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Kucharzyk KH, Meisel JE, Kara-Murdoch F, Murdoch RW, Higgins SA, Vainberg S, Bartling CM, Mullins L, Hatzinger PB, Löffler FE. Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9. J Proteome Res 2020; 19:1812-1823. [PMID: 32135063 DOI: 10.1021/acs.jproteome.0c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.
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Affiliation(s)
| | - Jayda E Meisel
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Fadime Kara-Murdoch
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Steven A Higgins
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Simon Vainberg
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Craig M Bartling
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Larry Mullins
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Paul B Hatzinger
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Department of Civil and Environmental Engineering, University of Tennessee, 851 Neyland Drive, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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Boudreau MA, Ding D, Meisel JE, Janardhanan J, Spink E, Peng Z, Qian Y, Yamaguchi T, Testero SA, O’Daniel PI, Leemans E, Lastochkin E, Song W, Schroeder VA, Wolter WR, Suckow MA, Mobashery S, Chang M. Structure-Activity Relationship for the Oxadiazole Class of Antibacterials. ACS Med Chem Lett 2020; 11:322-326. [PMID: 32184964 DOI: 10.1021/acsmedchemlett.9b00379] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/03/2019] [Indexed: 11/29/2022] Open
Abstract
A structure-activity relationship (SAR) for the oxadiazole class of antibacterials was evaluated by syntheses of 72 analogs and determination of the minimal-inhibitory concentrations (MICs) against the ESKAPE panel of bacteria. Selected compounds were further evaluated for in vitro toxicity, plasma protein binding, pharmacokinetics (PK), and a mouse model of methicillin-resistant Staphylococcus aureus (MRSA) infection. Oxadiazole 72c shows potent in vitro antibacterial activity, exhibits low clearance, a high volume of distribution, and 41% oral bioavailability, and shows efficacy in mouse models of MRSA infection.
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Affiliation(s)
- Marc A. Boudreau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Derong Ding
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jayda E. Meisel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeshina Janardhanan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Edward Spink
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zhihong Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yuanyuan Qian
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Takao Yamaguchi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sebastian A. Testero
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Peter I. O’Daniel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Erika Leemans
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Wei Song
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Valerie A. Schroeder
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - William R. Wolter
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mark A. Suckow
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Hohn M, Chang M, Meisel JE, Frost E, Schwegmann K, Hermann S, Schäfers M, Riemann B, Haufe G, Breyholz H, Wagner S. Synthesis and Preliminary In Vitroand In VivoEvaluation of Thiirane‐Based Slow‐Binding MMP Inhibitors as Potential Radiotracers for PET Imaging. ChemistrySelect 2018. [DOI: 10.1002/slct.201803093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Michael Hohn
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1 Building A1 D-48149 Münster Germany
- Organic Chemistry InstituteUniversity of Münster Corrensstr. 40 D-48149 Münster Germany
| | - Mayland Chang
- Department of Chemistry and Biochemistry, 354 McCourtney HallUniversity of Notre Dame Notre Dame IN 46556–5710 USA
| | - Jayda E. Meisel
- Chemical, BiologicalRadiological, Nuclearand Explosive DefenseBattelle Memorial Institute 505 King Avenue Columbus Ohio 43201 USA
| | - Emma Frost
- Department of Chemistry and Biochemistry, 354 McCourtney HallUniversity of Notre Dame Notre Dame IN 46556–5710 USA
| | - Katrin Schwegmann
- European Institute for Molecular Imaging (EIMI)University of Münster Waldeyerstraße 15 D-48149 Münster Germany
| | - Sven Hermann
- European Institute for Molecular Imaging (EIMI)University of Münster Waldeyerstraße 15 D-48149 Münster Germany
| | - Michael Schäfers
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1 Building A1 D-48149 Münster Germany
- European Institute for Molecular Imaging (EIMI)University of Münster Waldeyerstraße 15 D-48149 Münster Germany
- Cells in Motion (CiM) Cluster of ExcellenceUniversity of Münster D-48149 Münster Germany
| | - Burkhard Riemann
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1 Building A1 D-48149 Münster Germany
| | - Günter Haufe
- Organic Chemistry InstituteUniversity of Münster Corrensstr. 40 D-48149 Münster Germany
- Cells in Motion (CiM) Cluster of ExcellenceUniversity of Münster D-48149 Münster Germany
| | - Hans‐Jörg Breyholz
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1 Building A1 D-48149 Münster Germany
| | - Stefan Wagner
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1 Building A1 D-48149 Münster Germany
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Meisel JE, Chang M. Selective small-molecule inhibitors as chemical tools to define the roles of matrix metalloproteinases in disease. Biochim Biophys Acta Mol Cell Res 2017; 1864:2001-2014. [PMID: 28435009 DOI: 10.1016/j.bbamcr.2017.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/15/2017] [Accepted: 04/17/2017] [Indexed: 12/22/2022]
Abstract
The focus of this article is to highlight novel inhibitors and current examples where the use of selective small-molecule inhibitors has been critical in defining the roles of matrix metalloproteinases (MMPs) in disease. Selective small-molecule inhibitors are surgical chemical tools that can inhibit the targeted enzyme; they are the method of choice to ascertain the roles of MMPs and complement studies with knockout animals. This strategy can identify targets for therapeutic development as exemplified by the use of selective small-molecule MMP inhibitors in diabetic wound healing, spinal cord injury, stroke, traumatic brain injury, cancer metastasis, and viral infection. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Lockwood SY, Meisel JE, Monsma FJ, Spence DM. A Diffusion-Based and Dynamic 3D-Printed Device That Enables Parallel in Vitro Pharmacokinetic Profiling of Molecules. Anal Chem 2016; 88:1864-70. [PMID: 26727249 DOI: 10.1021/acs.analchem.5b04270] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The process of bringing a drug to market involves many steps, including the preclinical stage, where various properties of the drug candidate molecule are determined. These properties, which include drug absorption, distribution, metabolism, and excretion, are often displayed in a pharmacokinetic (PK) profile. While PK profiles are determined in animal models, in vitro systems that model in vivo processes are available, although each possesses shortcomings. Here, we present a 3D-printed, diffusion-based, and dynamic in vitro PK device. The device contains six flow channels, each with integrated porous membrane-based insert wells. The pores of these membranes enable drugs to freely diffuse back and forth between the flow channels and the inserts, thus enabling both loading and clearance portions of a standard PK curve to be generated. The device is designed to work with 96-well plate technology and consumes single-digit milliliter volumes to generate multiple PK profiles, simultaneously. Generation of PK profiles by use of the device was initially performed with fluorescein as a test molecule. Effects of such parameters as flow rate, loading time, volume in the insert well, and initial concentration of the test molecule were investigated. A prediction model was generated from this data, enabling the user to predict the concentration of the test molecule at any point along the PK profile within a coefficient of variation of ∼ 5%. Depletion of the analyte from the well was characterized and was determined to follow first-order rate kinetics, indicated by statistically equivalent (p > 0.05) depletion half-lives that were independent of the starting concentration. A PK curve for an approved antibiotic, levofloxacin, was generated to show utility beyond the fluorescein test molecule.
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Affiliation(s)
- Sarah Y Lockwood
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Jayda E Meisel
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Frederick J Monsma
- Merck Research Laboratories , Kenilworth, New Jersey 07033, United States
| | - Dana M Spence
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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Gross BC, Anderson KB, Meisel JE, McNitt MI, Spence DM. Polymer Coatings in 3D-Printed Fluidic Device Channels for Improved Cellular Adherence Prior to Electrical Lysis. Anal Chem 2015; 87:6335-41. [PMID: 25973637 DOI: 10.1021/acs.analchem.5b01202] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This paper describes the design and fabrication of a polyjet-based three-dimensional (3D)-printed fluidic device where poly(dimethylsiloxane) (PDMS) or polystyrene (PS) were used to coat the sides of a fluidic channel within the device to promote adhesion of an immobilized cell layer. The device was designed using computer-aided design software and converted into an .STL file prior to printing. The rigid, transparent material used in the printing process provides an optically transparent path to visualize endothelial cell adherence and supports integration of removable electrodes for electrical cell lysis in a specified portion of the channel (1 mm width × 0.8 mm height × 2 mm length). Through manipulation of channel geometry, a low-voltage power source (500 V max) was used to selectively lyse adhered endothelial cells in a tapered region of the channel. Cell viability was maintained on the device over a 5 day period (98% viable), though cell coverage decreased after day 4 with static media delivery. Optimal lysis potentials were obtained for the two fabricated device geometries, and selective cell clearance was achieved with cell lysis efficiencies of 94 and 96%. The bottleneck of unknown surface properties from proprietary resin use in fabricating 3D-printed materials is overcome through techniques to incorporate PDMS and PS.
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Affiliation(s)
- Bethany C Gross
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, United States
| | - Kari B Anderson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, United States
| | - Jayda E Meisel
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, United States
| | - Megan I McNitt
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, United States
| | - Dana M Spence
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, United States
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