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Shelef O, Kopp T, Tannous R, Arutkin M, Jospe-Kaufman M, Reuveni S, Shabat D, Fridman M. Enzymatic Activity Profiling Using an Ultrasensitive Array of Chemiluminescent Probes for Bacterial Classification and Characterization. J Am Chem Soc 2024; 146:5263-5273. [PMID: 38362863 PMCID: PMC10910560 DOI: 10.1021/jacs.3c11790] [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: 10/23/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Identification and characterization of bacterial species in clinical and industrial settings necessitate the use of diverse, labor-intensive, and time-consuming protocols as well as the utilization of expensive and high-maintenance equipment. Furthermore, while cutting-edge identification technologies such as mass spectrometry and PCR are highly effective in identifying bacterial pathogens, they fall short in providing additional information for identifying bacteria not present in the databases upon which these methods rely. In response to these challenges, we present a robust and general approach to bacterial identification based on their unique enzymatic activity profiles. This method delivers results within 90 min, utilizing an array of highly sensitive and enzyme-selective chemiluminescent probes. Leveraging our recently developed technology of chemiluminescent luminophores, which emit light under physiological conditions, we have crafted an array of probes designed to rapidly detect various bacterial enzymatic activities. The array includes probes for detecting resistance to the important and large class of β-lactam antibiotics. The analysis of chemiluminescent fingerprints from a diverse range of prominent bacterial pathogens unveiled distinct enzymatic activity profiles for each strain. The reported universally applicable identification procedure offers a highly sensitive and expeditious means to delineate bacterial enzymatic activity fingerprints. This opens new avenues for characterizing and identifying pathogens in research, clinical, and industrial applications.
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Affiliation(s)
| | | | | | - Maxence Arutkin
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moriah Jospe-Kaufman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shlomi Reuveni
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Shabat
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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2
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Salaemae W, Thompson AP, Gaiser BI, Lee KJ, Huxley MT, Sumby CJ, Polyak SW, Abell AD, Bruning JB, Wegener KL. Fortuitous In Vitro Compound Degradation Produces a Tractable Hit against Mycobacterium tuberculosis Dethiobiotin Synthetase: A Cautionary Tale of What Goes In Does Not Always Come Out. ACS Chem Biol 2023; 18:1985-1992. [PMID: 37651626 DOI: 10.1021/acschembio.3c00215] [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: 09/02/2023]
Abstract
We previously reported potent ligands and inhibitors of Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumann et al., ACS Chem Biol. 2021, 16, 2339-2347); here, the unconventional origin of the fragment compound they were derived from is described for the first time. Compound 1 (9b-hydroxy-6b,7,8,9,9a,9b-hexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified by an in silico fragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (KD = 0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket when 1 was soaked into MtDTBS crystals, but the density was inconsistent with the structure of 1. Here, we show that the lactone of 1 hydrolyzes to a carboxylic acid (2) under basic conditions, including those of the crystallography soak, with a subsequent ring opening of the component cyclobutane ring forming a cyclopentylacetic acid (3). Crystals soaked directly with authentic 3 produced an electron density that matched that of crystals soaked with presumed 1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed 3 enabled the subsequent compound development of nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.
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Affiliation(s)
- Wanisa Salaemae
- Biochemistry, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Andrew P Thompson
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Birgit I Gaiser
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kwang Jun Lee
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Michael T Huxley
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christopher J Sumby
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Steven W Polyak
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kate L Wegener
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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Wang C, Tian Z, Zhang M, Deng Y, Tian X, Feng L, Cui J, James TD, Ma X. Visual identification of gut bacteria and determination of natural inhibitors using a fluorescent probe selective for PGP-1. Anal Chim Acta 2022; 1191:339280. [PMID: 35033245 DOI: 10.1016/j.aca.2021.339280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/24/2021] [Accepted: 11/10/2021] [Indexed: 11/01/2022]
Abstract
PGP-1 is a bacterial hydrolase that can hydrolyze the amide bond of the l-pyroglutamate (L-pGlu) residue at the amino terminus of proteins and peptides. Guided by the biological function of PGP-1, an off-on NIR fluorescent probe DDPA was developed for the visual sensing of PGP-1 by conjugating pyroglutamic acid (recognition group) and DDAN (fluorophore). Using intestinal bacteria cultivation, eight bacteria strains with active PGP-1 were identified and cultivated efficiently using DDPA. In addition, three natural inhibitors against PGP-1 were isolated from the medical herb Psoralea corylifolia, which could be used to interfere with bacterial metabolism in the gut. As such, the fluorescent probe DDPA provides an efficient method and potential tool for the investigation of intestinal microbiota.
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Affiliation(s)
- Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Integrative Medicine, College of Pharmacy, Dalian, 116044, China
| | - Zhenhao Tian
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ming Zhang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Integrative Medicine, College of Pharmacy, Dalian, 116044, China; State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Ying Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Integrative Medicine, College of Pharmacy, Dalian, 116044, China
| | - Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, China.
| | - Jingnan Cui
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Tony D James
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, China; Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
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Synthesis and Antimicrobial Activity of Phosphonopeptide Derivatives Incorporating Single and Dual Inhibitors. Molecules 2020; 25:molecules25071557. [PMID: 32231126 PMCID: PMC7180716 DOI: 10.3390/molecules25071557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
In diagnostic microbiology, culture media are widely used for detection of pathogenic bacteria. Such media employ various ingredients to optimize detection of specific pathogens such as chromogenic enzyme substrates and selective inhibitors to reduce the presence of commensal bacteria. Despite this, it is rarely possible to inhibit the growth of all commensal bacteria, and thus pathogens can be overgrown and remain undetected. One approach to attempt to remedy this is the use of “suicide substrates” that can target specific bacterial enzymes and selectively inhibit unwanted bacterial species. With the purpose of identifying novel selective inhibitors, six novel phosphonopeptide derivatives based on d/l-fosfalin and β-chloro-l-alanine were synthesized and tested on 19 different strains of clinically relevant bacteria. Several compounds show potential as useful selective agents that could be exploited in the recovery of several bacterial pathogens including Salmonella, Pseudomonas aeruginosa, and Listeria.
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