific detection of pathogenic bacteria is urgent. In order to obtain an aptamer that can specifically recognize bacteria expressing KPC-2, we have established a method called Precision-SELEX. Precision-SELEX combined protein SELEX and bacterium SELEX. In this method, KPC-2 was used as a target protein, and Escherichia coli expressing KPC-2 (KPC-2 E. coli) was used as a target bacterium. After precision-SELEX, the same aptamer named XK-10 that can recognize KPC-2 and KPC-2 E. coli was obtained while the screening process could be shortened to 4 rounds. Dissociation equilibrium constants were calculated as 0.81 nM by SPR. In addition, XK-10 could specifically bind to KPC-2 E. coli, which was confirmed through flow cytometry and molecular Docking Simulations. The high-content imaging method could detect KPC-2 E. coli. In all, the Precision-SELEX provides an accurate and efficient method to screening aptamers for bacteria.
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Affiliation(s)
- Fang Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China
| | - Jing Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China
| | - Zecheng Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China
| | - Huixin Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China
| | - Wenchao Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China
| | - Shuyuan Xue
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210046, China.
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38
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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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Ding Y, Li Z, Xu C, Qin W, Wu Q, Wang X, Cheng X, Li L, Huang W. Fluorogenic Probes/Inhibitors of β-Lactamase and their Applications in Drug-Resistant Bacteria. Angew Chem Int Ed Engl 2020; 60:24-40. [PMID: 32592283 DOI: 10.1002/anie.202006635] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 01/08/2023]
Abstract
β-Lactam antibiotics are generally perceived as one of the greatest inventions of the 20th century, and these small molecular compounds have saved millions of lives. However, upon clinical application of antibiotics, the β-lactamase secreted by pathogenic bacteria can lead to the gradual development of drug resistance. β-Lactamase is a hydrolase that can efficiently hydrolyze and destroy β-lactam antibiotics. It develops and spreads rapidly in pathogens, and the drug-resistant bacteria pose a severe threat to human health and development. As a result, detecting and inhibiting the activities of β-lactamase are of great value for the rational use of antibiotics and the treatment of infectious diseases. At present, many specific detection methods and inhibitors of β-lactamase have been developed and applied in clinical practice. In this Minireview, we describe the resistance mechanism of bacteria producing β-lactamase and further summarize the fluorogenic probes, inhibitors of β-lactamase, and their applications in the treatment of infectious diseases. It may be valuable to design fluorogenic probes with improved selectivity, sensitivity, and effectiveness to further identify the inhibitors for β-lactamases and eventually overcome bacterial resistance.
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Affiliation(s)
- Yang Ding
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Zheng Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Chenchen Xu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Wenjing Qin
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Xuchun Wang
- College of Chemistry and Material Engineering, University of Science and Technology of Anhui, Bengbu, 233000, P. R. China
| | - Xiamin Cheng
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, P. R. China.,Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University (NPU), Xi'an, 710072, P. R. China
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Ding Y, Li Z, Xu C, Qin W, Wu Q, Wang X, Cheng X, Li L, Huang W. Fluorogenic Probes/Inhibitors of β‐Lactamase and their Applications in Drug‐Resistant Bacteria. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yang Ding
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Zheng Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Chenchen Xu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Wenjing Qin
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Xuchun Wang
- College of Chemistry and Material Engineering University of Science and Technology of Anhui Bengbu 233000 P. R. China
| | - Xiamin Cheng
- Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) Nanjing 211816 P. R. China
- Frontiers Science Center for Flexible Electronics (FSCFE) Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME) Northwestern Polytechnical University (NPU) Xi'an 710072 P. R. China
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41
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Fluorescent probes for investigating peptidoglycan biosynthesis in mycobacteria. Curr Opin Chem Biol 2020; 57:50-57. [DOI: 10.1016/j.cbpa.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 02/02/2023]
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Yu P, Yang JN, Yan JW, Meng ZZ, Hong WD, Roberts AP, Ward SA, Zhang L, Li S. A novel fluorescent probe for the detection of AmpC beta-lactamase and the application in screening beta-lactamase inhibitors. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 234:118257. [PMID: 32208355 DOI: 10.1016/j.saa.2020.118257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/01/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
The rapid detection of β-lactamases (Blas) and effective screening of Bla inhibitors are critically important and urgent for solving antibiotic resistance and improving precision medicine. Here a novel fluorescent probe CDC-559 was designed and synthesized, which can be used for the selective and direct detection of AmpC Blas. More importantly, it can realize screening the Bla inhibitors with sulbactam sodium and tazobactam as model compounds, and the half-maximal inhibitory concentration are 0.279 μM and 0.053 μM, respectively. CDC-559 can be applied not only to examine the resistance of bacterial strains, but also to categorize its mode of action specifically, which is consistent with the essential result of the Blas. The research suggests that CDC-559 probe has tremendous potential in the rapid detection of AmpC Blas as well as the strains with AmpC-encoded gene, which is instructive in promoting better antibiotic stewardship practices and developments.
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Affiliation(s)
- Pan Yu
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jia-Ning Yang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jin-Wu Yan
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Zhi-Zhong Meng
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - W David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Adam P Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Stephen A Ward
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Lei Zhang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Engineering and Technological Centre for Biopharmaceuticals, South China University of Technology, Guangzhou 510006, PR China.
| | - Shan Li
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
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Wang J, Xu W, Xue S, Yu T, Xie H. A minor structure modification serendipitously leads to a highly carbapenemase-specific fluorogenic probe. Org Biomol Chem 2020; 18:4029-4033. [PMID: 32432265 DOI: 10.1039/d0ob00114g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reported herein is a fluorogenic probe for the detection of carbapenemase activity. This reagent features carbapenem as an enzyme recognition motif and a carbon-carbon double bond between carbapenem and the fluorophore, exhibiting high specificity to all carbapenemases, including metallo carbapenemases and serine carbapenemases, over other β-lactamases.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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Jackson AC, Zaengle-Barone JM, Puccio EA, Franz KJ. A Cephalosporin Prochelator Inhibits New Delhi Metallo-β-lactamase 1 without Removing Zinc. ACS Infect Dis 2020; 6:1264-1272. [PMID: 32298084 DOI: 10.1021/acsinfecdis.0c00083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antibacterial drug resistance is a rapidly growing clinical threat, partially due to expression of β-lactamase enzymes, which confer resistance to bacteria by hydrolyzing and inactivating β-lactam antibiotics. The increasing prevalence of metallo-β-lactamases poses a unique challenge, as currently available β-lactamase inhibitors target the active site of serine β-lactamases but are ineffective against the zinc-containing active sites of metallo-β-lactamases. There is an urgent need for metallo-β-lactamase inhibitors and antibiotics that circumvent resistance mediated by metallo-β-lactamases in order to extend the utility of existing β-lactam antibiotics for treating infection. Here we investigated the antibacterial chelator-releasing prodrug PcephPT (2-((((6R,7R)-2-carboxy-8-oxo-7-(2-phenylacetamido)-5-thia-1-azabicyclo[4.2.0]oct-2-en-3-yl)methyl)thio) pyridine 1-oxide) as an inhibitor of New Delhi metallo-β-lactamase 1 (NDM-1). PcephPT is an experimental compound that we have previously shown inhibits growth of β-lactamase-expressing E. coli using a mechanism that is dependent on both copper availability and β-lactamase expression. Here, we found that PcephPT, in addition to being a copper-dependent antibacterial compound, inhibits hydrolysis activity of purified NDM-1with an IC50 of 7.6 μM without removing zinc from the active site and restores activity of the carbapenem antibiotic meropenem against NDM-1-producing E. coli. This work demonstrates that targeting a metal-binding pharmacophore to β-lactamase-producing bacteria is a promising strategy for inhibition of both bacterial growth and metallo-β-lactamases.
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Affiliation(s)
- Abigail C. Jackson
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | | | - Elena A. Puccio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Katherine J. Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
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Soleimany AP, Bhatia SN. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Trends Mol Med 2020; 26:450-468. [PMID: 32359477 DOI: 10.1016/j.molmed.2020.01.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
Diagnostics to accurately detect disease and monitor therapeutic response are essential for effective clinical management. Bioengineering, chemical biology, molecular biology, and computer science tools are converging to guide the design of diagnostics that leverage enzymatic activity to measure or produce biomarkers of disease. We review recent advances in the development of these 'activity-based diagnostics' (ABDx) and their application in infectious and noncommunicable diseases. We highlight efforts towards both molecular probes that respond to disease-specific catalytic activity to produce a diagnostic readout, as well as diagnostics that use enzymes as an engineered component of their sense-and-respond cascade. These technologies exemplify how integrating techniques from multiple disciplines with preclinical validation has enabled ABDx that may realize the goals of precision medicine.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Wyss Institute at Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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Maity S, Wang X, Das S, He M, Riley LW, Murthy N. A cephalosporin-chemiluminescent conjugate increases beta-lactamase detection sensitivity by four orders of magnitude. Chem Commun (Camb) 2020; 56:3516-3519. [PMID: 32101196 PMCID: PMC7666973 DOI: 10.1039/c9cc09498a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The expression of beta-lactamases in bacteria is a central cause of drug resistance. In this report, we present a beta-lactamase chemiluminescent probe, termed CCP, which can for the first time detect beta-lactamase activity via chemiluminescence and can detect beta lactamase with a sensitivity that is 4-orders of magnitude higher than the commercially available fluorescent lactamase substrate fluorocillin.
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Affiliation(s)
- Santanu Maity
- Department of Bioengineering, University of California, Berkeley, USA.
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Nabeta P, Seshadri P, Havumaki J, Mbhele S, Hendricks L, Perkins MD, Nicol MP, Denkinger CM. First clinical assessment of a prototype assay to detect the enzymatic activity of β-lactamase as a marker for pulmonary tuberculosis. Diagn Microbiol Infect Dis 2020; 97:115026. [PMID: 32173144 PMCID: PMC7262578 DOI: 10.1016/j.diagmicrobio.2020.115026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/15/2020] [Accepted: 02/15/2020] [Indexed: 10/29/2022]
Abstract
The objective was to evaluate the sensitivity and specificity of a novel prototype test, TB REaD™, a reporter enzyme fluorescence-based assay, for pulmonary tuberculosis and to determine the optimal threshold for test positivity. This blinded, prospective study enrolled 250 patients, of which 23.2% were Mycobacterium tuberculosis complex (MTB) culture-positive. At the manufacturer-set threshold, sensitivity of the assay was 93.1% (95% confidence interval [CI] 83.3-98.1) and specificity was 8.9% (95% CI 5.2-13.8). The highest accuracy was seen at a higher threshold: sensitivity 58.6% (95% CI 44.9-71.4), specificity 59.4% (95% CI 52.1%-66.4%), with sensitivity by smear status being 40.0% (95% CI 21.1-61.3) for smear-negative and 72.7% (95% CI 54.5-86.7) for smear-positive. This study demonstrated limited accuracy of the TB REaD™ prototype for detection of pulmonary TB. Further improvements are necessary, potentially exploring probes that are more specific to MTB.
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Affiliation(s)
- Pamela Nabeta
- FIND, Chemin des Mines 9, 1202, Geneva, Switzerland.
| | - Pratibha Seshadri
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, 330 Brookline Ave, 02215, Boston, USA.
| | | | - Silindile Mbhele
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, Cape Town, 7925, South Africa and National Health Laboratory Service, South Africa.
| | - Layla Hendricks
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, Cape Town, 7925, South Africa and National Health Laboratory Service, South Africa.
| | | | - Mark P Nicol
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, Cape Town, 7925, South Africa and National Health Laboratory Service, South Africa; School of Biomedical Sciences, University of Western Australia, Hackett Drive, Crawley, Perth, Australia 6009.
| | - Claudia M Denkinger
- FIND, Chemin des Mines 9, 1202, Geneva, Switzerland; Division of Tropical Medicine, Center of Infectious Diseases, University Hospital of Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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Takashima I, Inoue Y, Matsumoto N, Takagi A, Okuda K. A fluorogenic probe using a catalytic reaction for the detection of trace intracellular zinc. Chem Commun (Camb) 2020; 56:13327-13330. [DOI: 10.1039/d0cc05315e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A reaction-based fluorescent probe with cephem scaffold has been applied for signal amplification system to detect trace intracellular zinc.
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Affiliation(s)
- Ippei Takashima
- Laboratory of Bioorganic & Natural Products Chemistry
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
| | - Yohei Inoue
- Laboratory of Bioorganic & Natural Products Chemistry
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
| | | | - Akira Takagi
- Laboratory of Bioorganic & Natural Products Chemistry
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
| | - Kensuke Okuda
- Laboratory of Bioorganic & Natural Products Chemistry
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
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Performance of a Novel Fluorogenic Assay for Detection of Carbapenemase-Producing Enterobacteriaceae from Bacterial Colonies and Directly from Positive Blood Cultures. J Clin Microbiol 2019; 58:JCM.01026-19. [PMID: 31666362 DOI: 10.1128/jcm.01026-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Rapid and accurate detection of carbapenemase-producing Enterobacteriaceae (CPE) is critical for appropriate treatment and infection control. We compared a rapid fluorogenic assay using a carbapenem-based fluorogenic probe with other phenotypic assays: modified carbapenem inactivation method (mCIM), Carba NP test (CNP), and carbapenemase inhibition test (CIT). A total of 217 characterized isolates of Enterobacteriaceae were included as follows: 63 CPE; 48 non-carbapenemase-producing carbapenem-resistant Enterobacteriaceae (non-CP-CRE); 53 extended-spectrum β-lactamase producers; and 53 third-generation-cephalosporin-susceptible isolates. The fluorogenic assay using bacterial colonies (Fluore-C) was conducted by lysing the isolates followed by centrifugation and mixing the supernatant with fluorogenic probe. In addition, for the fluorogenic assay using spiked blood culture bottles (Fluore-Direct), pellets were obtained via the saponin preparation method, which can directly identify the pathogens using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The fluorescence signal was measured over 50 min using a fluorometer. The fluorescent signal of CPE was significantly higher than that of non-CPE in both Fluore-C (median relative fluorescence units [RFU] [range], 5,814 [240 to 32,009] versus 804 [36 to 2,480], respectively; P < 0.0001) and Fluore-Direct (median RFU [range], 10,355 [1,689 to 31,463] versus 1,068 [428 to 2,155], respectively; P < 0.0001) tests. Overall, positive and negative percent agreements of Fluore-C, mCIM, CNP, CIT, and Fluore-Direct were 100% and 98.7%, 98.3% and 97.5%, 88.1% and 100%, 96.4% and 98.7%, and 98.3% and 98.1%, respectively. The relatively lower positive percent agreement (PPA) of CNP was mainly observed in OXA-type CPE. The fluorogenic assay showed excellent performance with bacterial colonies and also directly from positive blood cultures. We included many non-CP-CRE isolates for strict evaluation. The fluorogenic assay will be a useful tool for clinical microbiology laboratories.
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Wang S, Xiao C, Guo L, Ling L, Li M, Li H, Guo X. Rapidly quantitative analysis of γ-glutamyltranspeptidase activity in the lysate and blood via a rational design of the molecular probe by matrix-assisted laser desorption ionization mass spectrometry. Talanta 2019; 205:120141. [DOI: 10.1016/j.talanta.2019.120141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
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