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Bioanalytical strategy for the characterization and bioanalysis of biologics: a global, nonregulated bioanalytical lab perspective. Bioanalysis 2023; 15:133-148. [PMID: 36891956 DOI: 10.4155/bio-2022-0215] [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: 03/10/2023] Open
Abstract
Over the past two decades, we have seen an increase in the complexity and diversity of biotherapeutic modalities pursued by biopharmaceutical companies. These biologics are multifaceted and susceptible to post-translational modifications and in vivo biotransformation that could impose challenges for bioanalysis. It is vital to characterize the functionality, stability and biotransformation products of these molecules to enable screening, identify potential liabilities at an early stage and devise a bioanalytical strategy. This article highlights our perspective on characterization and bioanalysis of biologics using hybrid LC-MS in our global nonregulated bioanalytical laboratories. AbbVie's suite of versatile, stage-appropriate characterization assays and quantitative bioanalytical approaches are discussed, along with guidance on their utility in answering project-specific questions to aid in decision-making.
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Tanner L, Mashabela GT, Omollo CC, de Wet TJ, Parkinson CJ, Warner DF, Haynes RK, Wiesner L. Intracellular Accumulation of Novel and Clinically Used TB Drugs Potentiates Intracellular Synergy. Microbiol Spectr 2021; 9:e0043421. [PMID: 34585951 PMCID: PMC8557888 DOI: 10.1128/spectrum.00434-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022] Open
Abstract
The therapeutic repertoire for tuberculosis (TB) remains limited despite the existence of many TB drugs that are highly active in in vitro models and possess clinical utility. Underlying the lack of efficacy in vivo is the inability of TB drugs to penetrate microenvironments inhabited by the causative agent, Mycobacterium tuberculosis, including host alveolar macrophages. Here, we determined the ability of the phenoxazine PhX1 previously shown to be active against M. tuberculosis in vitro to differentially penetrate murine compartments, including plasma, epithelial lining fluid, and isolated epithelial lining fluid cells. We also investigated the extent of permeation into uninfected and M. tuberculosis-infected human macrophage-like Tamm-Horsfall protein 1 (THP-1) cells directly and by comparing to results obtained in vitro in synergy assays. Our data indicate that PhX1 (4,750 ± 127.2 ng/ml) penetrates more effectively into THP-1 cells than do the clinically used anti-TB agents, rifampin (3,050 ± 62.9 ng/ml), moxifloxacin (3,374 ± 48.7 ng/ml), bedaquiline (4,410 ± 190.9 ng/ml), and linezolid (770 ± 14.1 ng/ml). Compound efficacy in infected cells correlated with intracellular accumulation, reinforcing the perceived importance of intracellular penetration as a key drug property. Moreover, we detected synergies deriving from redox-stimulatory combinations of PhX1 or clofazimine with the novel prenylated amino-artemisinin WHN296. Finally, we used compound synergies to elucidate the relationship between compound intracellular accumulation and efficacy, with PhX1/WHN296 synergy levels shown to predict drug efficacy. Collectively, our data support the utility of the applied assays in identifying in vitro active compounds with the potential for clinical development. IMPORTANCE This study addresses the development of novel therapeutic compounds for the eventual treatment of drug-resistant tuberculosis. Tuberculosis continues to progress, with cases of Mycobacterium tuberculosis (M. tuberculosis) resistance to first-line medications increasing. We assess new combinations of drugs with both oxidant and redox properties coupled with a third partner drug, with the focus here being on the potentiation of M. tuberculosis-active combinations of compounds in the intracellular macrophage environment. Thus, we determined the ability of the phenoxazine PhX1, previously shown to be active against M. tuberculosis in vitro, to differentially penetrate murine compartments, including plasma, epithelial lining fluid, and isolated epithelial lining fluid cells. In addition, the extent of permeation into human macrophage-like THP-1 cells and H37Rv-infected THP-1 cells was measured via mass spectrometry and compared to in vitro two-dimensional synergy and subsequent intracellular efficacy. Collectively, our data indicate that development of new drugs will be facilitated using the methods described herein.
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Affiliation(s)
- Lloyd Tanner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gabriel T. Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Charles C. Omollo
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Timothy J. de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Digby F. Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Richard K. Haynes
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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Ruddraraju KV, Aggarwal D, Niu C, Baker EA, Zhang RY, Wu L, Zhang ZY. Highly Potent and Selective N-Aryl Oxamic Acid-Based Inhibitors for Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. J Med Chem 2020; 63:9212-9227. [PMID: 32787087 DOI: 10.1021/acs.jmedchem.0c00302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tuberculosis is an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb). Mtb protein tyrosine phosphatase B (mPTPB) is a virulence factor required for Mtb survival in host macrophages. Consequently, mPTPB represents an exciting target for tuberculosis treatment. Here, we identified N-phenyl oxamic acid as a highly potent and selective monoacid-based phosphotyrosine mimetic for mPTPB inhibition. SAR studies on the initial hit, compound 4 (IC50 = 257 nM), resulted in several highly potent inhibitors with IC50 values lower than 20 nM for mPTPB. Among them, compound 4t showed a Ki of 2.7 nM for mPTPB with over 4500-fold preference over 25 mammalian PTPs. Kinetic, molecular docking, and site-directed mutagenesis analyses confirmed these compounds as active site-directed reversible inhibitors of mPTPB. These inhibitors can reverse the altered host cell immune responses induced by the bacterial phosphatase. Furthermore, the inhibitors possess molecular weights <400 Da, log D7.4 < 2.5, topological polar surface area < 75, ligand efficiency > 0.43, and good aqueous solubility and metabolic stability, thus offering excellent starting points for further therapeutic development.
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Affiliation(s)
- Kasi Viswanatharaju Ruddraraju
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Devesh Aggarwal
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Congwei Niu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Erica Anne Baker
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Li Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 4790, United States
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Zhao Y, Tietz O, Kuan WL, Haji-Dheere AK, Thompson S, Vallin B, Ronchi E, Tóth G, Klenerman D, Aigbirhio FI. A fluorescent molecular imaging probe with selectivity for soluble tau aggregated protein. Chem Sci 2020; 11:4773-4778. [PMID: 34122933 PMCID: PMC8159431 DOI: 10.1039/c9sc05620c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/19/2020] [Indexed: 01/25/2023] Open
Abstract
Soluble forms of aggregated tau misfolded protein, generally termed oligomers, are considered to be the most toxic species of the different assembly states that are the pathological components of neurodegenerative disorders. Therefore, a critical biomedical need exists for imaging probes that can identify and quantify them. We have designed and synthesized a novel fluorescent probe, pTP-TFE for which binding and selectivity profiles towards aggregated tau and Aβ proteins were assessed. Our results have shown pTP-TFE to be selective for early forms of soluble tau aggregates, with high affinity of dissociation constants (K d) = 66 nM, and tenfold selectivity over mature tau fibrils. Furthermore, we found that pTP-TFE is selective for tau over Aβ aggregates and had good cell permeability. This selectivity of pTP-TFE towards early forms of aggregated tau protein ex vivo was also supported with studies on human brain tissue containing tau and Aβ pathology. To the best of our knowledge, this is the first fluorescent molecule to be reported to have this form of selectivity profile, which suggests that pTP-TFE is a unique probe candidate for imaging-based detection of early stages of Alzheimer's disease and other tauopathies.
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Affiliation(s)
- Yanyan Zhao
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
| | - Ole Tietz
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
| | - Wei-Li Kuan
- John van Geest Centre for Brain Repair, Department of Clinical Neuroscience, University of Cambridge Cambridge UK
| | - Abdul K Haji-Dheere
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
| | - Stephen Thompson
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
| | - Benjamin Vallin
- John van Geest Centre for Brain Repair, Department of Clinical Neuroscience, University of Cambridge Cambridge UK
| | - Elisabetta Ronchi
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
| | - Gergely Tóth
- TTK-NAP B - Drug Discovery Research Group - Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences Budapest Hungary
| | - David Klenerman
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge UK
- UK Dementia Research Institute, University of Cambridge Cambridge UK
| | - Franklin I Aigbirhio
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge Cambridge UK
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Zgurskaya HI, Rybenkov VV. Permeability barriers of Gram-negative pathogens. Ann N Y Acad Sci 2020; 1459:5-18. [PMID: 31165502 PMCID: PMC6940542 DOI: 10.1111/nyas.14134] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Most clinical antibiotics do not have efficacy against Gram-negative pathogens, mainly because these cells are protected by the permeability barrier comprising the two membranes with active efflux. The emergence of multidrug-resistant Gram-negative strains threatens the utility even of last resort therapeutic treatments. Significant efforts at different levels of resolution are currently focused on finding a solution to this nonpermeation problem and developing new approaches to the optimization of drug activities against multidrug-resistant pathogens. The exceptional efficiency of the Gram-negative permeability barrier is the result of a complex interplay between the two opposing fluxes of drugs across the two membranes. In this review, we describe the current state of understanding of the problem and the recent advances in theoretical and empirical approaches to characterization of drug permeation and active efflux in Gram-negative bacteria.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma
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Widya M, Pasutti WD, Sachdeva M, Simmons RL, Tamrakar P, Krucker T, Six DA. Development and Optimization of a Higher-Throughput Bacterial Compound Accumulation Assay. ACS Infect Dis 2019; 5:394-405. [PMID: 30624052 DOI: 10.1021/acsinfecdis.8b00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Gram-negative bacterial permeability barrier, coupled with efflux, raises formidable challenges to antibiotic drug discovery. The absence of efficient assays to determine compound penetration into the cell and impact of efflux makes the process resource-intensive, small-scale, and lacking much success. Here, we present BacPK: a label-free, solid phase extraction-mass spectrometry (SPE-MS)-based assay that measures total cellular compound accumulation in Escherichia coli. The BacPK assay is a 96-well accumulation assay that takes advantage of 9 s/sample SPE-MS throughput. This enables the analysis of each compound in a four-point dose-response in isogenic strain pairs along with a no-cell control and 16-point external standard curve, all in triplicate. To validate the assay, differences in accumulation were examined for tetracycline (Tet) and two analogs, confirming that close analogs can differ greatly in accumulation. Tet cellular accumulation was also compared for isogenic strains exhibiting Tet resistance due to the expression of an efflux pump (TetA) or ribosomal protection protein (TetM), confirming only TetA affected cellular Tet accumulation. Finally, using a diverse set of antibacterial compounds, we confirmed the assay's ability to quantify differences in accumulation for isogenic strain pairs with efflux or permeability alterations that are consistent with differences in susceptibility seen for the compounds.
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8
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Prochnow H, Fetz V, Hotop SK, García-Rivera MA, Heumann A, Brönstrup M. Subcellular Quantification of Uptake in Gram-Negative Bacteria. Anal Chem 2018; 91:1863-1872. [PMID: 30485749 DOI: 10.1021/acs.analchem.8b03586] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Infections by Gram-negative pathogens represent a major health care issue of growing concern due to a striking lack of novel antibacterial agents over the course of the last decades. The main scientific problem behind the rational optimization of novel antibiotics is our limited understanding of small molecule translocation into, and their export from, the target compartments of Gram-negative species. To address this issue, a versatile, label-free assay to determine the intracellular localization and concentration of a given compound has been developed for Escherichia coli and its efflux-impaired ΔTolC mutant. The assay applies a fractionation procedure to antibiotic-treated bacterial cells to obtain periplasm, cytoplasm, and membrane fractions of high purity, as demonstrated by Western Blots of compartment-specific marker proteins. This is followed by an LC-MS/MS-based quantification of antibiotic content in each compartment. Antibiotic amounts could be converted to antibiotic concentrations by assuming that an E. coli cell is a cylinder flanked by two half spheres and calculating the volumes of bacterial compartments. The quantification of antibiotics from different classes, namely ciprofloxacin, tetracycline, trimethoprim, and erythromycin, demonstrated pronounced differences in uptake quantities and distribution patterns across the compartments. For example, in the case of ciprofloxacin, a higher amount of compound was located in the cytoplasm than in the periplasm (592 ± 50 pg vs 277 ± 13 pg per 3.9 × 109 cells), but owing to the smaller volume of the periplasmic compartment, its concentration in the cytoplasm was much lower (37 ± 3 vs 221 ± 10 pg/μL for the periplasm). For erythromycin and tetracycline, differences in MICs between WT and ΔTolC mutant strains were not reflected by equal differences in uptake, illustrating that additional experimental data are needed to predict antibiotic efficacy. We believe that our assay, providing the antibiotic concentration at the compartment in which the drug target is expressed, constitutes an essential piece of information for a more rational optimization of novel antibiotics against Gram-negative infections.
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Affiliation(s)
- Hans Prochnow
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Verena Fetz
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany.,School of Engineering and Science , Jacobs University Bremen , 28759 Bremen , Germany
| | - Sven-Kevin Hotop
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Mariel A García-Rivera
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Axel Heumann
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Mark Brönstrup
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany.,German Center for Infection Research (DZIF) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
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Tanner L, Denti P, Wiesner L, Warner DF. Drug permeation and metabolism in Mycobacterium tuberculosis: Prioritising local exposure as essential criterion in new TB drug development. IUBMB Life 2018; 70:926-937. [PMID: 29934964 PMCID: PMC6129860 DOI: 10.1002/iub.1866] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Anti-tuberculosis (TB) drugs possess diverse abilities to penetrate the different host tissues and cell types in which infecting Mycobacterium tuberculosis bacilli are located during active disease. This is important since there is increasing evidence that the respective "lesion-penetrating" properties of the front-line TB drugs appear to correlate well with their specific activity in standard combination therapy. In turn, these observations suggest that rational efforts to discover novel treatment-shortening drugs and drug combinations should incorporate knowledge about the comparative abilities of both existing and experimental anti-TB agents to access bacilli in defined physiological states at different sites of infection, as well as avoid elimination by efflux or inactivation by host or bacterial metabolism. However, while there is a fundamental requirement to understand the mode of action and pharmacological properties of any current or experimental anti-TB agent within the context of the obligate human host, this is complex and, until recently, has been severely limited by the available methodologies and models. Here, we discuss advances in analytical models and technologies which have enabled investigations of drug metabolism and pharmacokinetics (DMPK) for new TB drug development. In particular, we consider the potential to shift the focus of traditional pharmacokinetic-pharmacodynamic analyses away from plasma to a more specific "site of action" drug exposure as an essential criterion for drug development and the design of dosing strategies. Moreover, in summarising approaches to determine DMPK data for the "unit of infection" comprising host macrophage and intracellular bacillus, we evaluate the potential benefits of including these analyses at an early stage in the preclinical drug development algorithm. © 2018 IUBMB Life, 70(9):926-937, 2018.
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Affiliation(s)
- Lloyd Tanner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Paolo Denti
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Lubbe Wiesner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Digby F. Warner
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
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Lokesh D, Parkesh R, Kammara R. Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs. Sci Rep 2018; 8:11897. [PMID: 30093677 PMCID: PMC6085307 DOI: 10.1038/s41598-018-30429-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
Multiple mutations in the β subunit of the RNA polymerase (rpoβ) of Mycobacterium tuberculosis (Mtb) are the primary cause of resistance to rifamycin (RIF). In the present study, bifidobacterial rpoβ sequences were analyzed to characterize the mutations that contribute to the development of intrinsic resistance to RIF, isoniazid, streptomycin and pyrazinamide. Sequence variations, which mapped to cassettes 1 and 2 of the rpoβ pocket, are also found in multidrug-resistant Mtb (MDR Mtb). Growth curves in the presence of osmolytes and different concentrations of RIF showed that the bacteria adapted rapidly by shortening the growth curve lag time. Insight into the adapted rpoβ DNA sequences revealed that B. adolescentis harbored mutations both in the RIF pocket and in regions outside the pocket. The minimum inhibitory concentrations (MICs) and mutant prevention concentrations (MPCs) indicated that B. longum, B. adolescentis and B. animalis are resistant to antitubercular drugs. 3D-homology modeling and binding interaction studies using computational docking suggested that mutants had reduced binding affinity towards RIF. RIF-exposed/resistant bacteria exhibited variant protein profiles along with morphological differences, such as elongated and branched cells, surface conversion from rough to smooth, and formation of a concentrating ring.
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Affiliation(s)
- Dhanashree Lokesh
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India
| | - Raman Parkesh
- Principal Scientist, Protein Science Center, Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Rajagopal Kammara
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India.
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11
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Advances and challenges in bacterial compound accumulation assays for drug discovery. Curr Opin Chem Biol 2018; 44:9-15. [PMID: 29803973 DOI: 10.1016/j.cbpa.2018.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/03/2018] [Indexed: 11/21/2022]
Abstract
The identification of potent in vitro inhibitors of essential bacterial targets is relatively straightforward, however vanishingly few of these molecules have Gram-negative antibacterial potency and spectrum because of a failure to accumulate inside the bacteria. The Gram-negative bacterial cell envelope provides a formidable barrier to entry and couples with efflux pumps to prevent compound accumulation. Assays to measure the cellular permeation, efflux and accumulation of compounds in bacteria continue to be innovated and refined to guide drug discovery. Important advances in the label-free detection of compounds associated with or passing through bacteria rely on mass spectrometry This technique holds the promise of bacterial subcellular resolution and the throughput needed to test libraries of compounds to evaluate structure-accumulation relationships.
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12
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Antibiotic Hybrids: the Next Generation of Agents and Adjuvants against Gram-Negative Pathogens? Clin Microbiol Rev 2018. [PMID: 29540434 DOI: 10.1128/cmr.00077-17] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The global incidence of drug-resistant Gram-negative bacillary infections has been increasing, and there is a dire need to develop novel strategies to overcome this problem. Intrinsic resistance in Gram-negative bacteria, such as their protective outer membrane and constitutively overexpressed efflux pumps, is a major survival weapon that renders them refractory to current antibiotics. Several potential avenues to overcome this problem have been at the heart of antibiotic drug discovery in the past few decades. We review some of these strategies, with emphasis on antibiotic hybrids either as stand-alone antibacterial agents or as adjuvants that potentiate a primary antibiotic in Gram-negative bacteria. Antibiotic hybrid is defined in this review as a synthetic construct of two or more pharmacophores belonging to an established agent known to elicit a desired antimicrobial effect. The concepts, advances, and challenges of antibiotic hybrids are elaborated in this article. Moreover, we discuss several antibiotic hybrids that were or are in clinical evaluation. Mechanistic insights into how tobramycin-based antibiotic hybrids are able to potentiate legacy antibiotics in multidrug-resistant Gram-negative bacilli are also highlighted. Antibiotic hybrids indeed have a promising future as a therapeutic strategy to overcome drug resistance in Gram-negative pathogens and/or expand the usefulness of our current antibiotic arsenal.
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Lei C, Wang J, Liu Y, Liu X, Zhao G, Wang J. A feedback regulatory model for RifQ-mediated repression of rifamycin export in Amycolatopsis mediterranei. Microb Cell Fact 2018; 17:14. [PMID: 29375035 PMCID: PMC5787919 DOI: 10.1186/s12934-018-0863-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Due to the important role of rifamycin in curing tuberculosis infection, the study on rifamycin has never been stopped. Although RifZ, which locates within the rifamycin biosynthetic cluster, has recently been characterized as a pathway-specific regulator for rifamycin biosynthesis, little is known about the regulation of rifamycin export. RESULTS In this work, we proved that the expression of the rifamycin efflux pump (RifP) was regulated by RifQ, a TetR-family transcriptional regulator. Deletion of rifQ had little impact on bacterial growth, but resulted in improved rifamycin production, which was consistent with the reverse transcription PCR results that RifQ negatively regulated rifP's transcription. With electrophoretic mobility shift assay and DNase I Footprinting assay, RifQ was found to directly bind to the promoter region of rifP, and a typical inverted repeat was identified within the RifQ-protected sequences. The transcription initiation site of rifP was further characterized and found to be upstream of the RifQ binding sites, well explaining the RifQ-mediated repression of rifP's transcription in vivo. Moreover, rifamycin B (the end product of rifamycin biosynthesis) remarkably decreased the DNA binding affinity of RifQ, which led to derepression of rifamycin export, reducing the intracellular concentration of rifamycin B as well as its toxicity against the host. CONCLUSIONS Here, we proved that the export of rifamycin B was repressed by RifQ in Amycolatopsis mediterranei, and the RifQ-mediated repression could be specifically relieved by rifamycin B, the end product of rifamycin biosynthesis, based on which a feedback model was proposed for regulation of rifamycin export. With the findings here, one could improve the antibiotic yield by simply inactivating the negative regulator of the antibiotic transporter.
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Affiliation(s)
- Chao Lei
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Jingzhi Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Yuanyuan Liu
- Shanghai Tolo Biotechnology Company Limited, Shanghai, 200233, China
| | - Xinqiang Liu
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
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14
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Pagès JM. [Antibiotic transport and membrane permeability: new insights to fight bacterial resistance]. Biol Aujourdhui 2017; 211:149-154. [PMID: 29236663 DOI: 10.1051/jbio/2017020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 11/14/2022]
Abstract
A main challenge in medicinal chemistry is to determine the parameters modulating the in cellulo drug concentration needed for a therapeutic action. In Gram-negative antibacterial research, the concern is to evaluate the antibiotic permeation across the outer and inner membranes, that delineate the periplasm surrounding the bacterial cytoplasm. Passing through the membrane barrier to reach the inhibitory concentration inside the bacterium is the first pivotal step for antibiotics. The research and the development of new antimicrobials mostly rely on their capacity to reach critical concentrations in the vicinity of their intracellular target. Despite several decades of studies focused on antibiotic/drug activity against bacterial cells using different approaches, no consensus regarding the analysis of the kinetics and accumulation in individual bacterium and in bacterial populations is available to understand the drug translocation into living bacteria as a first step of drug action. Our TRANSLOCATION consortium supports the development of reliable and robust methods to quantify penetration and efflux processes in Gram-negative bacteria and recently we have developed a reliable and efficient method to determine the intra-bacterial concentration of fluorescent antibiotics. By using these powerful approaches, new concepts, "Resident Time Concentration Close to Target" (RTC2T) and "Structure Intracellular Concentration Activity Relationship" (SICAR), have been proposed in order to link chemical and structural aspects with the bacterial membrane and transport aspects. Using RTC2T and SICAR indexes, a new dissection of antibiotic translocation-transport can be obtained to better understand and improve the antibiotic pharmacophoric groups that are related to permeation and efflux.
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Affiliation(s)
- Jean-Marie Pagès
- UMR_MD1, Transporteurs Membranaires, Chimiorésistance et Drug Design, Faculté de Médecine et Faculté de Pharmacie, 27 boulevard Jean-Moulin, 13385 Marseille cedex 05, France
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15
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Hong S, Moritz TJ, Rath CM, Tamrakar P, Lee P, Krucker T, Lee LP. Assessing Antibiotic Permeability of Gram-Negative Bacteria via Nanofluidics. ACS NANO 2017; 11:6959-6967. [PMID: 28605582 DOI: 10.1021/acsnano.7b02267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While antibiotic resistance is increasing rapidly, drug discovery has proven to be extremely difficult. Antibiotic resistance transforms some bacterial infections into deadly medical conditions. A significant challenge in antibiotic discovery is designing potent molecules that enter Gram-negative bacteria and also avoid active efflux mechanisms. Critical analysis in rational drug design has been hindered by the lack of effective analytical tools to analyze the bacterial membrane permeability of small molecules. We design, fabricate, and characterize the nanofluidic device that actively loads more than 200 single bacterial cells in a nanochannel array. We demonstrate a gigaohm seal between the nanochannel walls and the loaded bacteria, restricting small molecule transport to only occur through the bacterial cell envelope. Quantitation of clindamycin translocation through wild-type and efflux-deficient (ΔtolC) Escherichia coli strains via nanofluidic-interfaced liquid chromatography mass spectrometry shows higher levels of translocation for wild-type E. coli than for an efflux-deficient strain. We believe that the assessment of compound permeability in Gram-negative bacteria via the nanofluidic analysis platform will be an impactful tool for compound permeation and efflux studies in bacteria to assist rational antibiotic design.
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Affiliation(s)
| | - Tobias J Moritz
- Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States
| | - Christopher M Rath
- Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States
| | - Pramila Tamrakar
- Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States
| | | | - Thomas Krucker
- Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States
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16
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Correlating uptake and activity of proline-rich antimicrobial peptides in Escherichia coli. Anal Bioanal Chem 2017; 409:5581-5592. [PMID: 28717895 DOI: 10.1007/s00216-017-0496-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/29/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023]
Abstract
Increasing death tolls accounted for by antimicrobial drug resistance demand novel antibiotic lead compounds. Among different promising candidate classes, proline-rich antimicrobial peptides (PrAMPs) are very favorable due to their intracellular mechanism, i.e., binding to the 70S ribosome and DnaK, after active uptake relying on bacterial transporters like SbmA and MdtM. Studies on peptide internalization as the first step of their complex mode of action rely typically on fluorophore or radioactive labeling and quantification using microscopy, flow cytometry, or radioactivity. Here, a liquid chromatography based assay was applied to quantify the unlabeled internalized full-length peptides and their proteolytic degradation products (metabolites) using UV absorbance and mass spectrometry. Knockout mutants lacking transporter proteins showed reduced PrAMP uptakes, explaining their reduced susceptibility against PrAMPs. Interestingly, major metabolites produced by bacterial proteases still bound to the 70S ribosome provide evidence that degradation by cytosolic proteases as a possible resistance mechanism is not very efficient. Graphical abstract The uptake of unlabeled proline-rich antimicrobial peptides (PrAMPs) is analyzed in Escherichia coli BW25113 wild-type and transporter knockout mutants ΔsbmA and BS2 (ΔsbmA yjiL::Tn10) by reversed-phase chromatography and quantified by UV detection or mass spectrometry with multi-reaction monitoring (scheme right). Internalized peptide amounts correlated to minimal inhibitory concentrations and bacterial transport activities based on the present transporter proteins (scheme left).
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17
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Tian H, Six DA, Krucker T, Leeds JA, Winograd N. Subcellular Chemical Imaging of Antibiotics in Single Bacteria Using C 60-Secondary Ion Mass Spectrometry. Anal Chem 2017; 89:5050-5057. [PMID: 28332827 PMCID: PMC5415874 DOI: 10.1021/acs.analchem.7b00466] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 12/20/2022]
Abstract
The inherent difficulty of discovering new and effective antibacterials and the rapid development of resistance particularly in Gram-negative bacteria, illustrates the urgent need for new methods that enable rational drug design. Here we report the development of 3D imaging cluster Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) as a label-free approach to chemically map small molecules in aggregated and single Escherichia coli cells, with ∼300 nm spatial resolution and high chemical sensitivity. The feasibility of quantitative analysis was explored, and a nonlinear relationship between treatment dose and signal for tetracycline and ampicillin, two clinically used antibacterials, was observed. The methodology was further validated by the observation of reduction in tetracycline accumulation in an E. coli strain expressing the tetracycline-specific efflux pump (TetA) compared to the isogenic control. This study serves as a proof-of-concept for a new strategy for chemical imaging at the nanoscale and has the potential to aid discovery of new antibacterials.
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Affiliation(s)
- Hua Tian
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - David A. Six
- Novartis
Institutes
for BioMedical Research, Inc., 5300
Chiron Way, Emeryville, California 94608-2916, United States
| | - Thomas Krucker
- Novartis
Institutes
for BioMedical Research, Inc., 5300
Chiron Way, Emeryville, California 94608-2916, United States
| | - Jennifer A. Leeds
- Novartis
Institutes
for BioMedical Research, Inc., 5300
Chiron Way, Emeryville, California 94608-2916, United States
| | - Nicholas Winograd
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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18
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Teuscher KB, Zhang M, Ji H. A Versatile Method to Determine the Cellular Bioavailability of Small-Molecule Inhibitors. J Med Chem 2017; 60:157-169. [PMID: 27935314 PMCID: PMC7771553 DOI: 10.1021/acs.jmedchem.6b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The determination of the cellular bioavailability of small-molecule inhibitors is a critical step for interpreting cell-based data and guiding inhibitor optimization. Herein, a HPLC-MS based protocol was developed to determine inhibitor cellular bioavailability. This generalizable protocol allows determination of the accurate intracellular concentrations and characterization of various properties of inhibitors including the extra- and intracellular stability, the dose- and time-dependence of the intracellular concentrations, the cell permeability, and the nonspecific binding with the cell culture plates, the extracellular matrices, and the cell membrane. The inhibitors of the protein-protein interactions, bromodomains, and the β-catenin/B-cell lymphoma 9 (BCL9) interaction were used to examine the protocol, and the cellular bioavailability of the inhibitors in cancer cells was determined. High nonspecific binding and low cellular uptake were observed for two bromodomain inhibitors. The two β-catenin/BCL9 inhibitors had low nonspecific binding but different cellular uptake. These inhibitors exhibited different stability kinetics in cells.
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Affiliation(s)
- Kevin B Teuscher
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States.,Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Min Zhang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States.,Department of Oncologic Sciences, University of South Florida College of Medicine , Tampa, Florida 33612, United States.,Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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19
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Taddeo VA, Genovese S, Carlucci G, Ferrone V, Patruno A, Ferrone A, de Medina P, Fiorito S, Epifano F. Quantitative profiling of 4'-geranyloxyferulic acid and its conjugate with l-nitroarginine methyl ester in mononuclear cells by high-performance liquid chromatography with fluorescence detection. J Pharm Biomed Anal 2016; 133:49-55. [PMID: 27856101 DOI: 10.1016/j.jpba.2016.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 12/25/2022]
Abstract
Oxyprenylated natural products were shown to exert in vitro and in vivo remarkable anti-cancer and anti-inflammatory effects. This paper describes a rapid, selective, and sensitive HPLC method with fluorescence detection for determination of 4'-geranyloxyferulic acid (GOFA) and its conjugate with l-nitroarginine methyl ester (GOFA-L-NAME) in mononuclear cells. Analytes were extracted from cells using methanol and eluted on a GraceSmart RP18 analytical column (250×4.6mm i.d., 5μm particle size) kept at 25°C. A mixture of formic acid 1% in water (A) and methanol (B) were used as mobile phase, at a flow-rate of 1.2mL/min in gradient elution. A fluorescence detector (excitation/emission wavelength of 319/398nm for GOFA and GOFA-L-NAME), was used for the two analytes. Calibration curves of GOFA and GOFA-L-NAME were linear over the concentration range of 1.0-50μg/mL, with correlation coefficients (r2)≥0.9995. Intra- and inter-assay precision do not exceed 6.8%. The accuracy was from 94% to 105% for quality control samples (2.0, 25.0 and 40μg/mL). The mean (RSD%) extraction recoveries (n=5) for GOFA and GOFA-L-NAME from spiked cells at 2.0, 25.0 and 40.0μg/mL were 92.4±1.5%, 94.7±0.9% and 93.8±1.1%, for GOFA and 95.3±1.2%, 94.8±1.0% and 93.9±1.3%, for GOFA-L-NAME. The limits of detection and quantification were 0.3μg/mL and 1.0μg/mL for GOFA and GOFA-L-NAME. This method was successfully applied to measure GOFA and GOFA-L-NAME concentrations in a mononuclear cells.
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Affiliation(s)
- Vito Alessandro Taddeo
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Salvatore Genovese
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Giuseppe Carlucci
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Vincenzo Ferrone
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Antonia Patruno
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Alessio Ferrone
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | | | - Serena Fiorito
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Francesco Epifano
- Department of Pharmacy, University "G. d'Annunzio" - Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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20
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Phetsang W, Pelingon R, Butler MS, KC S, Pitt ME, Kaeslin G, Cooper MA, Blaskovich MAT. Fluorescent Trimethoprim Conjugate Probes To Assess Drug Accumulation in Wild Type and Mutant Escherichia coli. ACS Infect Dis 2016; 2:688-701. [PMID: 27737551 PMCID: PMC5067704 DOI: 10.1021/acsinfecdis.6b00080] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Reduced
susceptibility to antimicrobials in Gram-negative bacteria may result
from multiple resistance mechanisms, including increased efflux pump
activity or reduced porin protein expression. Up-regulation of the
efflux pump system is closely associated with multidrug resistance
(MDR). To help investigate the role of efflux pumps on compound accumulation,
a fluorescence-based assay was developed using fluorescent derivatives
of trimethoprim (TMP), a broad-spectrum synthetic antibiotic that
inhibits an intracellular target, dihydrofolate reductase (DHFR).
Novel fluorescent TMP probes inhibited eDHFR activity
with comparable potency to TMP, but did not kill or inhibit growth
of wild type Escherichia coli. However,
bactericidal activity was observed against an efflux pump deficient E. coli mutant strain (ΔtolC). A simple and quick fluorescence assay was developed to measure
cellular accumulation of the TMP probe using either fluorescence spectroscopy
or flow cytometry, with validation by LC-MS/MS. This fluorescence
assay may provide a simple method to assess efflux pump activity with
standard laboratory equipment.
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Affiliation(s)
- Wanida Phetsang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ruby Pelingon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark S. Butler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sanjaya KC
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Miranda E. Pitt
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geraldine Kaeslin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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21
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Winton VJ, Aldrich C, Kiessling LL. Carboxylate Surrogates Enhance the Antimycobacterial Activity of UDP-Galactopyranose Mutase Probes. ACS Infect Dis 2016; 2:538-43. [PMID: 27626294 DOI: 10.1021/acsinfecdis.6b00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Uridine diphosphate galactopyranose mutase (UGM also known as Glf) is a biosynthetic enzyme required for construction of the galactan, an essential mycobacterial cell envelope polysaccharide. Our group previously identified two distinct classes of UGM inhibitors; each possesses a carboxylate moiety that is crucial for potency yet likely detrimental for cell permeability. To enhance the antimycobacterial potency, we sought to replace the carboxylate with a functional group mimic-an N-acylsulfonamide group. We therefore synthesized a series of N-acylsulfonamide analogs and tested their ability to inhibit UGM. For each inhibitor scaffold tested, the N-acylsulfonamide group functions as an effective carboxylate surrogate. Although the carboxylates and their surrogates show similar activity against UGM in a test tube, several N-acylsulfonamide derivatives more effectively block the growth of Mycobacterium smegmatis. These data suggest that the replacement of a carboxylate with an N-acylsulfonamide group could serve as a general strategy to augment antimycobacterial activity.
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Affiliation(s)
- Valerie J. Winton
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Claudia Aldrich
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- Department
of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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22
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Ravishankar S, Ambady A, Ramu H, Mudugal NV, Tunduguru R, Anbarasu A, Sharma UK, Sambandamurthy VK, Ramaiah S. An IPTG Inducible Conditional Expression System for Mycobacteria. PLoS One 2015; 10:e0134562. [PMID: 26247874 PMCID: PMC4527713 DOI: 10.1371/journal.pone.0134562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/12/2015] [Indexed: 12/21/2022] Open
Abstract
Conditional expression strains serve as a valuable tool to study the essentiality and to establish the vulnerability of a target under investigation in a drug discovery program. While essentiality implies an absolute requirement of a target function, vulnerability provides valuable information on the extent to which a target function needs to be depleted to achieve bacterial growth inhibition followed by cell death. The critical feature of an ideal conditional expression system is its ability to tightly regulate gene expression to achieve the full spectrum spanning from a high level of expression in order to support growth and near zero level of expression to mimic conditions of gene knockout. A number of bacterial conditional expression systems have been reported for use in mycobacteria. The utility of an isopropylthiogalactoside (IPTG) inducible system in mycobacteria has been reported for protein overexpression and anti-sense gene expression from a replicating multi-copy plasmid. Herein, we report the development of a versatile set of non-replicating IPTG inducible vectors for mycobacteria which can be used for generation of conditional expression strains through homologous recombination. The role of a single lac operator versus a double lac operator to regulate gene expression was evaluated by monitoring the expression levels of β-galactosidase in Mycobacterium smegmatis. These studies indicated a significant level of leaky expression from the vector with a single lac operator but none from the vector with double lac operator. The significance of the double lac operator vector for target validation was established by monitoring the growth kinetics of an inhA, a rpoB and a ftsZ conditional expression strain grown in the presence of different concentrations of IPTG. The utility of this inducible system in identifying target specific inhibitors was established by screening a focussed library of small molecules using an inhA and a rpoB conditional expression strain.
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Affiliation(s)
- Sudha Ravishankar
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
- * E-mail:
| | - Anisha Ambady
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Haripriya Ramu
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Naina Vinay Mudugal
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Anand Anbarasu
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| | - Umender K. Sharma
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Sudha Ramaiah
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
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23
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Evans JC, Mizrahi V. The application of tetracyclineregulated gene expression systems in the validation of novel drug targets in Mycobacterium tuberculosis. Front Microbiol 2015; 6:812. [PMID: 26300875 PMCID: PMC4523840 DOI: 10.3389/fmicb.2015.00812] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022] Open
Abstract
Although efforts to identify novel therapies for the treatment of tuberculosis have led to the identification of several promising drug candidates, the identification of high-quality hits from conventional whole-cell screens remains disappointingly low. The elucidation of the genome sequence of Mycobacterium tuberculosis (Mtb) facilitated a shift to target-based approaches to drug design but these efforts have proven largely unsuccessful. More recently, regulated gene expression systems that enable dose-dependent modulation of gene expression have been applied in target validation to evaluate the requirement of individual genes for the growth of Mtb both in vitro and in vivo. Notably, these systems can also provide a measure of the extent to which putative targets must be depleted in order to manifest a growth inhibitory phenotype. Additionally, the successful implementation of Mtb strains engineered to under-express specific molecular targets in whole-cell screens has enabled the simultaneous identification of cell-permeant inhibitors with defined mechanisms of action. Here, we review the application of tetracycline-regulated gene expression systems in the validation of novel drug targets in Mtb, highlighting both the strengths and limitations associated with this approach to target validation.
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Affiliation(s)
- Joanna C. Evans
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research UnitCape Town, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa
| | - Valerie Mizrahi
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research UnitCape Town, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa
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24
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Tommasi R, Brown DG, Walkup GK, Manchester JI, Miller AA. ESKAPEing the labyrinth of antibacterial discovery. Nat Rev Drug Discov 2015; 14:529-42. [DOI: 10.1038/nrd4572] [Citation(s) in RCA: 379] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Zhou Y, Joubran C, Miller-Vedam L, Isabella V, Nayar A, Tentarelli S, Miller A. Thinking Outside the “Bug”: A Unique Assay To Measure Intracellular Drug Penetration in Gram-Negative Bacteria. Anal Chem 2015; 87:3579-84. [DOI: 10.1021/ac504880r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ying Zhou
- Department
of Chemistry, Infection Innovative Medicines Unit, AstraZeneca-US, 53 Gatehouse
Drive, Waltham, Massachusetts 02451, United States
| | - Camil Joubran
- Department
of Chemistry, Infection Innovative Medicines Unit, AstraZeneca-US, 53 Gatehouse
Drive, Waltham, Massachusetts 02451, United States
| | - Lakshmi Miller-Vedam
- Department
of Biosciences, Infection Innovative Medicines Unit, AstraZeneca-US, Waltham, Massachusetts 02451, United States
| | - Vincent Isabella
- Department
of Biosciences, Infection Innovative Medicines Unit, AstraZeneca-US, Waltham, Massachusetts 02451, United States
| | - Asha Nayar
- Department
of Biosciences, Infection Innovative Medicines Unit, AstraZeneca-US, Waltham, Massachusetts 02451, United States
| | - Sharon Tentarelli
- Department
of Chemistry, Infection Innovative Medicines Unit, AstraZeneca-US, 53 Gatehouse
Drive, Waltham, Massachusetts 02451, United States
| | - Alita Miller
- Department
of Biosciences, Infection Innovative Medicines Unit, AstraZeneca-US, Waltham, Massachusetts 02451, United States
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26
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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27
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UDP-N-acetylmuramic acid l-alanine ligase (MurC) inhibition in a tolC mutant Escherichia coli strain leads to cell death. Antimicrob Agents Chemother 2014; 58:6165-71. [PMID: 25114134 DOI: 10.1128/aac.02890-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mur ligases play an essential role in the biosynthesis of bacterial peptidoglycan and hence are attractive antibacterial targets. A screen of the AstraZeneca compound library led to the identification of compound A, a pyrazolopyrimidine, as a potent inhibitor of Escherichia coli and Pseudomonas aeruginosa MurC. However, cellular activity against E. coli or P. aeruginosa was not observed. Compound A was active against efflux pump mutants of both strains. Experiments using an E. coli tolC mutant revealed accumulation of the MurC substrate and a decrease in the level of product upon treatment with compound A ,: indicating inhibition of MurC enzyme in these cells. Such a modulation was not observed in the E. coli wild-type cells. Further, overexpression of MurC in the E. coli tolC mutant led to an increase in the compound A MIC by ≥16-fold, establishing a correlation between MurC inhibition and cellular activity. In addition, estimation of the intracellular compound A level showed an accumulation of the compound over time in the tolC mutant strain. A significant compound A level was not detected in the wild-type E. coli strain even upon treatment with high concentrations of the compound. Therefore, the lack of MIC and absence of MurC inhibition in wild-type E. coli were possibly due to suboptimal compound concentration as a consequence of a high efflux level and/or poor permeativity of compound A.
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Abstract
Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.
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Koch A, Mizrahi V, Warner DF. The impact of drug resistance on Mycobacterium tuberculosis physiology: what can we learn from rifampicin? Emerg Microbes Infect 2014; 3:e17. [PMID: 26038512 PMCID: PMC3975073 DOI: 10.1038/emi.2014.17] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/12/2013] [Accepted: 12/30/2013] [Indexed: 01/08/2023]
Abstract
The emergence of drug-resistant pathogens poses a major threat to public health. Although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. The fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. Rifampicin (RIF) is a frontline anti-tuberculosis agent that targets the rpoB-encoded β subunit of the DNA-dependent RNA polymerase (RNAP). In Mycobacterium tuberculosis (Mtb), RIF resistance (RIF(R)) maps to mutations in rpoB that are likely to impact RNAP function and, therefore, the ability of the organism to cause disease. However, while numerous studies have assessed the impact of RIF(R) on key Mtb fitness indicators in vitro, the consequences of rpoB mutations for pathogenesis remain poorly understood. Here, we examine evidence from diverse bacterial systems indicating very specific effects of rpoB polymorphisms on cellular physiology, and consider these observations in the context of Mtb. In addition, we discuss the implications of these findings for the propagation of clinically relevant RIF(R) mutations. While our focus is on RIF, we also highlight results which suggest that drug-independent effects might apply to a broad range of resistance-associated mutations, especially in an obligate pathogen increasingly linked with multidrug resistance.
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Affiliation(s)
- Anastasia Koch
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Valerie Mizrahi
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Digby F Warner
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
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