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Gouws AC, Kruger HG, Gheysens O, Zeevaart JR, Govender T, Naicker T, Ebenhan T. Antibiotic-Derived Radiotracers for Positron Emission Tomography: Nuclear or "Unclear" Infection Imaging? Angew Chem Int Ed Engl 2022; 61:e202204955. [PMID: 35834311 PMCID: PMC9826354 DOI: 10.1002/anie.202204955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 01/11/2023]
Abstract
The excellent features of non-invasive molecular imaging, its progressive technology (real-time, whole-body imaging and quantification), and global impact by a growing infrastructure for positron emission tomography (PET) scanners are encouraging prospects to investigate new concepts, which could transform clinical care of complex infectious diseases. Researchers are aiming towards the extension beyond the routinely available radiopharmaceuticals and are looking for more effective tools that interact directly with causative pathogens. We reviewed and critically evaluated (challenges or pitfalls) antibiotic-derived PET radiopharmaceutical development efforts aimed at infection imaging. We considered both radiotracer development for infection imaging and radio-antibiotic PET imaging supplementing other tools for pharmacologic drug characterization; overall, a total of 20 original PET radiotracers derived from eleven approved antibiotics.
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Affiliation(s)
- Arno Christiaan Gouws
- Catalysis and Peptide Research UnitUniversity of KwaZulu-NatalDurban4000South Africa
| | | | - Olivier Gheysens
- Department of Nuclear MedicineCliniques Universitaires Saint-Luc, and Institute of Clinical and Experimental ResearchUniversité Catholique de LouvainBrusselsBelgium
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure NPCPretoria0001South Africa
- RadiochemistryThe South African Nuclear Energy CorporationBrits0420South Africa
- Preclinical Drug Development PlatformNorth West UniversityPotchefstroom2520South Africa
| | | | - Tricia Naicker
- Catalysis and Peptide Research UnitUniversity of KwaZulu-NatalDurban4000South Africa
| | - Thomas Ebenhan
- Nuclear Medicine Research Infrastructure NPCPretoria0001South Africa
- Preclinical Drug Development PlatformNorth West UniversityPotchefstroom2520South Africa
- Department of Nuclear MedicineUniversity of PretoriaPretoria0001South Africa
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2
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Lee IK, Jacome DA, Cho JK, Tu V, Young AJ, Dominguez T, Northrup JD, Etersque JM, Lee HS, Ruff A, Aklilu O, Bittinger K, Glaser LJ, Dorgan D, Hadjiliadis D, Kohli RM, Mach RH, Mankoff DA, Doot RK, Sellmyer MA. Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim. J Clin Invest 2022; 132:156679. [PMID: 36106638 PMCID: PMC9479701 DOI: 10.1172/jci156679] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 07/19/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Several molecular imaging strategies can identify bacterial infections in humans. PET affords the potential for sensitive infection detection deep within the body. Among PET-based approaches, antibiotic-based radiotracers, which often target key bacterial-specific enzymes, have considerable promise. One question for antibiotic radiotracers is whether antimicrobial resistance (AMR) reduces specific accumulation within bacteria, diminishing the predictive value of the diagnostic test. METHODS Using a PET radiotracer based on the antibiotic trimethoprim (TMP), [11C]-TMP, we performed in vitro uptake studies in susceptible and drug-resistant bacterial strains and whole-genome sequencing (WGS) in selected strains to identify TMP resistance mechanisms. Next, we queried the NCBI database of annotated bacterial genomes for WT and resistant dihydrofolate reductase (DHFR) genes. Finally, we initiated a first-in-human protocol of [11C]-TMP in patients infected with both TMP-sensitive and TMP-resistant organisms to demonstrate the clinical feasibility of the tool. RESULTS We observed robust [11C]-TMP uptake in our panel of TMP-sensitive and -resistant bacteria, noting relatively variable and decreased uptake in a few strains of P. aeruginosa and E. coli. WGS showed that the vast majority of clinically relevant bacteria harbor a WT copy of DHFR, targetable by [11C]-TMP, and that despite the AMR, these strains should be “imageable.” Clinical imaging of patients with [11C]-TMP demonstrated focal radiotracer uptake in areas of infectious lesions. CONCLUSION This work highlights an approach to imaging bacterial infection in patients, which could affect our understanding of bacterial pathogenesis as well as our ability to better diagnose infections and monitor response to therapy. TRIAL REGISTRATION ClinicalTrials.gov NCT03424525. FUNDING Institute for Translational Medicine and Therapeutics, Burroughs Wellcome Fund, NIH Office of the Director Early Independence Award (DP5-OD26386), and University of Pennsylvania NIH T32 Radiology Research Training Grant (5T32EB004311-12).
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Affiliation(s)
- Iris K. Lee
- Department of Radiology and
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Vincent Tu
- Department of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Jean M. Etersque
- Department of Radiology and
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Kyle Bittinger
- Department of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laurel J. Glaser
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Dorgan
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, and
| | - Denis Hadjiliadis
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, and
| | - Rahul M. Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Division of Infectious Disease, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Mark A. Sellmyer
- Department of Radiology and
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Gouws AC, Kruger HG, Gheysens O, Zeevaart JR, Govender T, Naiker T, Ebenhan T. Antibiotic‐Derived Radiotracers for Positron Emission Tomography: Nuclear or ‘Unclear’ Infection Imaging? Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arno Christiaan Gouws
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Hendrik Gerhardus Kruger
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Olivier Gheysens
- Cliniques Universitaires Saint-Luc Department of Nuclear Medicine BELGIUM
| | - Jan Rijn Zeevaart
- North-West University Potchefstroom Campus: North-West University Preclinical Drug Development Platform SOUTH AFRICA
| | | | - Tricia Naiker
- University of KwaZulu-Natal School of Health Sciences Catalysis and Peptide Research Unit SOUTH AFRICA
| | - Thomas Ebenhan
- University of Pretoria Nuclear Medicine Steve Biko and Malherbe St 0001 Pretoria SOUTH AFRICA
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4
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Krucinska J, Lombardo MN, Erlandsen H, Estrada A, Si D, Viswanathan K, Wright DL. Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Commun Biol 2022; 5:459. [PMID: 35562546 PMCID: PMC9106665 DOI: 10.1038/s42003-022-03384-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors. Critical residue variations in two of the most clinically prevalent DHFR isoforms are identified as a common structural element in trimethoprim-resistant DHFR which impose changes on enzyme catalysis and ligand-cofactor cooperativity.
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Affiliation(s)
- Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Michael N Lombardo
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment (COR2E), University of Connecticut, 91N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Debjani Si
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Kishore Viswanathan
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA.
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5
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Raji M, Le TM, Huynh T, Szekeres A, Nagy V, Zupkó I, Szakonyi Z. Divergent Synthesis, Antiproliferative and Antimicrobial Studies of 1,3-Aminoalcohol and 3-Amino-1,2-Diol Based Diaminopyrimidines. Chem Biodivers 2022; 19:e202200077. [PMID: 35349207 DOI: 10.1002/cbdv.202200077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
A series of novel diaminopyrimidines containing pinane moieties were synthesized via an efficient methodology starting from pinane-based aminoalcohols, aminodiols and 2,4-dichloropyrimidines. Bioassay tests demonstrated that compound 18a displayed much stronger antiproliferative activities against four human cancer cell lines (HeLa, Siha, MDA-MB-231, MCF-7 and A2780) than positive control cisplatin. In particular, compound 22a was found to be selective in inhibiting HeLa cell proliferation with cancer cell growth inhibition values higher than 95 %. Moreover, the in vitro screening of prepared compounds against different bacterial and fungal strains is reported. The results revealed that 12b and 17a, the most promising compounds, displayed selective inhibition for the Gram-positive bacteria (B. subtilis and S. aureus) with percent inhibition values ranging from 75 to 95 % at 10 μg/mL concentration. Both selective inhibition and the in vitro activity values demonstrated that these compounds have the potential to be developed into clinically important therapeutic choices for the treatment of infections caused by B. subtilis and S. aureus.
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Affiliation(s)
- Mounir Raji
- Institute of Pharmaceutical Chemistry, University of Szeged, 6720, Szeged, Eötvös u. 6, Hungary
| | - Tam Minh Le
- Institute of Pharmaceutical Chemistry, University of Szeged, 6720, Szeged, Eötvös u. 6, Hungary.,Stereochemistry Research Group of the Hungarian Academy of Sciences, 6720, Szeged, Eötvös u. 6, Hungary
| | - Thu Huynh
- Department of Microbiology, University of Szeged, 6726, Szeged, Közép fasor 52, Hungary
| | - András Szekeres
- Department of Microbiology, University of Szeged, 6726, Szeged, Közép fasor 52, Hungary
| | - Viktória Nagy
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, 6720, Szeged, Eötvös utca 6, Hungary
| | - István Zupkó
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, 6720, Szeged, Eötvös utca 6, Hungary.,Interdisciplinary Center of Natural Products, University of Szeged, 6720, Szeged, Hungary
| | - Zsolt Szakonyi
- Institute of Pharmaceutical Chemistry, University of Szeged, 6720, Szeged, Eötvös u. 6, Hungary.,Interdisciplinary Center of Natural Products, University of Szeged, 6720, Szeged, Hungary
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6
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Jacome DA, Northrup JD, Ruff AJ, Reilly SW, Lee IK, Blizard GS, Sellmyer MA. A Chemical Approach for Programmable Protein Outputs Based on Engineered Cell Interactions. ACS Chem Biol 2021; 16:52-57. [PMID: 33351606 DOI: 10.1021/acschembio.0c00935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cell-cell interactions and communication are crucial to the proper function of complex mammalian physiology including neurocognitive and immune system functions. While many tools are available for observing and perturbing intracellular processes, relatively few exist to probe intercellular processes. Current techniques for studying interactions often rely on direct protein contact, and few can manipulate diverse, functional outputs with tunable protein expression. To address these limitations, we have developed a small-molecule approach based on a trimethoprim prodrug-enzyme pair capable of reporting the presence of two different engineered cell populations with programmable protein outputs. The approach relies on bacterial nitroreductase enzyme catalysis, which is orthogonal to normal mammalian biology, and diffusion of trimethoprim from "activator" cells to "receiver" cells. We test this strategy, which can theoretically regulate many different types of proteins, using biochemical and in vitro culture assays with optical and cytokine protein readouts. This describes the first small-molecule approach capable of detecting and controlling engineered cell-cell outputs, and we anticipate future applications that are especially relevant to the field of immuno-oncology.
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Affiliation(s)
- Daniel A. Jacome
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Justin D. Northrup
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Andrew J. Ruff
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sean W. Reilly
- Department of Process Research and Development, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Iris K. Lee
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Gabrielle S. Blizard
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark A. Sellmyer
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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7
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Sellmyer MA, Richman SA, Lohith K, Hou C, Weng CC, Mach RH, O'Connor RS, Milone MC, Farwell MD. Imaging CAR T Cell Trafficking with eDHFR as a PET Reporter Gene. Mol Ther 2019; 28:42-51. [PMID: 31668558 DOI: 10.1016/j.ymthe.2019.10.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 01/11/2023] Open
Abstract
Cell-based therapeutics have considerable promise across diverse medical specialties; however, reliable human imaging of the distribution and trafficking of genetically engineered cells remains a challenge. We developed positron emission tomography (PET) probes based on the small-molecule antibiotic trimethoprim (TMP) that can be used to image the expression of the Escherichia coli dihydrofolate reductase enzyme (eDHFR) and tested the ability of [18F]-TMP, a fluorine-18 probe, to image primary human chimeric antigen receptor (CAR) T cells expressing the PET reporter gene eDHFR, yellow fluorescent protein (YFP), and Renilla luciferase (rLuc). Engineered T cells showed an approximately 50-fold increased bioluminescent imaging signal and 10-fold increased [18F]-TMP uptake compared to controls in vitro. eDHFR-expressing anti-GD2 CAR T cells were then injected into mice bearing control GD2- and GD2+ tumors. PET/computed tomography (CT) images acquired on days 7 and 13 demonstrated early residency of CAR T cells in the spleen followed by on-target redistribution to the GD2+ tumors. This was corroborated by autoradiography and anti-human CD8 immunohistochemistry. We found a high sensitivity of detection for identifying tumor-infiltrating CD8 CAR T cells, ∼11,000 cells per mm3. These data suggest that the [18F]-TMP/eDHFR PET pair offers important advantages that could better allow investigators to monitor immune cell trafficking to tumors in patients.
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Affiliation(s)
- Mark A Sellmyer
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sarah A Richman
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katheryn Lohith
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Catherine Hou
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi-Chang Weng
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan 33302, Taiwan
| | - Robert H Mach
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roddy S O'Connor
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Milone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael D Farwell
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Mourad AK, Mohammed FK, Tammam GH, Mohammed SR. An Efficient Access to Pyrimidine‐based Polyfunctional Heterocycles with Anticipated Antibacterial Activity. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Asmaa Kamal Mourad
- Department of Chemistry, Faculty of ScienceFayoum University 63514 Fayoum Egypt
| | - Fatehia K. Mohammed
- Department of Chemistry, Faculty of ScienceFayoum University 63514 Fayoum Egypt
| | - Gamal Hassan Tammam
- Department of Chemistry, Faculty of ScienceFayoum University 63514 Fayoum Egypt
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9
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Sellmyer MA, Lee I, Hou C, Weng CC, Li S, Lieberman BP, Zeng C, Mankoff DA, Mach RH. Bacterial infection imaging with [ 18F]fluoropropyl-trimethoprim. Proc Natl Acad Sci U S A 2017; 114:8372-8377. [PMID: 28716936 PMCID: PMC5547613 DOI: 10.1073/pnas.1703109114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is often overlap in the diagnostic features of common pathologic processes such as infection, sterile inflammation, and cancer both clinically and using conventional imaging techniques. Here, we report the development of a positron emission tomography probe for live bacterial infection based on the small-molecule antibiotic trimethoprim (TMP). [18F]fluoropropyl-trimethoprim, or [18F]FPTMP, shows a greater than 100-fold increased uptake in vitro in live bacteria (Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa) relative to controls. In a rodent myositis model, [18F]FPTMP identified live bacterial infection without demonstrating confounding increased signal in the same animal from other etiologies including chemical inflammation (turpentine) and cancer (breast carcinoma). Additionally, the biodistribution of [18F]FPTMP in a nonhuman primate shows low background in many important tissues that may be sites of infection such as the lungs and soft tissues. These results suggest that [18F]FPTMP could be a broadly useful agent for the sensitive and specific imaging of bacterial infection with strong translational potential.
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Affiliation(s)
- Mark A Sellmyer
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Iljung Lee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Catherine Hou
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Chi-Chang Weng
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Shihong Li
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Brian P Lieberman
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Chenbo Zeng
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - David A Mankoff
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert H Mach
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
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10
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Targeting bacterial central metabolism for drug development. ACTA ACUST UNITED AC 2014; 21:1423-32. [PMID: 25442374 DOI: 10.1016/j.chembiol.2014.08.020] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/25/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022]
Abstract
Current antibiotics, derived mainly from natural sources, inhibit a narrow spectrum of cellular processes, namely DNA replication, protein synthesis, and cell wall biosynthesis. With the worldwide explosion of drug resistance, there is renewed interest in the investigation of alternate essential cellular processes, including bacterial central metabolic pathways, as a drug target space for the next generation of antibiotics. However, the validation of targets in central metabolism is more complex, as essentiality of such targets can be conditional and/or contextual. Bearing in mind our enhanced understanding of prokaryotic central metabolism, a key question arises: can central metabolism be bacteria's Achilles' heel and a therapeutic target for the development of new classes of antibiotics? In this review, we draw lessons from oncology and attempt to address some of the open questions related to feasibility of targeting bacterial central metabolism as a strategy for developing new antibacterial drugs.
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11
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Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol 2011; 19:307-14. [PMID: 21561773 DOI: 10.1016/j.tim.2011.03.008] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/29/2011] [Accepted: 03/31/2011] [Indexed: 11/23/2022]
Abstract
Recent advances in liquid chromatography and mass spectrometry have enabled the highly parallel, quantitative measurement of metabolites within a cell and the ability to trace their biochemical fates. In Mycobacterium tuberculosis (Mtb), these advances have highlighted major gaps in our understanding of central carbon metabolism (CCM) that have prompted fresh interpretations of the composition and structure of its metabolic pathways and the phenotypes of Mtb strains in which CCM genes have been deleted. High-throughput screens have demonstrated that small chemical compounds can selectively inhibit some enzymes of Mtb's CCM while sparing homologs in the host. Mtb's CCM has thus emerged as a frontier for both fundamental and translational research.
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12
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Chemical Probes of Escherichia coli Uncovered through Chemical-Chemical Interaction Profiling with Compounds of Known Biological Activity. ACTA ACUST UNITED AC 2010; 17:852-62. [DOI: 10.1016/j.chembiol.2010.06.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/25/2010] [Accepted: 06/04/2010] [Indexed: 01/25/2023]
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13
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Bourne CR, Bunce RA, Bourne PC, Berlin KD, Barrow EW, Barrow WW. Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. Antimicrob Agents Chemother 2009; 53:3065-73. [PMID: 19364848 PMCID: PMC2704665 DOI: 10.1128/aac.01666-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/03/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (< or =12.8 microg/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2(1)2(1)2(1), and X-ray diffraction data were collected to a 2.3-A resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA.
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14
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Frey KM, Liu J, Lombardo MN, Bolstad DB, Wright DL, Anderson AC. Crystal structures of wild-type and mutant methicillin-resistant Staphylococcus aureus dihydrofolate reductase reveal an alternate conformation of NADPH that may be linked to trimethoprim resistance. J Mol Biol 2009; 387:1298-308. [PMID: 19249312 PMCID: PMC2723953 DOI: 10.1016/j.jmb.2009.02.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 02/11/2009] [Accepted: 02/18/2009] [Indexed: 01/07/2023]
Abstract
Both hospital- and community-acquired Staphylococcus aureus infections have become major health concerns in terms of morbidity, suffering and cost. Trimethoprim-sulfamethoxazole (TMP-SMZ) is an alternative treatment for methicillin-resistant S. aureus (MRSA) infections. However, TMP-resistant strains have arisen with point mutations in dihydrofolate reductase (DHFR), the target for TMP. A single point mutation, F98Y, has been shown biochemically to confer the majority of this resistance to TMP. Using a structure-based approach, we have designed a series of novel propargyl-linked DHFR inhibitors that are active against several trimethoprim-resistant enzymes. We screened this series against wild-type and mutant (F98Y) S. aureus DHFR and found that several are active against both enzymes and specifically that the meta-biphenyl class of these inhibitors is the most potent. In order to understand the structural basis of this potency, we determined eight high-resolution crystal structures: four each of the wild-type and mutant DHFR enzymes bound to various propargyl-linked DHFR inhibitors. In addition to explaining the structure-activity relationships, several of the structures reveal a novel conformation for the cofactor, NADPH. In this new conformation that is predominantly associated with the mutant enzyme, the nicotinamide ring is displaced from its conserved location and three water molecules complete a network of hydrogen bonds between the nicotinamide ring and the protein. In this new position, NADPH has reduced interactions with the inhibitor. An equilibrium between the two conformations of NADPH, implied by their occupancies in the eight crystal structures, is influenced both by the ligand and the F98Y mutation. The mutation induced equilibrium between two NADPH-binding conformations may contribute to decrease TMP binding and thus may be responsible for TMP resistance.
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Affiliation(s)
| | | | | | | | | | - Amy C. Anderson
- Corresponding author: Mailing address: Dept of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269. Phone: (860)486-6145. Fax: (860)486-6857.
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15
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Schüttelkopf AW, Hardy LW, Beverley SM, Hunter WN. Structures of Leishmania major pteridine reductase complexes reveal the active site features important for ligand binding and to guide inhibitor design. J Mol Biol 2005; 352:105-16. [PMID: 16055151 DOI: 10.1016/j.jmb.2005.06.076] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 06/29/2005] [Accepted: 06/30/2005] [Indexed: 11/23/2022]
Abstract
Pteridine reductase (PTR1) is an NADPH-dependent short-chain reductase found in parasitic trypanosomatid protozoans. The enzyme participates in the salvage of pterins and represents a target for the development of improved therapies for infections caused by these parasites. A series of crystallographic analyses of Leishmania major PTR1 are reported. Structures of the enzyme in a binary complex with the cofactor NADPH, and ternary complexes with cofactor and biopterin, 5,6-dihydrobiopterin, and 5,6,7,8-tetrahydrobiopterin reveal that PTR1 does not undergo any major conformational changes to accomplish binding and processing of substrates, and confirm that these molecules bind in a single orientation at the catalytic center suitable for two distinct reductions. Ternary complexes with cofactor and CB3717 and trimethoprim (TOP), potent inhibitors of thymidylate synthase and dihydrofolate reductase, respectively, have been characterized. The structure with CB3717 reveals that the quinazoline moiety binds in similar fashion to the pterin substrates/products and dominates interactions with the enzyme. In the complex with TOP, steric restrictions enforced on the trimethoxyphenyl substituent prevent the 2,4-diaminopyrimidine moiety from adopting the pterin mode of binding observed in dihydrofolate reductase, and explain the inhibition properties of a range of pyrimidine derivates. The molecular detail provided by these complex structures identifies the important interactions necessary to assist the structure-based development of novel enzyme inhibitors of potential therapeutic value.
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Affiliation(s)
- Alexander W Schüttelkopf
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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16
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Kovalevskaya NV, Smurnyy YD, Polshakov VI, Birdsall B, Bradbury AF, Frenkiel T, Feeney J. Solution structure of human dihydrofolate reductase in its complex with trimethoprim and NADPH. JOURNAL OF BIOMOLECULAR NMR 2005; 33:69-72. [PMID: 16222560 DOI: 10.1007/s10858-005-1475-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 07/26/2005] [Indexed: 05/04/2023]
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17
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Affiliation(s)
- Ivan M Kompis
- ARPIDA Ltd, Dammstrasse 36, 4142 Münchenstein, Switzerland
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18
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Schneider P, Hawser S, Islam K. Iclaprim, a novel diaminopyrimidine with potent activity on trimethoprim sensitive and resistant bacteria. Bioorg Med Chem Lett 2003; 13:4217-21. [PMID: 14623005 DOI: 10.1016/j.bmcl.2003.07.023] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Iclaprim, a new selective dihydrofolate inhibitor was synthesized based on rational drug design. Iclaprim's interaction with a resistant Staphylococcus aureus dihydrofolate reductase (DHFR) is outlined in comparison to trimethoprim (TMP). This compound is active against methicillin, TMP and vancomycin resistant strains. Arpida Ltd. is developing Iclaprim for serious hospital infections from Gram-positive pathogens and respiratory tract infections.
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Affiliation(s)
- Peter Schneider
- Arpida Ltd, Dammstrasse 36, CH-4142, Muenchenstein, Switzerland.
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19
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Zolli-Juran M, Cechetto JD, Hartlen R, Daigle DM, Brown ED. High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorg Med Chem Lett 2003; 13:2493-6. [PMID: 12852950 DOI: 10.1016/s0960-894x(03)00480-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This communication describes the high-throughput screen of a diverse library of 50,000 small molecules against Escherichia coli dihydrofolate reductase to detect inhibitors. Sixty-two compounds were identified as having significant inhibitory activity against the enzyme. Secondary screening of these revealed twelve molecules that were competitive with dihydrofolate, nine of which have not been previously characterized as inhibitors of dihydrofolate reductase. These novel molecules ranged in potency (K(i)) from 26 nM to 11 microM and may represent fresh starting points for new small molecule therapeutics directed against dihydrofolate reductase.
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Affiliation(s)
- Michela Zolli-Juran
- McMaster HTS Lab, Department of Biochemistry, McMaster University, Hamilton, ON, Canada L8N 3Z5
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20
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Suling WJ, Seitz LE, Pathak V, Westbrook L, Barrow EW, Zywno-Van-Ginkel S, Reynolds RC, Piper JR, Barrow WW. Antimycobacterial activities of 2,4-diamino-5-deazapteridine derivatives and effects on mycobacterial dihydrofolate reductase. Antimicrob Agents Chemother 2000; 44:2784-93. [PMID: 10991861 PMCID: PMC90152 DOI: 10.1128/aac.44.10.2784-2793.2000] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Development of new antimycobacterial agents for Mycobacterium avium complex (MAC) infections is important particularly for persons coinfected with human immunodeficiency virus. The objectives of this study were to evaluate the in vitro activity of 2, 4-diamino-5-methyl-5-deazapteridines (DMDPs) against MAC and to assess their activities against MAC dihydrofolate reductase recombinant enzyme (rDHFR). Seventy-seven DMDP derivatives were evaluated initially for in vitro activity against one to three strains of MAC (NJ168, NJ211, and/or NJ3404). MICs were determined with 10-fold dilutions of drug and a colorimetric (Alamar Blue) microdilution broth assay. MAC rDHFR 50% inhibitory concentrations versus those of human rDHFR were also determined. Substitutions at position 5 of the pteridine moiety included -CH(3), -CH(2)CH(3), and -CH(2)OCH(3) groups. Additionally, different substituted and unsubstituted aryl groups were linked at position 6 through a two-atom bridge of either -CH(2)NH, -CH(2)N(CH(3)), -CH(2)CH(2), or -CH(2)S. All but 4 of the 77 derivatives were active against MAC NJ168 at concentrations of < or =13 microg/ml. Depending on the MAC strain used, 81 to 87% had MICs of < or =1.3 microg/ml. Twenty-one derivatives were >100-fold more active against MAC rDHFR than against human rDHFR. In general, selectivity was dependent on the composition of the two-atom bridge at position 6 and the attached aryl group with substitutions at the 2' and 5' positions on the phenyl ring. Using this assessment, a rational synthetic approach was implemented that resulted in a DMDP derivative that had significant intracellular activity against a MAC-infected Mono Mac 6 monocytic cell line. These results demonstrate that it is possible to synthesize pteridine derivatives that have selective activity against MAC.
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Affiliation(s)
- W J Suling
- Bacteriology and Mycology Research Unit, Southern Research Institute, Birmingham, Alabama 35205, USA
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21
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Adrian PV, Thomson CJ, Klugman KP, Amyes SG. New gene cassettes for trimethoprim resistance, dfr13, and Streptomycin-spectinomycin resistance, aadA4, inserted on a class 1 integron. Antimicrob Agents Chemother 2000; 44:355-61. [PMID: 10639362 PMCID: PMC89683 DOI: 10.1128/aac.44.2.355-361.2000] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous survey of 357 trimethoprim-resistant isolates of aerobic gram-negative bacteria from commensal fecal flora, hybridization experiments showed that 25% (90 of 357) of the isolates failed to hybridize to specific oligonucleotide probes for dihydrofolate reductase types 1, 2b, 3, 5, 6, 7, 8, 9, 10, and 12. Subsequent cloning and sequencing of a plasmid-borne trimethoprim resistance gene from one of these isolates revealed a new dihydrofolate reductase gene, dfr13, which occurred as a cassette integrated in a site-specific manner in a class 1 integron. The gene product shared 84% amino acid identity with dfr12 and exhibited a trimethoprim inhibition profile similar to that of dfr12. Gene probing experiments with an oligonucleotide probe specific for this gene showed that 12.3% (44 of 357) of the isolates which did not hybridize to probes for other dihydrofolate reductases hybridized to this probe. Immediately downstream of dfr13, a new cassette, an aminoglycoside resistance gene of the class AADA ¿ANT(3")(9)-I, which encodes streptomycin-spectinomycin resistance, was identified. This gene shares 57% identity with the consensus aadA1 (ant(3")-Ia) and has been called aadA4 (ant(3")-Id). The 3' end of the aadA4 cassette was truncated by IS26, which was contiguous with a truncated form of Tn3. On the same plasmid, pUK2381, a second copy of IS26 was associated with sul2, which suggests that both integrase and transposase activities have played major roles in the arrangement and dissemination of antibiotic resistance genes dfr13, aadA4, bla(TEM-1), and sul2.
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Affiliation(s)
- P V Adrian
- Department of Medical Microbiology, University of the Witwatersrand, and the South African Institute for Medical Research, Johannesburg, South Africa.
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22
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Polshakov VI, Birdsall B, Frenkiel TA, Gargaro AR, Feeney J. Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate. Protein Sci 1999; 8:467-81. [PMID: 10091649 PMCID: PMC2144292 DOI: 10.1110/ps.8.3.467] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We have determined the three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase and the anticancer drug trimetrexate. Two thousand seventy distance, 345 dihedral angle, and 144 hydrogen bond restraints were obtained from analysis of multidimensional NMR spectra recorded for complexes containing 15N-labeled protein. Simulated annealing calculations produced a family of 22 structures fully consistent with the constraints. Several intermolecular protein-ligand NOEs were obtained by using a novel approach monitoring temperature effects of NOE signals resulting from dynamic processes in the bound ligand. At low temperature (5 degrees C) the trimethoxy ring of bound trimetrexate is flipping sufficiently slowly to give narrow signals in slow exchange, which give good NOE cross peaks. At higher temperature these broaden and their NOE cross peaks disappear thus allowing the signals in the lower-temperature spectrum to be identified as NOEs involving ligand protons. The binding site for trimetrexate is well defined and this was compared with the binding sites in related complexes formed with methotrexate and trimethoprim. No major conformational differences were detected between the different complexes. The 2,4-diaminopyrimidine-containing moieties in the three drugs bind essentially in the same binding pocket and the remaining parts of their molecules adapt their conformations such that they can make effective van der Waals interactions with essentially the same set of hydrophobic amino acids, the side-chain orientations and local conformations of which are not greatly changed in the different complexes (similar chi1 and chi2 values).
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Affiliation(s)
- V I Polshakov
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
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23
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Zywno-van Ginkel S, Dooley TP, Suling WJ, Barrow WW. Identification and cloning of the Mycobacterium avium folA gene, required for dihydrofolate reductase activity. FEMS Microbiol Lett 1997; 156:69-78. [PMID: 9368362 DOI: 10.1111/j.1574-6968.1997.tb12707.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Dihydrofolate reductase is an essential bacterial enzyme necessary for the maintenance of intracellular folate pools in a biochemically active reduced state. In this report, the Mycobacterium avium folA gene was identified by functional genetic complementation, sequenced, and expressed for the first time. It has an open reading frame of 543 bp with a G + C content of 73%. The translated polypeptide sequence shows 58% identity to the consensus sequence of the conserved regions from eight other bacterial dihydrofolate reductases. Recombinant M. avium dihydrofolate reductase was expressed actively in Escherichia coli, and SDS-PAGE analysis revealed a 20 kDa species, agreeable with that predicted from the polypeptide sequence:
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Fresta M, Furneri PM, Mezzasalma E, Nicolosi VM, Puglisi G. Correlation of trimethoprim and brodimoprim physicochemical and lipid membrane interaction properties with their accumulation in human neutrophils. Antimicrob Agents Chemother 1996; 40:2865-73. [PMID: 9124856 PMCID: PMC163637 DOI: 10.1128/aac.40.12.2865] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Dipalmitoylphosphatidylcholine vesicles were used as a biological membrane model to investigate the interaction and the permeation properties of trimethoprim and brodimoprim as a function of drug protonation. The drug-membrane interaction was studied by differential scanning calorimetry. Both drugs interacted with the hydrophilic phospholipid head groups when in a protonated form. An experiment on the permeation of the two drugs through dipalmitoylphosphatidylcholine biomembranes showed higher diffusion rate constants when the two drugs were in the uncharged form; lowering of the pH (formation of protonated species) caused a reduction of permeation. Drug uptake by human neutrophil cells was also investigated. Both drugs may accumulate within neutrophils; however, brodimoprim does so to a greater extent. This accumulation is probably due to a pH gradient driving force, which allows the two drugs to move easily from the extracellular medium (pH approximately 7.3) into the internal cell compartments (acid pH). Once protonated, both drugs are less able to permeate and can be trapped by the neutrophils. This investigation showed the importance of the physicochemical properties of brodimoprim and trimethoprim in determining drug accumulation and membrane permeation pathways.
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Affiliation(s)
- M Fresta
- Department of Pharmaceutical Sciences, University of Catania, Italy
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