1
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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2
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Brady M, Shchepetkina VI, González-Recio I, Martínez-Chantar ML, Buccella D. Ratiometric Fluorescent Sensors Illuminate Cellular Magnesium Imbalance in a Model of Acetaminophen-Induced Liver Injury. J Am Chem Soc 2023; 145:21841-21850. [PMID: 37782839 PMCID: PMC10571084 DOI: 10.1021/jacs.3c05704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Indexed: 10/04/2023]
Abstract
Magnesium(II) plays catalytic, structural, regulatory, and signaling roles in living organisms. Abnormal levels of this metal have been associated with numerous pathologies, including cardiovascular disease, diabetes, metabolic syndrome, immunodeficiency, cancer, and, most recently, liver pathologies affecting humans. The role of Mg2+ in the pathophysiology of liver disease, however, has been occluded by concomitant changes in concentration of interfering divalent cations, such as Ca2+, which complicates the interpretation of experiments conducted with existing molecular Mg2+ indicators. Herein, we introduce a new quinoline-based fluorescent sensor, MagZet1, that displays a shift in its excitation and emission wavelengths, affording ratiometric detection of cellular Mg2+ by both fluorescence microscopy and flow cytometry. The new sensor binds the target metal with a submillimolar dissociation constant─well suited for detection of changes in free Mg2+ in cells─and displays a 10-fold selectivity against Ca2+. Furthermore, the fluorescence ratio is insensitive to changes in pH in the physiological range, providing an overall superior performance over existing indicators. We provide insights into the metal selectivity profile of the new sensor based on computational modeling, and we apply it to shed light on a decrease in cytosolic free Mg2+ and altered expression of metal transporters in cellular models of drug-induced liver injury caused by acetaminophen overdose.
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Affiliation(s)
- Michael Brady
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | | | - Irene González-Recio
- Liver
Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE),
Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building
801A, 48160 Derio, Spain
| | - María L. Martínez-Chantar
- Liver
Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE),
Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building
801A, 48160 Derio, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Carlos III National
Health Institute, 28029 Madrid, Spain
| | - Daniela Buccella
- Department
of Chemistry, New York University, New York, New York 10003, United States
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3
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Hu XL, Xiao W, Lei Y, Green A, Lee X, Maradana MR, Gao Y, Xie X, Wang R, Chennell G, Basson MA, Kille P, Maret W, Bewick GA, Zhou Y, Hogstrand C. Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier. Nat Commun 2023; 14:5431. [PMID: 37669965 PMCID: PMC10480478 DOI: 10.1038/s41467-023-41168-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Zinc and plant-derived ligands of the aryl hydrocarbon receptor (AHR) are dietary components affecting intestinal epithelial barrier function. Here, we explore whether zinc and the AHR pathway are linked. We show that dietary supplementation with an AHR pre-ligand offers protection against inflammatory bowel disease in a mouse model while protection fails in mice lacking AHR in the intestinal epithelium. AHR agonist treatment is also ineffective in mice fed zinc depleted diet. In human ileum organoids and Caco-2 cells, AHR activation increases total cellular zinc and cytosolic free Zn2+ concentrations through transcription of genes for zinc importers. Tight junction proteins are upregulated through zinc inhibition of nuclear factor kappa-light-chain-enhancer and calpain activity. Our data show that AHR activation by plant-derived dietary ligands improves gut barrier function at least partly via zinc-dependent cellular pathways, suggesting that combined dietary supplementation with AHR ligands and zinc might be effective in preventing inflammatory gut disorders.
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Affiliation(s)
- Xiuchuan Lucas Hu
- Institute of Pediatrics, Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Nutritional Sciences, King's College London, London, UK
| | - Wenfeng Xiao
- Institute of Pediatrics, Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Fudan University, Shanghai, China
| | - Yuxian Lei
- Department of Diabetes, Cardiovascular and Metabolic Medicine & Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Adam Green
- Department of Nutritional Sciences, King's College London, London, UK
| | - Xinyi Lee
- Department of Nutritional Sciences, King's College London, London, UK
| | | | - Yajing Gao
- Institute of Pediatrics, Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Fudan University, Shanghai, China
| | - Xueru Xie
- Institute of Pediatrics, Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Fudan University, Shanghai, China
| | - Rui Wang
- Department of Nutritional Sciences, King's College London, London, UK
| | - George Chennell
- Clinical Neuroscience Department, King's College London, London, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology and MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Pete Kille
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Wolfgang Maret
- Department of Nutritional Sciences, King's College London, London, UK
| | - Gavin A Bewick
- Department of Diabetes, Cardiovascular and Metabolic Medicine & Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Yufeng Zhou
- Institute of Pediatrics, Children's Hospital of Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Fudan University, Shanghai, China.
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4
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Okuda K, Takashima I, Takagi A. Advances in reaction-based synthetic fluorescent probes for studying the role of zinc and copper ions in living systems. J Clin Biochem Nutr 2023; 72:1-12. [PMID: 36777081 PMCID: PMC9899921 DOI: 10.3164/jcbn.22-92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/01/2022] [Indexed: 12/15/2022] Open
Abstract
Recently, the behavior of essential trace metal elements in living organisms has attracted more and more attention as their dynamics have been found to be tightly regulated by metallothionines, transporters, etc. As the physiological and/or pathological roles of such metal elements are critical, there have been many non-invasive methods developed to determine their cellular functions, mainly by small molecule fluorescent probes. In this review, we focus on probes that detect intracellular zinc and monovalent copper. Both zinc and copper act not only as tightly bound cofactors of enzymes and proteins but also as signaling factors as labile or loosely bound species. Many fluorescent probes that detect mobile zinc or monovalent copper are recognition-based probes, whose detection is hindered by the abundance of intracellular chelators such as glutathione which interfere with the interaction between probe and metal. In contrast, reaction-based probes release fluorophores triggered by zinc or copper and avoid interference from such intracellular chelators, allowing the detection of even low concentrations of such metals. Here, we summarize the current status of the cumulative effort to develop such reaction-based probes and discuss the strategies adopted to overcome their shortcomings.
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Affiliation(s)
- Kensuke Okuda
- Laboratory of Bioorganic & Natural Products Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-kita, Higashinada-ku, Kobe 658-8558, Japan,To whom correspondence should be addressed. E-mail:
| | - Ippei Takashima
- Laboratory of Bioorganic & Natural Products Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-kita, Higashinada-ku, Kobe 658-8558, Japan
| | - Akira Takagi
- Laboratory of Bioorganic & Natural Products Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-kita, Higashinada-ku, Kobe 658-8558, Japan
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5
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Goldberg JM, Lippard SJ. Mobile zinc as a modulator of sensory perception. FEBS Lett 2023; 597:151-165. [PMID: 36416529 PMCID: PMC10108044 DOI: 10.1002/1873-3468.14544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Mobile zinc is an abundant transition metal ion in the central nervous system, with pools of divalent zinc accumulating in regions of the brain engaged in sensory perception and memory formation. Here, we present essential tools that we developed to interrogate the role(s) of mobile zinc in these processes. Most important are (a) fluorescent sensors that report the presence of mobile zinc and (b) fast, Zn-selective chelating agents for measuring zinc flux in animal tissue and live animals. The results of our studies, conducted in collaboration with neuroscientist experts, are presented for sensory organs involved in hearing, smell, vision, and learning and memory. A general principle emerging from these studies is that the function of mobile zinc in all cases appears to be downregulation of the amplitude of the response following overstimulation of the respective sensory organs. Possible consequences affecting human behavior are presented for future investigations in collaboration with interested behavioral scientists.
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Affiliation(s)
| | - Stephen J Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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6
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Yu T, Ahmad Malik A, Anuwongcharoen N, Eiamphungporn W, Nantasenamat C, Piacham T. Towards combating antibiotic resistance by exploring the quantitative structure-activity relationship of NDM-1 inhibitors. EXCLI JOURNAL 2022; 21:1331-1351. [PMID: 36540675 PMCID: PMC9755517 DOI: 10.17179/excli2022-5380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, has added up to the totality of antimicrobial resistance control, animal husbandry and food safety. Thus far, there have been no effective drugs for neutralizing NDM-1. This study explores the structure-activity relationship of NDM-1 inhibitors. IC50 values of NDM-1 inhibitors were compiled from both the ChEMBL database and literature. After curation, a final set of 686 inhibitors were used for machine learning model building using the random forest algorithm against 12 sets of molecular fingerprints. Benchmark results indicated that the KlekotaRothCount fingerprint provided the best overall performance with an accuracy of 0.978 and 0.778 for the training and testing set, respectively. Model interpretation revealed that nitrogen-containing features (KRFPC 4080, KRFPC 3882, KRFPC 677, KRFPC 3608, KRFPC 3750, KRFPC 4287 and KRFPC 3943), sulfur-containing substructures (KRFPC 2855 and KRFPC 4843), aromatic features (KRFPC 1566, KRFPC 1564, KRFPC 1642, KRFPC 3608, KRFPC 4287 and KRFPC 3943), carbonyl features (KRFPC 1193 and KRFPC 3025), aliphatic features (KRFPC 2975, KRFPC 297, KRFPC 3224 and KRFPC 669) are features contributing to NDM-1 inhibitory activity. It is anticipated that findings from this study would help facilitate the drug discovery of NDM-1 inhibitors by providing guidelines for further lead optimization.
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Affiliation(s)
- Tianshi Yu
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Aijaz Ahmad Malik
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nuttapat Anuwongcharoen
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Theeraphon Piacham
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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7
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A Cephalosporin-Tripodalamine Conjugate Inhibits Metallo-β-Lactamase with High Efficacy and Low Toxicity. Antimicrob Agents Chemother 2022; 66:e0035222. [PMID: 36094199 PMCID: PMC9578398 DOI: 10.1128/aac.00352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wide spread of metallo-β-lactamase (MBL)-expressing bacteria has greatly threatened human health, and there is an urgent need for inhibitors against MBLs. Herein, we present a cephalosporin-tripodalamine conjugate (DPASC) as a potent MBL inhibitor with a block-release design. The cephalosporin tag blocks the ligand binding site to reduce toxicity and is cleaved by MBLs to release active ligands to inhibit MBLs in situ. The screening of MBL-expressing pathogenic strains with 16 μg/mL DPASC showed a decrease of the minimum inhibitory concentration of meropenem (MEM) by 16 to 512-fold, and its toxicity was minimal to human HepG2 cells, with an IC50 exceeding 512 μg/mL. An in vivo infection model with Galleria mellonella larvae showed an increased 3-day survival rate of 87% with the coadministration of DPASC and MEM, compared to 50% with MEM alone and no toxicity at a dose of 256 mg/kg of DPASC. Our findings with DPASC demonstrate that it is an effective MBL inhibitor and that the block-release strategy could be useful for the development of new MBL inhibitors.
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8
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Lou J, Sagar R, Best MD. Metabolite-Responsive Liposomes Employing Synthetic Lipid Switches Driven by Molecular Recognition Principles. Acc Chem Res 2022; 55:2882-2891. [PMID: 36174148 DOI: 10.1021/acs.accounts.2c00446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The ability to exert control over lipid properties, including structure, charge, function, and self-assembly characteristics is a powerful tool that can be implemented to achieve a wide range of biomedical applications. Examples in this arena include the development of caged lipids for controlled activation of signaling properties, metabolic labeling strategies for tracking lipid biosynthesis, lipid activity probes for identifying cognate binding partners, approaches for in situ membrane assembly, and liposome triggered release strategies. In this Account, we describe recent advancements in the latter area entailing the development of stimuli-responsive liposomes through programmable changes to lipid self-assembly properties, which can be harnessed to drive the release of encapsulated contents toward applications including drug delivery. We will focus on an emerging paradigm involving liposomal platforms that are sensitized toward chemical agents ranging from metal cations to small organic molecules that exhibit dysregulation in disease states. This has been achieved by developing synthetic lipid switches that are designed to undergo programmed conformational changes upon the recognition of specific target analytes. These structural alterations are leveraged to perturb the packing of lipids within the membrane and thereby drive the release of encapsulated contents.We provide an overview of the inspiration, design, and characterization of liposomes that selectively respond to wide-ranging target analytes. This series of studies began with the development of calcium-responsive liposomes utilizing a lipid switch inspired by sensors including indo-1. Following this successful demonstration, we next showed that the selectivity of the lipid switch could be altered among different metal cations by producing a liposomal platform for which release is induced through zinc binding. Our next goal was to develop metabolite-responsive liposomes in which switching is driven by molecular recognition events involving phosphorylated small molecules. In this work, screening of lipid switches designed to interact with phosphorylated metabolites led to the identification of liposomal formulations that selectivity release contents in the presence of adenosine triphosphate (ATP). Finally, we were able to modulate the metabolite selectivity by rationally designing a modified lipid switch structure that is activated through complexation of inositol-(1,4,5)-trisphosphate (IP3). These projects show the progression of our approaches for liposome release triggered by molecular recognition principles, building from ion-responsive lipid switches to structures that are activated by small molecules. These "smart" liposomal platforms provide an important addition to the toolbox for controlled cargo release since they respond to ions or small molecules that are commonly overproduced by diseased cells.
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Affiliation(s)
- Jinchao Lou
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
| | - Ruhani Sagar
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
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9
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Weiss A, Murdoch CC, Edmonds KA, Jordan MR, Monteith AJ, Perera YR, Rodríguez Nassif AM, Petoletti AM, Beavers WN, Munneke MJ, Drury SL, Krystofiak ES, Thalluri K, Wu H, Kruse ARS, DiMarchi RD, Caprioli RM, Spraggins JM, Chazin WJ, Giedroc DP, Skaar EP. Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis. Cell 2022; 185:2148-2163.e27. [PMID: 35584702 DOI: 10.1016/j.cell.2022.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/07/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Zinc (Zn) is an essential micronutrient and cofactor for up to 10% of proteins in living organisms. During Zn limitation, specialized enzymes called metallochaperones are predicted to allocate Zn to specific metalloproteins. This function has been putatively assigned to G3E GTPase COG0523 proteins, yet no Zn metallochaperone has been experimentally identified in any organism. Here, we functionally characterize a family of COG0523 proteins that is conserved across vertebrates. We identify Zn metalloprotease methionine aminopeptidase 1 (METAP1) as a COG0523 client, leading to the redesignation of this group of COG0523 proteins as the Zn-regulated GTPase metalloprotein activator (ZNG1) family. Using biochemical, structural, genetic, and pharmacological approaches across evolutionarily divergent models, including zebrafish and mice, we demonstrate a critical role for ZNG1 proteins in regulating cellular Zn homeostasis. Collectively, these data reveal the existence of a family of Zn metallochaperones and assign ZNG1 an important role for intracellular Zn trafficking.
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Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Caitlin C Murdoch
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew J Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Aslin M Rodríguez Nassif
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Amber M Petoletti
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sydney L Drury
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Evan S Krystofiak
- Cell Imaging Shared Resource, Vanderbilt University, Nashville, TN 37232, USA
| | - Kishore Thalluri
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Angela R S Kruse
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Richard M Caprioli
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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10
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Li J, Ho DJ, Henault M, Yang C, Neri M, Ge R, Renner S, Mansur L, Lindeman A, Kelly B, Tumkaya T, Ke X, Soler-Llavina G, Shanker G, Russ C, Hild M, Gubser Keller C, Jenkins JL, Worringer KA, Sigoillot FD, Ihry RJ. DRUG-seq Provides Unbiased Biological Activity Readouts for Neuroscience Drug Discovery. ACS Chem Biol 2022; 17:1401-1414. [PMID: 35508359 PMCID: PMC9207813 DOI: 10.1021/acschembio.1c00920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Unbiased transcriptomic RNA-seq data has provided deep insights into biological processes. However, its impact in drug discovery has been narrow given high costs and low throughput. Proof-of-concept studies with Digital RNA with pertUrbation of Genes (DRUG)-seq demonstrated the potential to address this gap. We extended the DRUG-seq platform by subjecting it to rigorous testing and by adding an open-source analysis pipeline. The results demonstrate high reproducibility and ability to resolve the mechanism(s) of action for a diverse set of compounds. Furthermore, we demonstrate how this data can be incorporated into a drug discovery project aiming to develop therapeutics for schizophrenia using human stem cell-derived neurons. We identified both an on-target activation signature, induced by a set of chemically distinct positive allosteric modulators of the N-methyl-d-aspartate (NMDA) receptor, and independent off-target effects. Overall, the protocol and open-source analysis pipeline are a step toward industrializing RNA-seq for high-complexity transcriptomics studies performed at a saturating scale.
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Affiliation(s)
| | | | | | | | - Marilisa Neri
- Chemical and Biological Therapeutics, Novartis Institutes for BioMedical Research, Basel, 4056, Switzerland
| | | | - Steffen Renner
- Chemical and Biological Therapeutics, Novartis Institutes for BioMedical Research, Basel, 4056, Switzerland
| | | | | | | | | | | | | | | | | | | | - Caroline Gubser Keller
- Chemical and Biological Therapeutics, Novartis Institutes for BioMedical Research, Basel, 4056, Switzerland
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11
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Liu R, Kowada T, Du Y, Amagai Y, Matsui T, Inaba K, Mizukami S. Organelle-Level Labile Zn 2+ Mapping Based on Targetable Fluorescent Sensors. ACS Sens 2022; 7:748-757. [PMID: 35238552 PMCID: PMC8963189 DOI: 10.1021/acssensors.1c02153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although many Zn2+ fluorescent probes have been developed, there remains a lack of consensus on the labile Zn2+ concentrations ([Zn2+]) in several cellular compartments, as the fluorescence properties and zinc affinity of the fluorescent probes are greatly affected by the pH and redox environments specific to organelles. In this study, we developed two turn-on-type Zn2+ fluorescent probes, namely, ZnDA-2H and ZnDA-3H, with low pH sensitivity and suitable affinity (Kd = 5.0 and 0.16 nM) for detecting physiological labile Zn2+ in various cellular compartments, such as the cytosol, nucleus, ER, and mitochondria. Due to their sufficient membrane permeability, both probes were precisely localized to the target organelles in HeLa cells using HaloTag labeling technology. Using an in situ standard quantification method, we identified the [Zn2+] in the tested organelles, resulting in the subcellular [Zn2+] distribution as [Zn2+]ER < [Zn2+]mito < [Zn2+]cyto ∼ [Zn2+]nuc.
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Affiliation(s)
- Rong Liu
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Toshiyuki Kowada
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi 980-8577, Japan,Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan,Department
of Chemistry, Faculty of Science, Tohoku
University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuyin Du
- Department
of Chemistry, Faculty of Science, Tohoku
University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuta Amagai
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Toshitaka Matsui
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi 980-8577, Japan,Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan,Department
of Chemistry, Faculty of Science, Tohoku
University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kenji Inaba
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi 980-8577, Japan,Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan,Department
of Chemistry, Faculty of Science, Tohoku
University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan,AMED-CREST,
Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Shin Mizukami
- Graduate
School of Life Sciences, Tohoku University, 2-1-1 Katahira,
Aoba-ku, Sendai, Miyagi 980-8577, Japan,Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan,Department
of Chemistry, Faculty of Science, Tohoku
University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan,AMED-CREST,
Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan,
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12
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Corona-Motolinia ND, Martínez-Valencia B, Noriega L, Sánchez-Gaytán BL, Melendez FJ, García-García A, Choquesillo-Lazarte D, Rodríguez-Diéguez A, Castro ME, González-Vergara E. Tris(2-Pyridylmethylamine)V(O)2 Complexes as Counter Ions of Diprotonated Decavanadate Anion: Potential Antineoplastic Activity. Front Chem 2022; 10:830511. [PMID: 35252118 PMCID: PMC8888438 DOI: 10.3389/fchem.2022.830511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
The synthesis and theoretical-experimental characterization of a novel diprotanated decavanadate is presented here due to our search for novel anticancer metallodrugs. Tris(2-pyridylmethyl)amine (TPMA), which is also known to have anticancer activity in osteosarcoma cell lines, was introduced as a possible cationic species that could act as a counterpart for the decavanadate anion. However, the isolated compound contains the previously reported vanadium (V) dioxido-tpma moieties, and the decavanadate anion appears to be diprotonated. The structural characterization of the compound was performed by infrared spectroscopy and single-crystal X-ray diffraction. In addition, DFT calculations were used to analyze the reactive sites involved in the donor-acceptor interactions from the molecular electrostatic potential maps. The level of theory mPW1PW91/6–31G(d)-LANL2DZ and ECP = LANL2DZ for the V atom was used. These insights about the compounds’ main interactions were supported by analyzing the noncovalent interactions utilizing the AIM and Hirshfeld surfaces approach. Molecular docking studies with small RNA fragments were used to assess the hypothesis that decavanadate’s anticancer activity could be attributed to its interaction with lncRNA molecules. Thus, a combination of three potentially beneficial components could be evaluated in various cancer cell lines.
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Affiliation(s)
- Nidia D. Corona-Motolinia
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Beatriz Martínez-Valencia
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Lisset Noriega
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Brenda L. Sánchez-Gaytán
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Francisco J. Melendez
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Amalia García-García
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | | | - María Eugenia Castro
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- *Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
| | - Enrique González-Vergara
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- *Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
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13
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Sagar R, Lou J, Watson AJ, Best MD. Zinc Triggered Release of Encapsulated Cargo from Liposomes via a Synthetic Lipid Switch. Bioconjug Chem 2021; 32:2485-2496. [PMID: 34870414 DOI: 10.1021/acs.bioconjchem.1c00425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Liposomes are effective nanocarriers due to their ability to encapsulate and deliver a wide variety of therapeutics. However, therapeutic potential would be improved by enhanced control over the release of drug cargo. Zinc ions provide exciting new targets for stimuli-responsive lipid design due to their overly abundant concentrations associated with diseased cells. Herein, we report zinc-triggered release of liposomal contents exploiting synthetic lipid switches designed to undergo conformational changes in the presence of this ion. Initially, Nile red leakage assays were conducted that validated successful dose-dependent triggering of release using zinc-responsive lipids (ZRLs). In addition, dynamic light scattering and confocal microscopy experiments showed that zinc treatment led to morphological changes in lipid nanoparticles only when ZRLs were present in formulations. Next, zinc-binding experiments conducted in a solution (NMR, MS) or membrane (zeta potential) context confirmed ZRL-Zn complexation. Finally, polar cargo release from liposomes was achieved. The results from these wide-ranging experiments using four different compounds indicated that zinc-responsive properties varied based on ZRL structure, providing insights into the structural requirements for activity. This work has established zinc-responsive liposomal platforms toward the development of clinical triggered release formulations.
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Affiliation(s)
- Ruhani Sagar
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
| | - Jinchao Lou
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
| | - Alexa J Watson
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, Tennessee 37996, United States
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14
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Rivera JF, Baral AJ, Nadat F, Boyd G, Smyth R, Patel H, Burman EL, Alameer G, Boxall SA, Jackson BR, Baxter EJ, Laslo P, Green AR, Kent DG, Mullally A, Chen E. Zinc-dependent multimerization of mutant calreticulin is required for MPL binding and MPN pathogenesis. Blood Adv 2021; 5:1922-1932. [PMID: 33821991 PMCID: PMC8045488 DOI: 10.1182/bloodadvances.2020002402] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/17/2021] [Indexed: 01/30/2023] Open
Abstract
Calreticulin (CALR) is mutated in the majority of JAK2/MPL-unmutated myeloproliferative neoplasms (MPNs). Mutant CALR (CALRdel52) exerts its effect by binding to the thrombopoietin receptor MPL to cause constitutive activation of JAK-STAT signaling. In this study, we performed an extensive mutagenesis screen of the CALR globular N-domain and revealed 2 motifs critical for CALRdel52 oncogenic activity: (1) the glycan-binding lectin motif and (2) the zinc-binding domain. Further analysis demonstrated that the zinc-binding domain was essential for formation of CALRdel52 multimers, which was a co-requisite for MPL binding. CALRdel52 variants incapable of binding zinc were unable to homomultimerize, form CALRdel52-MPL heteromeric complexes, or stimulate JAK-STAT signaling. Finally, treatment with zinc chelation disrupted CALRdel52-MPL complexes in hematopoietic cells in conjunction with preferential eradication of cells expressing CALRdel52 relative to cells expressing other MPN oncogenes. In addition, zinc chelators exhibited a therapeutic effect in preferentially impairing growth of CALRdel52-mutant erythroblasts relative to unmutated erythroblasts in primary cultures of MPN patients. Together, our data implicate zinc as an essential cofactor for CALRdel52 oncogenic activity by enabling CALRdel52 multimerization and interaction with MPL, and suggests that perturbation of intracellular zinc levels may represent a new approach to abrogate the oncogenic activity of CALRdel52 in the treatment of MPNs.
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Affiliation(s)
- Jeanne F Rivera
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
- Division of Haematology and Immunology, Leeds Institute for Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - April J Baral
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Fatima Nadat
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Grace Boyd
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Rachael Smyth
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Hershna Patel
- School of Life Sciences, University of Westminster, London, United Kingdom
| | - Emma L Burman
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Ghadah Alameer
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Sally A Boxall
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - Brian R Jackson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
| | - E Joanna Baxter
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Peter Laslo
- Division of Haematology and Immunology, Leeds Institute for Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anthony R Green
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - David G Kent
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA; and
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Edwin Chen
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and
- School of Life Sciences, University of Westminster, London, United Kingdom
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15
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Yadav O, Ansari M, Ansari A. Electronic structures, bonding and energetics of non-heme mono and dinuclear iron-TPA complexes: a computational exploration. Struct Chem 2021. [DOI: 10.1007/s11224-021-01775-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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16
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Zhang C, Maslar D, Minckley TF, LeJeune KD, Qin Y. Spontaneous, synchronous zinc spikes oscillate with neural excitability and calcium spikes in primary hippocampal neuron culture. J Neurochem 2021; 157:1838-1849. [PMID: 33638177 DOI: 10.1111/jnc.15334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Zinc has been suggested to act as an intracellular signaling molecule due to its regulatory effects on numerous protein targets including enzymes, transcription factors, ion channels, neurotrophic factors, and postsynaptic scaffolding proteins. However, intracellular zinc concentration is tightly maintained at steady levels under natural physiological conditions. Dynamic changes in intracellular zinc concentration have only been detected in certain types of cells that are exposed to pathologic stimuli or upon receptor ligand binding. Unlike calcium, the ubiquitous signaling metal ion that can oscillate periodically and spontaneously in various cells, spontaneous zinc oscillations have never been reported. In this work, we made the novel observation that the developing neurons generated spontaneous and synchronous zinc spikes in primary hippocampal cultures using a fluorescent zinc sensor, FluoZin-3. Blocking of glutamate receptor-dependent calcium influx depleted the zinc spikes, suggesting that these zinc spikes were driven by the glutamate-mediated spontaneous neural excitability and calcium spikes that have been characterized in early developing neurons. Simultaneous imaging of calcium or pH together with zinc, we uncovered that a downward pH spike was evoked with each zinc spike and this transient cellular acidification occurred downstream of calcium spikes but upstream of zinc spikes. Our results suggest that spontaneous, synchronous zinc spikes were generated through calcium influx-induced cellular acidification, which liberates zinc from intracellular zinc binding ligands. Given that changes in zinc concentration can modulate activities of proteins essential for synapse maturation and neuronal differentiation, these zinc spikes might act as important signaling roles in neuronal development.
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Affiliation(s)
- Chen Zhang
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Drew Maslar
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Taylor F Minckley
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kate D LeJeune
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, USA
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17
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Schizophrenia-associated SLC39A8 polymorphism is a loss-of-function allele altering glutamate receptor and innate immune signaling. Transl Psychiatry 2021; 11:136. [PMID: 33608496 PMCID: PMC7895948 DOI: 10.1038/s41398-021-01262-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/02/2021] [Indexed: 11/08/2022] Open
Abstract
Schizophrenia is a complex and heterogenous disease that presents with abnormalities in glutamate signaling and altered immune and inflammatory signals. Genome-wide association studies have indicated specific genes and pathways that may contribute to schizophrenia. We assessed the impact of the functional missense variant SLC39A8 (ZIP8)-A391T (ZIP8A391T) on zinc transport, glutamate signaling, and the neuroinflammatory response. The ZIP8A391T mutation resulted in reduced zinc transport into the cell, suggesting a loss in the tight control of zinc in the synaptic cleft. Electrophysiological recordings from perturbed neurons revealed a significant reduction in NMDA- and AMPA-mediated spontaneous EPSCs (sEPSCs) and a reduction in GluN2A and GluA1/2/3 receptor surface expression. All phenotypes were rescued by re-expression of wild-type ZIP8 (ZIP8WT) or application of the membrane-impermeable zinc chelator ZX1. ZIP8 reduction also resulted in decreased BBB integrity, increased IL-6/IL-1β protein expression, and increased NFκB following TNFα stimulation, indicating that ZIP8 loss-of-function may exacerbate immune and inflammatory signals. Together, our findings demonstrate that the A391T missense mutation results in alterations in glutamate and immune function and provide novel therapeutic targets relevant to schizophrenia.
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18
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Pratt EP, Anson KJ, Tapper JK, Simpson DM, Palmer AE. Systematic Comparison of Vesicular Targeting Signals Leads to the Development of Genetically Encoded Vesicular Fluorescent Zn 2+ and pH Sensors. ACS Sens 2020; 5:3879-3891. [PMID: 33305939 DOI: 10.1021/acssensors.0c01231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetically encoded fluorescent sensors have been widely used to illuminate secretory vesicle dynamics and the vesicular lumen, including Zn2+ and pH, in living cells. However, vesicular sensors have a tendency to mislocalize and are susceptible to the acidic intraluminal pH. In this study, we performed a systematic comparison of five different vesicular proteins to target the fluorescent protein mCherry and a Zn2+ Förster resonance energy transfer (FRET) sensor to secretory vesicles. We found that motifs derived from vesicular cargo proteins, including chromogranin A (CgA), target vesicular puncta with greater efficacy than transmembrane proteins. To characterize vesicular Zn2+ levels, we developed CgA-Zn2+ FRET sensor fusions with existing sensors ZapCY1 and eCALWY-4 and characterized subcellular localization and the influence of pH on sensor performance. We simultaneously monitored Zn2+ and pH in individual secretory vesicles by leveraging the acceptor fluorescent protein as a pH sensor and found that pH influenced FRET measurements in situ. While unable to characterize vesicular Zn2+ at the single-vesicle level, we were able to monitor Zn2+ dynamics in populations of vesicles and detected high vesicular Zn2+ in MIN6 cells compared to lower levels in the prostate cancer cell line LnCaP. The combination of CgA-ZapCY1 and CgA-eCALWY-4 allows for measurement of Zn2+ from pM to nM ranges.
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Affiliation(s)
- Evan P.S. Pratt
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, UCB 596, Boulder, Colorado 80309-0401, United States
| | - Kelsie J. Anson
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, UCB 596, Boulder, Colorado 80309-0401, United States
| | - Justin K. Tapper
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, UCB 596, Boulder, Colorado 80309-0401, United States
| | - David M. Simpson
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, UCB 596, Boulder, Colorado 80309-0401, United States
| | - Amy E. Palmer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, UCB 596, Boulder, Colorado 80309-0401, United States
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19
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Hyperpolarized 15N-labeled, deuterated tris (2-pyridylmethyl)amine as an MRI sensor of freely available Zn 2. Commun Chem 2020; 3. [PMID: 34212118 PMCID: PMC8244538 DOI: 10.1038/s42004-020-00426-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dynamic nuclear polarization (DNP) coupled with 15N magnetic resonance imaging (MRI) provides an opportunity to image quantitative levels of biologically important metal ions such as Zn2+, Mg2+ or Ca2+ using appropriately designed 15N enriched probes. For example, a Zn-specific probe could prove particularly valuable for imaging the tissue distribution of freely available Zn2+ ions, an important known metal ion biomarker in the pancreas, in prostate cancer, and in several neurodegenerative diseases. In the present study, we prepare the cell-permeable, 15N-enriched, d6-deuterated version of the well-known Zn2+ chelator, tris(2-pyridylmethyl)amine (TPA) and demonstrate that the polarized ligand had favorable T1 and linewidth characteristics for 15N MRI. Examples of how polarized TPA can be used to quantify freely available Zn2+ in homogenized human prostate tissue and intact cells are presented.
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20
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Pratt EPS, Damon LJ, Anson KJ, Palmer AE. Tools and techniques for illuminating the cell biology of zinc. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118865. [PMID: 32980354 DOI: 10.1016/j.bbamcr.2020.118865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Zinc (Zn2+) is an essential micronutrient that is required for a wide variety of cellular processes. Tools and methods have been instrumental in revealing the myriad roles of Zn2+ in cells. This review highlights recent developments fluorescent sensors to measure the labile Zn2+ pool, chelators to manipulate Zn2+ availability, and fluorescent tools and proteomics approaches for monitoring Zn2+-binding proteins in cells. Finally, we close with some highlights on the role of Zn2+ in regulating cell function and in cell signaling.
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Affiliation(s)
- Evan P S Pratt
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Leah J Damon
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Kelsie J Anson
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Amy E Palmer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America.
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21
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Jung W, Sengupta K, Wendel BM, Helmann JD, Chen P. Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria. Nucleic Acids Res 2020; 48:2199-2208. [PMID: 32009151 PMCID: PMC7049717 DOI: 10.1093/nar/gkaa056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 11/12/2022] Open
Abstract
Microorganisms use zinc-sensing regulators to alter gene expression in response to changes in the availability of zinc, an essential micronutrient. Under zinc-replete conditions, the Fur-family metalloregulator Zur binds to DNA tightly in its metallated repressor form to Zur box operator sites, repressing the transcription of zinc uptake transporters. Derepression comes from unbinding of the regulator, which, under zinc-starvation conditions, exists in its metal-deficient non-repressor forms having no significant affinity with Zur box. While the mechanism of transcription repression by Zur is well-studied, little is known on how derepression by Zur could be facilitated. Using single-molecule/single-cell measurements, we find that in live Escherichia coli cells, Zur's unbinding rate from DNA is sensitive to Zur protein concentration in a first-of-its-kind biphasic manner, initially impeded and then facilitated with increasing Zur concentration. These results challenge conventional models of protein unbinding being unimolecular processes and independent of protein concentration. The facilitated unbinding component likely occurs via a ternary complex formation mechanism. The impeded unbinding component likely results from Zur oligomerization on chromosome involving inter-protein salt-bridges. Unexpectedly, a non-repressor form of Zur is found to bind chromosome tightly, likely at non-consensus sequence sites. These unusual behaviors could provide functional advantages in Zur's facile switching between repression and derepression.
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Affiliation(s)
- Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kushal Sengupta
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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22
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Lo MN, Damon LJ, Wei Tay J, Jia S, Palmer AE. Single cell analysis reveals multiple requirements for zinc in the mammalian cell cycle. eLife 2020; 9:e51107. [PMID: 32014109 PMCID: PMC7000218 DOI: 10.7554/elife.51107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/30/2019] [Indexed: 01/01/2023] Open
Abstract
Zinc is widely recognized as essential for growth and proliferation, yet the mechanisms of how zinc deficiency arrests these processes remain enigmatic. Here we induce subtle zinc perturbations and track asynchronously cycling cells throughout division using fluorescent reporters, high throughput microscopy, and quantitative analysis. Zinc deficiency induces quiescence and resupply stimulates synchronized cell-cycle reentry. Monitoring cells before and after zinc deprivation we found the position of cells within the cell cycle determined whether they either went quiescent or entered another cell cycle but stalled in S-phase. Stalled cells exhibited prolonged S-phase, were defective in DNA synthesis and had increased DNA damage levels, suggesting a role for zinc in maintaining genome integrity. Finally, we demonstrate zinc deficiency-induced quiescence occurs independently of DNA-damage response pathways, and is distinct from mitogen removal and spontaneous quiescence. This suggests a novel pathway to quiescence and reveals essential micronutrients play a role in cell cycle regulation.
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Affiliation(s)
- Maria N Lo
- Department of BiochemistryUniversity of Colorado, BoulderBoulderUnited States
- BioFrontiers InstituteUniversity of Colorado, BoulderBoulderUnited States
| | - Leah J Damon
- Department of BiochemistryUniversity of Colorado, BoulderBoulderUnited States
- BioFrontiers InstituteUniversity of Colorado, BoulderBoulderUnited States
| | - Jian Wei Tay
- Department of BiochemistryUniversity of Colorado, BoulderBoulderUnited States
- BioFrontiers InstituteUniversity of Colorado, BoulderBoulderUnited States
| | - Shang Jia
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
| | - Amy E Palmer
- Department of BiochemistryUniversity of Colorado, BoulderBoulderUnited States
- BioFrontiers InstituteUniversity of Colorado, BoulderBoulderUnited States
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23
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Koebke KJ, Batelu S, Kandegedara A, Smith SR, Stemmler TL. Refinement of protein Fe(II) binding characteristics utilizing a competition assay exploiting small molecule ferrous chelators. J Inorg Biochem 2020; 203:110882. [PMID: 31683123 DOI: 10.1016/j.jinorgbio.2019.110882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Iron is the most prevalent metal in biology. Its chemical and redox versatility allows it to direct activity of many Fe binding proteins. While iron's biological applications are diverse, challenges inherent in having Fe(II) present at high abundance means cells must ensure delivery to the correct recipient, while also ensuring its chemistry is regulated. Having a detailed understanding of the biophysical characteristics of a protein's iron binding characteristics allows us to understand general cellular metal homeostasis events. Unfortunately, most spectroscopic techniques available to measure metal binding affinity require protein be in a homogeneous state. Homogeneity creates an artificial environment when measuring metal binding since within cells numerous additional metal binding biomolecules compete with the target. Here we investigate commercially available Fe(II) chelators with spectral markers coupled to metal binding and release. Our goal was to determine their utility as competitors while measuring aspects of metal binding by apoproteins during a metal binding competition assay. Adding chelators during apoprotein metal binding mimics heterogeneous metal binding environments present in vivo, and provides a more realistic metal binding affinity measurement. Ferrous chelators explored within this report include: Rhod-5N, Magfura-2, Fura-4F, Fura-2, and TPA (Tris-(2-byridyl-methyl)amine; each forms a 1:1 complex with Fe(II) and combined cover a binding range of 5 orders of magnitude (micromolar to nanomolar Kd). These chelators were used to calibrate binding affinities for yeast and fly frataxin (Yfh1 and Dfh, respectively), involved in mitochondrial FeS cluster bioassembly.
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Affiliation(s)
- Karl J Koebke
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Ashoka Kandegedara
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sheila R Smith
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI 48101, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA.
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24
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Wang S, Korenchan DE, Perez PM, Taglang C, Hayes TR, Sriram R, Bok R, Hong AS, Wu Y, Li H, Wang Z, Kurhanewicz J, Wilson DM, Flavell RR. Amino Acid-Derived Sensors for Specific Zn 2+ Detection Using Hyperpolarized 13 C Magnetic Resonance Spectroscopy. Chemistry 2019; 25:11842-11846. [PMID: 31338914 PMCID: PMC6742520 DOI: 10.1002/chem.201902771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/14/2019] [Indexed: 11/05/2022]
Abstract
Alterations in Zn2+ concentration are seen in normal tissues and in disease states, and for this reason imaging of Zn2+ is an area of active investigation. Herein, enriched [1-13 C]cysteine and [1-13 C2 ]iminodiacetic acid were developed as Zn2+ -specific imaging probes using hyperpolarized 13 C magnetic resonance spectroscopy. [1-13 C]cysteine was used to accurately quantify Zn2+ in complex biological mixtures. These sensors can be employed to detect Zn2+ via imaging mechanisms including changes in 13 C chemical shift, resonance linewidth, or T1 .
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Affiliation(s)
- Sinan Wang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - David E Korenchan
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Paola M Perez
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Céline Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Thomas R Hayes
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Renuka Sriram
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Robert Bok
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Andrew S Hong
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Yunkou Wu
- Department of Radiology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Henry Li
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Zhen Wang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - John Kurhanewicz
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94107, USA
| | - David M Wilson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
| | - Robert R Flavell
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA (USA, 94107, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94107, USA
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25
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Scaramuzzo FA, Badetti E, Licini G, Zonta C. Extending substrate sensing capabilities of zinc tris(2‐pyridylmethyl)amine‐based stereodynamic probe. Chirality 2019; 31:375-383. [DOI: 10.1002/chir.23064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/16/2023]
Affiliation(s)
| | - Elena Badetti
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padova Padova Italy
| | - Giulia Licini
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padova Padova Italy
| | - Cristiano Zonta
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padova Padova Italy
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26
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Uh K, Ryu J, Zhang L, Errington J, Machaty Z, Lee K. Development of novel oocyte activation approaches using Zn2+ chelators in pigs. Theriogenology 2019; 125:259-267. [DOI: 10.1016/j.theriogenology.2018.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/31/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
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27
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Su X, Jessop PG, Cunningham MF. ATRP Catalyst Removal and Ligand Recycling Using CO2-Switchable Materials. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xin Su
- Department of Chemical Engineering, Queen’s University, 19 Division Street, Kingston, Ontario, Canada K7L 3N6
| | - Philip G. Jessop
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| | - Michael F. Cunningham
- Department of Chemical Engineering, Queen’s University, 19 Division Street, Kingston, Ontario, Canada K7L 3N6
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28
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Schnaars C, Kildahl-Andersen G, Prandina A, Popal R, Radix S, Le Borgne M, Gjøen T, Andresen AMS, Heikal A, Økstad OA, Fröhlich C, Samuelsen Ø, Lauksund S, Jordheim LP, Rongved P, Åstrand OAH. Synthesis and Preclinical Evaluation of TPA-Based Zinc Chelators as Metallo-β-lactamase Inhibitors. ACS Infect Dis 2018; 4:1407-1422. [PMID: 30022668 DOI: 10.1021/acsinfecdis.8b00137] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rise of antimicrobial resistance (AMR) worldwide and the increasing spread of multi-drug-resistant organisms expressing metallo-β-lactamases (MBL) require the development of efficient and clinically available MBL inhibitors. At present, no such inhibitor is available, and research is urgently needed to advance this field. We report herein the development, synthesis, and biological evaluation of chemical compounds based on the selective zinc chelator tris-picolylamine (TPA) that can restore the bactericidal activity of Meropenem (MEM) against Pseudomonas aeruginosa and Klebsiella pneumoniae expressing carbapenemases Verona integron-encoded metallo-β-lactamase (VIM-2) and New Delhi metallo-β-lactamase 1 (NDM-1), respectively. These adjuvants were prepared via standard chemical methods and evaluated in biological assays for potentiation of MEM against bacteria and toxicity (IC50) against HepG2 human liver carcinoma cells. One of the best compounds, 15, lowered the minimum inhibitory concentration (MIC) of MEM by a factor of 32-256 at 50 μM within all tested MBL-expressing clinical isolates and showed no activity toward serine carbapenemase expressing isolates. Biochemical assays with purified VIM-2 and NDM-1 and 15 resulted in inhibition kinetics with kinact/ KI of 12.5 min-1 mM-1 and 0.500 min-1 mM-1, respectively. The resistance frequency of 15 at 50 μM was in the range of 10-7 to 10-9. 15 showed good tolerance in HepG2 cells with an IC50 well above 100 μM, and an in vivo study in mice showed no acute toxic effects even at a dose of 128 mg/kg.
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Affiliation(s)
| | | | - Anthony Prandina
- Université de Lyon, Université Lyon 1, Faculté de
Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry,
SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7, 69373 Lyon Cedex 8, France
| | | | - Sylvie Radix
- Université de Lyon, Université Lyon 1, Faculté de
Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry,
SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7, 69373 Lyon Cedex 8, France
| | - Marc Le Borgne
- Université de Lyon, Université Lyon 1, Faculté de
Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry,
SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7, 69373 Lyon Cedex 8, France
| | | | | | - Adam Heikal
- Centre for Integrative
Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Ole Andreas Økstad
- Centre for Integrative
Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Christopher Fröhlich
- Norwegian National
Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- NorStruct, Department of Chemistry, Faculty of Science and Technology,
SIVA Innovation Centre, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National
Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Department of Pharmacy, UiT − The Arctic University of Norway, 9037 Tromsø, Norway
| | - Silje Lauksund
- Norwegian National
Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Lars Petter Jordheim
- Université Lyon, Université Claude Bernard Lyon 1, INSERM
1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche
en Cancérologie de Lyon, Lyon 69008, France
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29
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Pierre VC, Harris SM, Pailloux SL. Comparing Strategies in the Design of Responsive Contrast Agents for Magnetic Resonance Imaging: A Case Study with Copper and Zinc. Acc Chem Res 2018; 51:342-351. [PMID: 29356506 DOI: 10.1021/acs.accounts.7b00301] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Magnetic resonance imaging (MRI) has emerged over the years as one of the preferred modalities for medical diagnostic and biomedical research. It has the advantage over other imaging modalities such as positron emission tomography and X-ray of affording high resolution three-dimensional images of the body without using harmful radiation. The use of contrast agents has further expanded this technique by increasing the contrast between regions where they accumulate and background tissues. As MRI most often measures the relaxation rate of water throughout the body, contrast agents function by modulating the intensity of the water signal either via improved relaxation or via saturation transfer to selected exchangeable proton. Among the growing class of MRI contrast agents, a subset of them called "smart" contrast agents function as responsive probes. Their ability to increase or decrease their signal intensity is modulated by the presence of an analyte. These probes offer the unique ability to image the distribution of an analyte in vivo, thereby opening new possibilities for diagnostics and for elucidating the role of specific analytes in various pathologies or biological processes. A number of different strategies can be exploited to design responsive MRI contrast agents. The majority of contrast agents are based on GdIII complexes. These complexes can be rendered responsive in either of two ways: either by modulating the number of inner-sphere water molecules, q, or via modulating the rotational correlation time, τR, of the contrast agent upon substrate binding. The longitudinal relaxivity increases with the number of inner-sphere water molecules. GdIII complexes can be rendered responsive if they contain a recognition moiety that can bind to both the open coordination site of GdIII and to the analyte. When the recognition moiety leaves the lanthanide ion to bind to the analyte, q increases and therefore so does the relaxivity. The dependence of relaxivity on rotational correlation time is more complex and more pronounced at lower magnetic fields. In general, slower tumbling macromolecules have longer rotational correlation times and higher relaxivities. Analyte-triggered formation of macromolecules thus also increases relaxivity. Such macromolecules can either be analyte-templated supramolecular assemblies, or analyte-enhanced protein-contrast agent complexes. Chemical Exchange Saturation Transfer (CEST) agents are a newer class of contrast agents that offer the possibility of multifrequency and thus ratiometric imaging, which in turn enables quantitative mapping of the concentration of an analyte in vivo under conditions where the concentration of the contrast agent is not known. Such agents can be rendered responsive if the analyte changes the number of exchangeable proton(s), its exchange rate, or its chemical shift. All of these approaches have been successfully employed for detecting and imaging both copper and zinc, including in vivo. Magnetic Iron Oxide Nanoparticles (MIONs) are powerful MRI transverse relaxation agents. They can also be rendered responsive to an analyte if the latter can control the aggregation of the nanoparticles. For metal ions, this can be achieved via chemical functionalities that only react to form conjugates in the presence of the metal ion analyte.
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Affiliation(s)
- Valérie C. Pierre
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Sarah M. Harris
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Sylvie L. Pailloux
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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30
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Goldberg JM, Wang F, Sessler CD, Vogler NW, Zhang DY, Loucks WH, Tzounopoulos T, Lippard SJ. Photoactivatable Sensors for Detecting Mobile Zinc. J Am Chem Soc 2018; 140:2020-2023. [PMID: 29384658 PMCID: PMC5935517 DOI: 10.1021/jacs.7b12766] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fluorescent sensors for mobile zinc are valuable for studying complex biological systems. Because these sensors typically bind zinc rapidly and tightly, there has been little temporal control over the activity of the probe after its application to a sample. The ability to control the activity of a zinc sensor in vivo during imaging experiments would greatly improve the time resolution of the measurement. Here, we describe photoactivatable zinc sensors that can be triggered with short pulses of UV light. These probes are prepared by functionalizing a zinc sensor with protecting groups that render the probe insensitive to metal ions. Photoinduced removal of the protecting groups restores the binding site, allowing for zinc-responsive changes in fluorescence that can be observed in live cells and tissues.
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Affiliation(s)
- Jacob M. Goldberg
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fang Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Chanan D. Sessler
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nathan W. Vogler
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Daniel Y. Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - William H. Loucks
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thanos Tzounopoulos
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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31
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Blakemore LJ, Trombley PQ. Zinc as a Neuromodulator in the Central Nervous System with a Focus on the Olfactory Bulb. Front Cell Neurosci 2017; 11:297. [PMID: 29033788 PMCID: PMC5627021 DOI: 10.3389/fncel.2017.00297] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/06/2017] [Indexed: 12/19/2022] Open
Abstract
The olfactory bulb (OB) is central to the sense of smell, as it is the site of the first synaptic relay involved in the processing of odor information. Odor sensations are first transduced by olfactory sensory neurons (OSNs) before being transmitted, by way of the OB, to higher olfactory centers that mediate olfactory discrimination and perception. Zinc is a common trace element, and it is highly concentrated in the synaptic vesicles of subsets of glutamatergic neurons in some brain regions including the hippocampus and OB. In addition, zinc is contained in the synaptic vesicles of some glycinergic and GABAergic neurons. Thus, zinc released from synaptic vesicles is available to modulate synaptic transmission mediated by excitatory (e.g., N-methyl-D aspartate (NMDA), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)) and inhibitory (e.g., gamma-aminobutyric acid (GABA), glycine) amino acid receptors. Furthermore, extracellular zinc can alter the excitability of neurons through effects on a variety of voltage-gated ion channels. Consistent with the notion that zinc acts as a regulator of neuronal activity, we and others have shown zinc modulation (inhibition and/or potentiation) of amino acid receptors and voltage-gated ion channels expressed by OB neurons. This review summarizes the locations and release of vesicular zinc in the central nervous system (CNS), including in the OB. It also summarizes the effects of zinc on various amino acid receptors and ion channels involved in regulating synaptic transmission and neuronal excitability, with a special emphasis on the actions of zinc as a neuromodulator in the OB. An understanding of how neuroactive substances such as zinc modulate receptors and ion channels expressed by OB neurons will increase our understanding of the roles that synaptic circuits in the OB play in odor information processing and transmission.
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Affiliation(s)
- Laura J Blakemore
- Program in Neuroscience, Florida State UniversityTallahassee, FL, United States.,Department of Biological Science, Florida State UniversityTallahassee, FL, United States
| | - Paul Q Trombley
- Program in Neuroscience, Florida State UniversityTallahassee, FL, United States.,Department of Biological Science, Florida State UniversityTallahassee, FL, United States
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32
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The zinc paradigm for metalloneurochemistry. Essays Biochem 2017; 61:225-235. [DOI: 10.1042/ebc20160073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/10/2017] [Accepted: 03/28/2017] [Indexed: 01/06/2023]
Abstract
Neurotransmission and sensory perception are shaped through metal ion–protein interactions in various brain regions. The term "metalloneurochemistry" defines the unique field of bioinorganic chemistry focusing on these processes, and zinc has been the leading target of metalloneurochemists in the almost 15 years since the definition was introduced. Zinc in the hippocampus interacts with receptors that dictate ion flow and neurotransmitter release. Understanding the intricacies of these interactions is crucial to uncovering the role that zinc plays in learning and memory. Based on receptor similarities and zinc-enriched neurons (ZENs) in areas of the brain responsible for sensory perception, such as the olfactory bulb (OB), and dorsal cochlear nucleus (DCN), zinc participates in odor and sound perception. Development and improvement of methods which allow for precise detection and immediate manipulation of zinc ions in neuronal cells and in brain slices will be critical in uncovering the synaptic action of zinc and, more broadly, the bioinorganic chemistry of cognition.
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33
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Qin Y, Sammond DW, Braselmann E, Carpenter MC, Palmer AE. Development of an Optical Zn 2+ Probe Based on a Single Fluorescent Protein. ACS Chem Biol 2016; 11:2744-2751. [PMID: 27467056 DOI: 10.1021/acschembio.6b00442] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Various fluorescent probes have been developed to reveal the biological functions of intracellular labile Zn2+. Here, we present Green Zinc Probe (GZnP), a novel genetically encoded Zn2+ sensor design based on a single fluorescent protein (single-FP). The GZnP sensor is generated by attaching two zinc fingers (ZF) of the transcription factor Zap1 (ZF1 and ZF2) to the two ends of a circularly permuted green fluorescent protein (cpGFP). Formation of ZF folds induces interaction between the two ZFs, which induces a change in the cpGFP conformation, leading to an increase in fluorescence. A small sensor library is created to include mutations in the ZFs, cpGFP and linkers between ZF and cpGFP to improve signal stability, sensor brightness and dynamic range based on rational protein engineering, and computational design by Rosetta. Using a cell-based library screen, we identify sensor GZnP1, which demonstrates a stable maximum signal, decent brightness (QY = 0.42 at apo state), as well as specific and sensitive response to Zn2+ in HeLa cells (Fmax/Fmin = 2.6, Kd = 58 pM, pH 7.4). The subcellular localizing sensors mito-GZnP1 (in mitochondria matrix) and Lck-GZnP1 (on plasma membrane) display sensitivity to Zn2+ (Fmax/Fmin = 2.2). This sensor design provides freedom to be used in combination with other optical indicators and optogenetic tools for simultaneous imaging and advancing our understanding of cellular Zn2+ function.
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Affiliation(s)
- Yan Qin
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Deanne W. Sammond
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Esther Braselmann
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Margaret C. Carpenter
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Amy E. Palmer
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
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34
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Zinc-sensitive MRI contrast agent detects differential release of Zn(II) ions from the healthy vs. malignant mouse prostate. Proc Natl Acad Sci U S A 2016; 113:E5464-71. [PMID: 27562169 DOI: 10.1073/pnas.1609450113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Many secretory tissues release Zn(II) ions along with other molecules in response to external stimuli. Here we demonstrate that secretion of Zn(II) ions from normal, healthy prostate tissue is stimulated by glucose in fasted mice and that release of Zn(II) can be monitored by MRI. An ∼50% increase in water proton signal enhancement is observed in T1-weighted images of the healthy mouse prostate after infusion of a Gd-based Zn(II) sensor and an i.p. bolus of glucose. Release of Zn(II) from intracellular stores was validated in human epithelial prostate cells in vitro and in surgically exposed prostate tissue in vivo using a Zn(II)-sensitive fluorescent probe known to bind to the extracellular surface of cells. Given the known differences in intracellular Zn(II) stores in healthy versus malignant prostate tissues, the Zn(II) sensor was then evaluated in a transgenic adenocarcinoma of the mouse prostate (TRAMP) model in vivo. The agent proved successful in detecting small malignant lesions as early as 11 wk of age, making this noninvasive MR imaging method potentially useful for identifying prostate cancer in situations where it may be difficult to detect using current multiparametric MRI protocols.
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35
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Zinc Chelation Mediates the Lysosomal Disruption without Intracellular ROS Generation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:6724585. [PMID: 27123155 PMCID: PMC4829717 DOI: 10.1155/2016/6724585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/23/2016] [Accepted: 03/08/2016] [Indexed: 01/28/2023]
Abstract
We report the molecular mechanism for zinc depletion caused by TPEN (N,N,N′,N′-Tetrakis(2-pyridylmethyl)ethylenediamine) in neuroblastoma cells. The activation of p38 MAP kinase and subsequently caspase 3 is not due to or followed by redox imbalance or ROS generation, though these are commonly observed in literature. We found that TPEN is not responsible for ROS generation and the mechanism involves essentially lysosomal disruption caused by intracellular zinc depletion. We also observed a modest activation of Bax and no changes in the Bcl-2 proteins. As a result, we suggest that TPEN causes intracellular zinc depletion which can influence the breakdown of lysosomes and cell death without ROS generation.
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36
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Zhang G, Gruskos JJ, Afzal MS, Buccella D. Visualizing changes in mitochondrial Mg 2+ during apoptosis with organelle-targeted triazole-based ratiometric fluorescent sensors. Chem Sci 2015; 6:6841-6846. [PMID: 29861926 PMCID: PMC5947525 DOI: 10.1039/c5sc02442k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/15/2015] [Indexed: 12/31/2022] Open
Abstract
Magnesium is one of the most abundant metals in cells and is essential for a wide range of cellular processes. Magnesium imbalance has been linked to a variety of diseases, but the scarcity of sensors suitable for detection of Mg2+ with subcellular resolution has hampered the study of compartmentalization and mobilization of this ion in the context of physiological and pathological processes. We report herein a family of fluorescent probes for targeted detection of free Mg2+ in specific intracellular organelles, and its application in the study of programmed cell death. The new sensors feature a triazole unit that plays both structural and electronic roles by serving as an attachment group for targeting moieties, and modulating a possible internal charge transfer process for ratiometric ion sensing. A probe decorated with an alkylphosphonium group was employed for the detection of mitochondrial Mg2+ in live HeLa cells, providing the first direct observation of an increase in free Mg2+ levels in this organelle in the early stages of Staurosporine-induced apoptosis.
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Affiliation(s)
- G Zhang
- Department of Chemistry , New York University , New York 10003 , USA .
| | - J J Gruskos
- Department of Chemistry , New York University , New York 10003 , USA .
| | - M S Afzal
- Department of Chemistry , New York University , New York 10003 , USA .
| | - D Buccella
- Department of Chemistry , New York University , New York 10003 , USA .
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37
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Libardo MDJ, Angeles-Boza AM. Bioinorganic Chemistry of Antimicrobial and Host-Defense Peptides. COMMENT INORG CHEM 2014. [DOI: 10.1080/02603594.2014.960923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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