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Magaji UF, Coremen M, Karabulut Bulan O, Sacan O, Yanardag R. Biochemical and Histological Effects of Moringa oleifera Extract against Valproate-Induced Kidney Damage. J Med Food 2024; 27:533-544. [PMID: 38836511 DOI: 10.1089/jmf.2023.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
Valproic acid is an effective treatment for generalized seizure and related neurological defects. Despite its efficacy and acceptability, its use is associated with adverse drug effects. Moringa oleifera leaves are rich in phytochemical and nutritional components. It has excellent antioxidant and ethnobotanical benefits, thus popular among folk medicines and nutraceuticals. In the present study, 70% ethanol extract of moringa leaves was assessed for its in vivo biochemical and histological effects against valproate-induced kidney damage. Female Sprague-Dawley rats were randomly divided into four groups: Group I: control animals given physiological saline (n = 8); Group II: Moringa extract-administered group (0.3 g/kg b.w./day, n = 8); Group III: valproate-administered animals (0.5 g/kg b.w./day, n = 15); and Group IV: valproate + moringa extract (given similar doses of both valproate and moringa extract, n = 12) administered group. Treatments were administered orally for 15 days, the animals were fasted overnight, anesthetized, and then tissue samples harvested. In the valproate-administered experimental group, serum urea and uric acid were elevated. In the kidney tissue of the valproate rats, glutathione was depleted, antioxidant enzyme activities (superoxide dismutase, catalase, glutathione reductase, glutathione S-transferase, and glutathione peroxidase) disrupted, while oxidative stress biomarker, inflammatory proteins (Tumor necrosis factor-alpha and interleukin-6), histological damage scores, and the number of PCNA-positive cells were elevated. M. oleifera attenuated all these biochemical defects through its plethora of diverse antioxidant and therapeutic properties.
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Affiliation(s)
- Umar Faruk Magaji
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
- Department of Biochemistry and Molecular Biology, Federal University Birnin Kebbi, Birnin Kebbi, Nigeria
| | - Melis Coremen
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | - Omur Karabulut Bulan
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | - Ozlem Sacan
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
| | - Refiye Yanardag
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
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Bazzicalupi C, Grimmer C, Nikolayenko IV. Old Acquaintances and Novel Complex Structures for the Ni(II) and Cu(II) Complexes of bis-Chelate Oxime-Amide Ligands. Molecules 2024; 29:522. [PMID: 38276599 PMCID: PMC10819512 DOI: 10.3390/molecules29020522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
In the process of systematically studying the methylhydroxyiminoethaneamide bis-chelate ligands with polymethylene spacers of different lengths, L1-L3, and their transition metal complexes, a number of new Ni(II) and Cu(II) species have been isolated, and their molecular and crystal structures were determined using single-crystal X-ray diffraction. In all of these compounds, the divalent metal is coordinated by the ligand donor atoms in a square-planar arrangement. In addition, a serendipitously discovered new type of neutral Ni(II) complex, where the propane spacer of ligand L2 underwent oxidation to the propene spacer, and one of the amide groups was oxidised to the ketoimine, is also reported. The resulting ligand L2' affords the formation of neutral planar Ni(II) complexes, which are assembled in the solid state on top of each other, and yield two polymorphic structures. In both structures, the resulting infinite, exclusively parallel metal ion columns in ligand insulation may serve as precursor materials for sub-nano-conducting connectors. Overall, this paper reports the synthesis and characterisation of seven new anionic, cationic, and neutral Ni(II) and Cu(II) complexes, their crystal structures, as well as experimental and computed UV-Vis absorption spectra for two structurally similar Ni(II) complexes, yellow and red.
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Affiliation(s)
- Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Craig Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg 3200, South Africa; (C.G.); (I.V.N.)
| | - Igor Vasyl Nikolayenko
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg 3200, South Africa; (C.G.); (I.V.N.)
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Ling ZN, Jiang YF, Ru JN, Lu JH, Ding B, Wu J. Amino acid metabolism in health and disease. Signal Transduct Target Ther 2023; 8:345. [PMID: 37699892 PMCID: PMC10497558 DOI: 10.1038/s41392-023-01569-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/12/2023] [Accepted: 07/13/2023] [Indexed: 09/14/2023] Open
Abstract
Amino acids are the building blocks of protein synthesis. They are structural elements and energy sources of cells necessary for normal cell growth, differentiation and function. Amino acid metabolism disorders have been linked with a number of pathological conditions, including metabolic diseases, cardiovascular diseases, immune diseases, and cancer. In the case of tumors, alterations in amino acid metabolism can be used not only as clinical indicators of cancer progression but also as therapeutic strategies. Since the growth and development of tumors depend on the intake of foreign amino acids, more and more studies have targeted the metabolism of tumor-related amino acids to selectively kill tumor cells. Furthermore, immune-related studies have confirmed that amino acid metabolism regulates the function of effector T cells and regulatory T cells, affecting the function of immune cells. Therefore, studying amino acid metabolism associated with disease and identifying targets in amino acid metabolic pathways may be helpful for disease treatment. This article mainly focuses on the research of amino acid metabolism in tumor-oriented diseases, and reviews the research and clinical research progress of metabolic diseases, cardiovascular diseases and immune-related diseases related to amino acid metabolism, in order to provide theoretical basis for targeted therapy of amino acid metabolism.
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Affiliation(s)
- Zhe-Nan Ling
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China
| | - Yi-Fan Jiang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China
| | - Jun-Nan Ru
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China
| | - Jia-Hua Lu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China
| | - Bo Ding
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, Zhejiang Province, 310003, P.R. China.
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, Zhejiang Province, P.R. China.
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang Province, P.R. China.
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang Province, P.R. China.
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Xu Z, Chen L, Liu Y, Chen C, Sun Y, Miao Y, Wu T, Niu J, Wei J, Cao X. Study on the Interaction between Deuterium Clopidogrel and Omeprazole. Pharmacology 2022; 107:308-316. [DOI: 10.1159/000521721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/20/2021] [Indexed: 11/19/2022]
Abstract
<b><i>Introduction:</i></b> Dual antiplatelet therapy with aspirin in combination with a P2Y<sub>12</sub> receptor antagonist is a cornerstone for treating patients with acute coronary syndrome and in percutaneous coronary intervention. However, as this combination of antiplatelet therapy increases the risk of bleeding, proton pump inhibitors (PPIs) are currently recommended to prevent gastrointestinal ulcers and bleeding. The cytochrome P450 (CYP450) isoenzyme system metabolizes both clopidogrel (CLP) and PPIs. Unfortunately, omeprazole (OM) reduce the antiplatelet activity of CLP and increases the probability of recurrence of cardiovascular events by competitively inhibiting the CYP450 isoenzyme CYP2C19. <b><i>Methods:</i></b> To address these abovementioned problems, we designed and synthesized deuterium CLP (D-CL) using selective deuterium technology. Our previous research results showed that D-CL had better pharmacokinetic and pharmacodynamic properties. Thus, the HPLC-MS/MS method, cocktail method, Born method, electro-stimulated thrombus generation, and thrombus elastography were used to detect the production of thiol active metabolites (AM), CYP450 enzyme activities, platelet aggregation, time and length of thrombus formation, and the maximum clot strength after combination therapy. We investigated the pharmacokinetics and pharmacodynamics properties of D-CL combined with OM. <b><i>Results:</i></b> As compared to CLP, D-CL was less affected when combined with OM, which was reflected in lower inhibitory effects of CYP450 enzyme activities, a greater area under the curve of AM, and better antiplatelet and antithrombotic effects. <b><i>Conclusion:</i></b> D-CL may reduce drug-drug interactions and address the clinical disadvantages of CLP.
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Xu Z, Miao Y, Wu T, Chen L, Gao M, Sun Y, Liu Y, Niu J, Cai D, Li X, Chen C, Liu S, Gu J, Cao X. Evaluation of efficacy and safety after replacement of methyl hydrogen with deuterium at methyl formate of Clopidogrel. Eur J Pharm Sci 2022; 172:106157. [DOI: 10.1016/j.ejps.2022.106157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/03/2022]
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Lennartz M, Gehrig E, Weidemann S, Gorbokon N, Menz A, Büscheck F, Hube-Magg C, Hinsch A, Reiswich V, Höflmayer D, Fraune C, Jacobsen F, Bernreuther C, Lebok P, Sauter G, Wilczak W, Steurer S, Burandt E, Marx AH, Simon R, Krech T, Clauditz TS, Minner S, Dum D, Uhlig R. Large-Scale Tissue Microarray Evaluation Corroborates High Specificity of High-Level Arginase-1 Immunostaining for Hepatocellular Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11122351. [PMID: 34943588 PMCID: PMC8699869 DOI: 10.3390/diagnostics11122351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
Arginase-1 catalyzes the conversion of arginine to ornithine and urea. Because of its predominant expression in hepatocytes, it serves as a marker for hepatocellular carcinoma, although other tumor entities can also express arginase-1. To comprehensively determine arginase-1 expression in normal and neoplastic tissues, tissue microarrays containing 14,912 samples from 117 different tumor types and 608 samples of 76 different normal tissue types were analyzed by immunohistochemistry. In normal tissues, arginase-1 was expressed in the liver, the granular layer of the epidermis, and in granulocytes. Among tumors, a nuclear and cytoplasmic arginase-1 immunostaining was predominantly observed in hepatocellular carcinoma, where 96% of 49 cancers were at least moderately positive. Although 22 additional tumor categories showed occasional arginase immunostaining, strong staining was exceedingly rare in these entities. Staining of a few tumor cells was observed in squamous cell carcinomas of various sites. Staining typically involved maturing cells with the beginning of keratinization in these tumors and was significantly associated with a low grade in 635 squamous cell carcinomas of various sites (p = 0.003). Teratoma, urothelial carcinoma and pleomorphic adenomas sometimes also showed arginase expression in areas with squamous differentiation. In summary, arginase-1 immunohistochemistry is highly sensitive and specific for hepatocellular carcinoma if weak and focal staining is disregarded.
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Affiliation(s)
- Maximilian Lennartz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Eva Gehrig
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Sören Weidemann
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Natalia Gorbokon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Anne Menz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Viktor Reiswich
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Christoph Fraune
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Christian Bernreuther
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Patrick Lebok
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Andreas H. Marx
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
- Department of Pathology, Academic Hospital Fuerth, 90766 Fuerth, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
- Correspondence: ; Tel.: +49-40-74105-7214
| | - Till Krech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
- Institute of Pathology, Clinical Center Osnabrueck, 49076 Osnabrueck, Germany
| | - Till S. Clauditz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - David Dum
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
| | - Ria Uhlig
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (E.G.); (S.W.); (N.G.); (A.M.); (F.B.); (C.H.-M.); (A.H.); (V.R.); (D.H.); (C.F.); (F.J.); (C.B.); (P.L.); (G.S.); (W.W.); (S.S.); (E.B.); (A.H.M.); (T.K.); (T.S.C.); (S.M.); (D.D.); (R.U.)
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7
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Chen MC, Korth CC, Harnett MD, Elenko E, Lickliter JD. A Randomized Phase 1 Evaluation of Deupirfenidone, a Novel Deuterium-Containing Drug Candidate for Interstitial Lung Disease and Other Inflammatory and Fibrotic Diseases. Clin Pharmacol Drug Dev 2021; 11:220-234. [PMID: 34779583 DOI: 10.1002/cpdd.1040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/19/2021] [Indexed: 11/07/2022]
Abstract
LYT-100 (deupirfenidone) is a selectively deuterated form of pirfenidone under development for the treatment of inflammatory and fibrotic diseases, including interstitial lung disease. Adverse events associated with antifibrotics can be a barrier to adoption and persistence in patients with interstitial lung diseases, most of whom are not on standard-of-care therapy. LYT-100 is designed to have a differentiated pharmacokinetic (PK) profile from pirfenidone and could offer a differentiated safety profile compared to current standard-of-care drugs while retaining the biochemical potency and specificity of pirfenidone. We conducted a phase 1b study to ascertain the safety, tolerability, steady-state PK profile, and food effect of LYT-100. This was a 2-part study. Part 1 assessed multiple ascending doses of LYT-100 from 100, 250, 500, 750, and 1000 mg twice daily given over 5 days without titration. Part 2 assessed the effects of fed vs fasting conditions on the PK profile of a single 500-mg dose of LYT-100. All doses up to 1000 mg were well tolerated, with adverse events being mild and transient. Exposure was slightly lower in the fed condition. LYT-100 was well tolerated and has a dose-proportional PK profile. The ratio of parent to major metabolite concentration was higher than reported with pirfenidone, which is consistent with an effect of deuteration on metabolism. No maximum tolerated dose was identified up to 1000 mg twice-daily dosing. These results support further clinical development of LYT-100, particularly considering the adverse event profile of current standard-of-care drugs.
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8
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Khoshnejad M, Perales-Puchalt A, Dia Y, Xiao P, Patel A, Xu Z, Zhu X, Yun K, Baboo I, Qureshi R, Humeau L, Muthumani K, Weiner DB. Synthetic DNA Delivery of an Engineered Arginase Enzyme Can Modulate Specific Immunity In Vivo. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:652-663. [PMID: 32802913 PMCID: PMC7406982 DOI: 10.1016/j.omtm.2020.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022]
Abstract
Arginase is a complex and unique enzyme that plays diverse roles in health and disease. By metabolizing arginine, it can shape the outcome of innate and adaptive immune responses. The immunomodulatory capabilities of arginase could potentially be applied for local immunosuppression or induction of immune tolerance. With the use of an enhanced DNA delivery approach, we designed and studied a DNA-encoded secretable arginase enzyme as a tool for immune modulation and evaluated its immunomodulatory function in vivo. Strong immunosuppression of cluster of differentiation 4 (CD4) and CD8 T cells, as well as macrophages and dendritic cells, was observed in vitro in the presence of an arginase-rich supernatant. To further evaluate the efficacy of DNA-encoded arginase on in vivo immunosuppression against an antigen, a cancer antigen vaccine model was used in the presence or absence of DNA-encoded arginase. Significant in vivo immunosuppression was observed in the presence of DNA-encoded arginase. The efficacy of this DNA-encoded arginase delivery was examined in a local, imiquimod-induced, psoriasis-like, skin-inflammation model. Pretreatment of animals with the synthetic DNA-encoded arginase led to significant decreases in skin acanthosis, proinflammatory cytokines, and costimulatory molecules in extracted macrophages and dendritic cells. These results draw attention to the potential of direct in vivo-delivered arginase to function as an immunomodulatory agent for treatment of local inflammation or autoimmune diseases.
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Affiliation(s)
- Makan Khoshnejad
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alfredo Perales-Puchalt
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Yaya Dia
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Peng Xiao
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ami Patel
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xizhou Zhu
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Kun Yun
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ishana Baboo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Rehman Qureshi
- Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Laurent Humeau
- Inovio Pharmaceuticals, Inc., Plymouth Meeting, PA 19462, USA
| | - Kar Muthumani
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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9
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The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases. Catalysts 2020. [DOI: 10.3390/catal10091038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.
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10
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S. Clemente G, van Waarde A, F. Antunes I, Dömling A, H. Elsinga P. Arginase as a Potential Biomarker of Disease Progression: A Molecular Imaging Perspective. Int J Mol Sci 2020; 21:E5291. [PMID: 32722521 PMCID: PMC7432485 DOI: 10.3390/ijms21155291] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
Arginase is a widely known enzyme of the urea cycle that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. The action of arginase goes beyond the boundaries of hepatic ureogenic function, being widespread through most tissues. Two arginase isoforms coexist, the type I (Arg1) predominantly expressed in the liver and the type II (Arg2) expressed throughout extrahepatic tissues. By producing L-ornithine while competing with nitric oxide synthase (NOS) for the same substrate (L-arginine), arginase can influence the endogenous levels of polyamines, proline, and NO•. Several pathophysiological processes may deregulate arginase/NOS balance, disturbing the homeostasis and functionality of the organism. Upregulated arginase expression is associated with several pathological processes that can range from cardiovascular, immune-mediated, and tumorigenic conditions to neurodegenerative disorders. Thus, arginase is a potential biomarker of disease progression and severity and has recently been the subject of research studies regarding the therapeutic efficacy of arginase inhibitors. This review gives a comprehensive overview of the pathophysiological role of arginase and the current state of development of arginase inhibitors, discussing the potential of arginase as a molecular imaging biomarker and stimulating the development of novel specific and high-affinity arginase imaging probes.
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Affiliation(s)
- Gonçalo S. Clemente
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (G.S.C.); (A.v.W.); (I.F.A.)
| | - Aren van Waarde
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (G.S.C.); (A.v.W.); (I.F.A.)
| | - Inês F. Antunes
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (G.S.C.); (A.v.W.); (I.F.A.)
| | - Alexander Dömling
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Philip H. Elsinga
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (G.S.C.); (A.v.W.); (I.F.A.)
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11
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Hwangbo SA, Kim JW, Jung SJ, Jin KS, Lee JO, Kim JS, Park SY. Characterization of a Dimeric Arginase From Zymomonas mobilis ZM4. Front Microbiol 2019; 10:2755. [PMID: 32038508 PMCID: PMC6988801 DOI: 10.3389/fmicb.2019.02755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/12/2019] [Indexed: 12/23/2022] Open
Abstract
Many organisms have genes to protect themselves from toxic conditions such as high ethanol and/or ammonia concentrations. When a high ethanol condition is induced to Zymomonas mobilis ZM4, a representative ethanologenic organism, this bacterium overexpresses several genes to overcome this ethanol stress. Among them, we characterized a gene product annotated as an arginase (zmARG) from Z. mobilis ZM4. Even though all of the arginase-determining sequence motifs are not strictly conserved in zmARG, this enzyme converts L-arginine to urea and L-ornithine in the presence of a divalent manganese ion. The revealed high-resolution crystal structure of zmARG shows that it has a typical globular α/β arginase fold with a protruded C-terminal helix. Two zinc ions reside in the active site, where one metal ion is penta-coordinated and the other has six ligands, discerning this zmARG from the reported arginases with two hexa-liganded metal ions. zmARG forms a dimeric structure in solution as well as in the crystalline state. The dimeric assembly of zmARG is formed mainly by interaction formed between the C-terminal α-helix of one molecule and the α/β hydrolase fold of another molecule. The presented findings demonstrate the first reported dimeric arginase formed by the C-terminal tail and has two metal ions coordinated by different number of ligands.
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Affiliation(s)
- Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea.,Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, South Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Sun-Ju Jung
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
| | - Jie-Oh Lee
- Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, South Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
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12
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Koruza K, Lafumat B, Nyblom M, Mahon BP, Knecht W, McKenna R, Fisher SZ. Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX. Acta Crystallogr D Struct Biol 2019; 75:895-903. [PMID: 31588921 PMCID: PMC6778848 DOI: 10.1107/s2059798319010027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX-inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal contacts and packing reveals different arrangements of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography.
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Affiliation(s)
- K. Koruza
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B. Lafumat
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - M. Nyblom
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B. P. Mahon
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - W. Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - R. McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - S. Z. Fisher
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
- Scientific Activities Division, European Spallation Source ERIC, Odarslövsvägen 113, 224 84 Lund, Sweden
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13
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Van Zandt MC, Jagdmann GE, Whitehouse DL, Ji M, Savoy J, Potapova O, Cousido-Siah A, Mitschler A, Howard EI, Pyle AM, Podjarny AD. Discovery of N-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II. J Med Chem 2019; 62:8164-8177. [PMID: 31408339 DOI: 10.1021/acs.jmedchem.9b00931] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent efforts to identify new highly potent arginase inhibitors have resulted in the discovery of a novel family of (3R,4S)-3-amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic acid analogues with up to a 1000-fold increase in potency relative to the current standards, 2-amino-6-boronohexanoic acid (ABH) and N-hydroxy-nor-l-arginine (nor-NOHA). The lead candidate, with an N-2-amino-3-phenylpropyl substituent (NED-3238), example 43, inhibits arginase I and II with IC50 values of 1.3 and 8.1 nM, respectively. Herein, we report the design, synthesis, and structure-activity relationships for this novel series of inhibitors, along with X-ray crystallographic data for selected examples bound to human arginase II.
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Affiliation(s)
- Michael C Van Zandt
- New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States
| | - G Erik Jagdmann
- New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States
| | - Darren L Whitehouse
- New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States
| | - Minkoo Ji
- New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States
| | - Jennifer Savoy
- New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States
| | - Olga Potapova
- Department of Molecular, Cellular and Developmental Biology and Department of Chemistry, Howard Hughes Medical Institute , Yale University , 219 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Alexandra Cousido-Siah
- Department of Integrative Biology, IGBMC, CNRS, INSERM , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch , France
| | - Andre Mitschler
- Department of Integrative Biology, IGBMC, CNRS, INSERM , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch , France
| | - Eduardo I Howard
- Instituto de Fisica de Liquidos y Sistemas Biologicos (IFLYSIB) , CONICET , Calle 59 Numero 789 , 1900 La Plata , Buenos Aires , Argentina
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology and Department of Chemistry, Howard Hughes Medical Institute , Yale University , 219 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Alberto D Podjarny
- Department of Integrative Biology, IGBMC, CNRS, INSERM , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch , France
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14
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Garcia AR, Oliveira DMP, Claudia F Amaral A, Jesus JB, Rennó Sodero AC, Souza AMT, Supuran CT, Vermelho AB, Rodrigues IA, Pinheiro AS. Leishmania infantum arginase: biochemical characterization and inhibition by naturally occurring phenolic substances. J Enzyme Inhib Med Chem 2019; 34:1100-1109. [PMID: 31124384 PMCID: PMC6534257 DOI: 10.1080/14756366.2019.1616182] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Inhibition of Leishmania arginase leads to a decrease in parasite growth and infectivity and thus represents an attractive therapeutic strategy. We evaluated the inhibitory potential of selected naturally occurring phenolic substances on Leishmania infantum arginase (ARGLi) and investigated their antileishmanial activity in vivo. ARGLi exhibited a Vmax of 0.28 ± 0.016 mM/min and a Km of 5.1 ± 1.1 mM for L-arginine. The phenylpropanoids rosmarinic acid and caffeic acid (100 µM) showed percentages of inhibition of 71.48 ± 0.85% and 56.98 ± 5.51%, respectively. Moreover, rosmarinic acid and caffeic acid displayed the greatest effects against L. infantum with IC50 values of 57.3 ± 2.65 and 60.8 ± 11 μM for promastigotes, and 7.9 ± 1.7 and 21.9 ± 5.0 µM for intracellular amastigotes, respectively. Only caffeic acid significantly increased nitric oxide production by infected macrophages. Altogether, our results broaden the current spectrum of known arginase inhibitors and revealed promising drug candidates for the therapy of visceral leishmaniasis.
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Affiliation(s)
- Andreza R Garcia
- a Graduate Program in Pharmaceutical Sciences , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Danielle M P Oliveira
- b Department of Biochemistry , Institute of Chemistry, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Ana Claudia F Amaral
- c Department of Natural Products , Farmanguinhos, FIOCRUZ , Rio de Janeiro , Brazil
| | - Jéssica B Jesus
- d Department of Drugs and Medicines , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Ana Carolina Rennó Sodero
- d Department of Drugs and Medicines , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Alessandra M T Souza
- d Department of Drugs and Medicines , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Claudiu T Supuran
- e Neurofarba Department , Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche , Florence , Italy
| | - Alane B Vermelho
- f Department of General Microbiology , Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Igor A Rodrigues
- a Graduate Program in Pharmaceutical Sciences , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil.,g Department of Natural Products and Food , School of Pharmacy, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
| | - Anderson S Pinheiro
- b Department of Biochemistry , Institute of Chemistry, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
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15
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Kress T, Walrant A, Bodenhausen G, Kurzbach D. Long-Lived States in Hyperpolarized Deuterated Methyl Groups Reveal Weak Binding of Small Molecules to Proteins. J Phys Chem Lett 2019; 10:1523-1529. [PMID: 30864805 DOI: 10.1021/acs.jpclett.9b00149] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We introduce a method for the detection of weak interactions of small molecules such as metabolites or medicaments that contain deuterated methyl groups with proteins in solution. The technique relies on long-lived imbalances of spin state populations, which are generated by dissolution dynamic nuclear polarization (D-DNP) and feature lifetimes that depend on the frequency of internal rotation of deuterated methyl groups. We demonstrate the technique for interactions between deuterated dimethyl sulfoxide (DMSO- d6) and bovine serum albumin (BSA) or trypsin, where the methyl group rotation is slowed down upon protein binding, which causes a marked reduction in the lifetime of the population imbalances.
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Affiliation(s)
- Thomas Kress
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
- Faculty of Chemistry, Institute of Biological Chemistry , University of Vienna , Währinger Strasse 38 , 1090 Vienna , Austria
| | - Astrid Walrant
- Laboratoire des Biomolécules, LBM, École Normale Supérieure , Sorbonne Université, École Normale Supérieure, PSL University, CNRS , 75005 Paris , France
| | - Geoffrey Bodenhausen
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry , University of Vienna , Währinger Strasse 38 , 1090 Vienna , Austria
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16
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Ortega-Pierres MG, Argüello-García R. Giardia duodenalis: Role of secreted molecules as virulent factors in the cytotoxic effect on epithelial cells. ADVANCES IN PARASITOLOGY 2019; 106:129-169. [PMID: 31630757 DOI: 10.1016/bs.apar.2019.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During the course of giardiasis in humans and experimental models, G. duodenalis trophozoites express and secrete several proteins (ESPs) affecting structural, cellular and soluble components of the host intestinal milieu. These include the toxin-like molecules CRP136 and ESP58 that induce intestinal hyper-peristalsis. After the completion of the Giardia genome database and using up-to date transcriptomic and proteomic approaches, secreted 'virulence factors' have also been identified and experimentally characterized. This repertoire includes arginine deiminase (ADI) that competes for arginine, an important energy source for trophozoites, some high-cysteine membrane proteins (HCMPs) and VSP88, a versatile variant surface protein (VSP) that functions as an extracellular protease. Another giardial protein, enolase, moonlights as a metabolic enzyme that interacts with the fibrinolytic system and damages host epithelial cells. Other putative Giardia virulence factors are cysteine proteases that degrade multiple host components including mucin, villin, tight junction proteins, immunoglobulins, defensins and cytokines. One of these proteases, named giardipain-1, decreases transepithelial electrical resistance and induces apoptosis in epithelial cells. A putative role for tenascins, present in the Giardia's secretome, is interfering with the host epidermal growth factor. Based on the roles that these molecules play, drugs may be designed to interfere with their functions. This review presents a comprehensive description of secreted Giardia virulence factors. It further describes their cytotoxic mechanisms and roles in the pathophysiology of giardiasis, and then assesses their potential as targets for drug development.
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Affiliation(s)
- M Guadalupe Ortega-Pierres
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico City, Mexico.
| | - Raúl Argüello-García
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico City, Mexico
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17
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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18
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From Initial Hit to Crystal Optimization with Microseeding of Human Carbonic Anhydrase IX—A Case Study for Neutron Protein Crystallography. CRYSTALS 2018. [DOI: 10.3390/cryst8110434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human carbonic anhydrase IX (CA IX) is a multi-domain membrane protein that is therefore difficult to express or crystalize. To prepare crystals that are suitable for neutron studies, we are using only the catalytic domain of CA IX with six surface mutations, named surface variant (SV). The crystallization of CA IX SV, and also partly deuterated CA IX SV, was enabled by the use of microseed matrix screening (MMS). Only three drops with crystals were obtained after initial sparse matrix screening, and these were used as seeds in subsequent crystallization trials. Application of MMS, commercial screens, and refinement resulted in consistent crystallization and diffraction-quality crystals. The crystallization protocols and strategies that resulted in consistent crystallization are presented. These results demonstrate not only the use of MMS in the growth of large single crystals for neutron studies with defined conditions, but also that MMS enabled re-screening to find new conditions and consistent crystallization success.
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19
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Credille CV, Dick BL, Morrison CN, Stokes RW, Adamek RN, Wu NC, Wilson IA, Cohen SM. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem 2018; 61:10206-10217. [PMID: 30351002 DOI: 10.1021/acs.jmedchem.8b01363] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PAN endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PAN endonuclease, a class of highly active and selective fragments was developed that displays IC50 values <50 nM. This SAR led to structurally distinct molecules that also displayed IC50 values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.
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Affiliation(s)
- Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States.,The Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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20
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Schneider F, Erisson L, Beygi H, Bradbury M, Cohen-Barak O, Grachev ID, Guzy S, Loupe PS, Levi M, McDonald M, Savola JM, Papapetropoulos S, Tracewell WG, Velinova M, Spiegelstein O. Pharmacokinetics, metabolism and safety of deuterated L-DOPA (SD-1077)/carbidopa compared to L-DOPA/carbidopa following single oral dose administration in healthy subjects. Br J Clin Pharmacol 2018; 84:2422-2432. [PMID: 29959802 PMCID: PMC6138493 DOI: 10.1111/bcp.13702] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/12/2018] [Accepted: 06/22/2018] [Indexed: 11/29/2022] Open
Abstract
AIMS SD-1077, a selectively deuterated precursor of dopamine (DA) structurally related to L-3,4-dihydroxyphenylalanine (L-DOPA), is under development for treatment of motor symptoms of Parkinson's disease. Preclinical models have shown slower metabolism of central deuterated DA. The present study investigated the peripheral pharmacokinetics (PK), metabolism and safety of SD-1077. METHODS Plasma and urine PK of drug and metabolites and safety after a single oral 150 mg SD-1077 dose were compared to 150 mg L-DOPA, each in combination with 37.5 mg carbidopa (CD) in a double-blind, two-period, crossover study in healthy volunteers (n = 16). RESULTS Geometric least squares mean ratios (GMRs) and 90% confidence intervals (90% CI) of SD-1077 vs. L-DOPA for Cmax , AUC0-t , and AUC0-inf were 88.4 (75.9-103.1), 89.5 (84.1-95.3), and 89.6 (84.2-95.4), respectively. Systemic exposure to DA was significantly higher after SD-1077/CD compared to that after L-DOPA/CD, with GMRs (90% CI) of 1.8 (1.45-2.24; P = 0.0005) and 2.06 (1.68-2.52; P < 0.0001) for Cmax and AUC0-t and a concomitant reduction in the ratio of 3,4-dihydroxyphenylacetic acid/DA confirming slower metabolic breakdown of DA by monoamine oxidase (MAO). There were increases in systemic exposures to metabolites of catechol O-methyltransferase (COMT) reaction, 3-methoxytyramine (3-MT) and 3-O-methyldopa (3-OMD) with GMRs (90% CI) for SD-1077/CD to L-DOPA/CD for 3-MT exposure of 1.33 (1.14-1.56; P = 0.0077) and 1.66 (1.42-1.93; P < 0.0001) for Cmax and AUC0-t , respectively and GMRs (90% CI) for 3-OMD of 1.19 (1.15, 1.23; P < 0.0001) and 1.31 (1.27, 1.36; P < 0.0001) for Cmax and AUC0-t . SD-1077/CD exhibited comparable tolerability and safety to L-DOPA/CD. CONCLUSIONS SD-1077/CD demonstrated the potential to prolong exposure to central DA at comparable peripheral PK and safety to the reference L-DOPA/CD combination. A single dose of SD-1077 is safe for further clinical development in Parkinson's disease patients.
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Affiliation(s)
- Frank Schneider
- Global Research and Development, Teva Pharmaceutical Industries, Berlin, Germany
| | - Lavi Erisson
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - Hooman Beygi
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - Margaret Bradbury
- Formerly Global Research and Development Teva Pharmaceuticals, currently Prana Biotechnology, San Francisco, CA, USA
| | - Orit Cohen-Barak
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
| | - Igor D Grachev
- Global Research and Development, Teva Pharmaceutical Industries, Malvern, PA, USA
| | - Serge Guzy
- Pop-Pharm Pharmacometrics Service, Albany, CA, USA
| | - Pippa S Loupe
- Global Research and Development, Teva Pharmaceutical Industries, Overland Park, KS, USA
| | - Micha Levi
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - Mirna McDonald
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | | | | | - William G Tracewell
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - Maria Velinova
- PRA Health Sciences, Early Development Services, Groningen, the Netherlands
| | - Ofer Spiegelstein
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
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21
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Koruza K, Lafumat B, Végvári Á, Knecht W, Fisher S. Deuteration of human carbonic anhydrase for neutron crystallography: Cell culture media, protein thermostability, and crystallization behavior. Arch Biochem Biophys 2018. [DOI: 10.1016/j.abb.2018.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Maharem TM, Zahran WE, Hassan RE, Abdel Fattah MM. Unique properties of arginase purified from camel liver cytosol. Int J Biol Macromol 2018; 108:88-97. [DOI: 10.1016/j.ijbiomac.2017.11.141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
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23
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Abstract
Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12C, 14N, and nonexchangeable 1H by 13C, 15N, and 2H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis.
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24
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Synthesis of deuterium-enriched and fluorine-substituted plinabulin derivatives and evaluation of their antitumor activities. Mol Divers 2017; 21:577-583. [DOI: 10.1007/s11030-017-9742-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 04/16/2017] [Indexed: 01/16/2023]
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25
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Krzemińska A, Moliner V, Świderek K. Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease. J Am Chem Soc 2016; 138:16283-16298. [PMID: 27935692 DOI: 10.1021/jacs.6b06856] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labeling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal·mol-1. On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mold for future drug design.
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Affiliation(s)
- Agnieszka Krzemińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
| | - Katarzyna Świderek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland.,Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
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26
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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27
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Yukawa T, Fujimori I, Kamei T, Nakada Y, Sakauchi N, Yamada M, Ohba Y, Ueno H, Takiguchi M, Kuno M, Kamo I, Nakagawa H, Fujioka Y, Igari T, Ishichi Y, Tsukamoto T. Design, synthesis, and biological evaluation of a novel series of peripheral-selective noradrenaline reuptake inhibitors-Part 2. Bioorg Med Chem 2016; 24:3207-17. [PMID: 27255177 DOI: 10.1016/j.bmc.2016.05.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 11/29/2022]
Abstract
Peripherally selective inhibition of noradrenaline reuptake is a novel mechanism for the treatment of stress urinary incontinence to overcome adverse effects associated with central action. Herein, we describe our medicinal chemistry approach to discover peripheral-selective noradrenaline reuptake inhibitors to avert the risk of P-gp-mediated DDI at the blood-brain barrier. We observed that steric shielding of the hydrogen-bond acceptors and donors (HBA and HBD) of compound 1 reduced the multidrug resistance protein 1 (MDR1) efflux ratio; however, the resulting compound 6, a methoxyacetamide derivative, was mainly metabolized by CYP2D6 and CYP2C19 in the in vitro phenotyping study, implying the risk of PK variability based on the genetic polymorphism of the CYPs. Replacement of the hydrogen atom with a deuterium atom in a strategic, metabolically hot spot led to compound 13, which was mainly metabolized by CYP3A4. To our knowledge, this study represents the first report of the effect of deuterium replacement for a major metabolic enzyme. The compound 13, N-{[(6S,7R)-7-(4-chloro-3-fluorophenyl)-1,4-oxazepan-6-yl]methyl}-2-[(2H(3))methyloxy]acetamide hydrochloride, which exhibited peripheral NET selective inhibition at tested doses in rats, increased urethral resistance in a dose-dependent manner.
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Affiliation(s)
- Tomoya Yukawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Ikuo Fujimori
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Taku Kamei
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshihisa Nakada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Nobuki Sakauchi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masami Yamada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusuke Ohba
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroyuki Ueno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Maiko Takiguchi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masako Kuno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Izumi Kamo
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Nakagawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasushi Fujioka
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoko Igari
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuji Ishichi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tetsuya Tsukamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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28
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Li F, Jiang W, Czarnik AW, Li W. Combinatorial synthesis of deuterium-enriched (S)-oxybutynin. Mol Divers 2016; 20:605-10. [PMID: 26852022 DOI: 10.1007/s11030-016-9660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The concept of deuterium enrichment has gained more attention due to its advantages in the studies of clinical pharmacokinetics and metabolic profiles. In addition, it is cost and time efficient to develop deuterium-enriched drugs. Herein we built a combinatorial library of deuterated (S)-oxybutynins which all 8 D-compounds were characterized by MS, [Formula: see text] NMR and [Formula: see text]C NMR.
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Affiliation(s)
- Feng Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China.,Marine Biomedical Research Institute of Qingdao, Qingdao, 266073, People's Republic of China
| | - Wenfeng Jiang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China.,Marine Biomedical Research Institute of Qingdao, Qingdao, 266073, People's Republic of China
| | - Anthony W Czarnik
- Department of Chemistry, University of Nevada, Reno, Reno, 89557-0216, USA.
| | - Wenbao Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China. .,Marine Biomedical Research Institute of Qingdao, Qingdao, 266073, People's Republic of China.
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29
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Li F, Jiang W, Czarnik AW, Li W. Combinatorial synthesis of deuterium-enriched atorvastatin. Mol Divers 2016; 20:453-9. [PMID: 26809618 DOI: 10.1007/s11030-015-9655-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/29/2015] [Indexed: 11/30/2022]
Abstract
It becomes more and more difficult to discover a new drug by existing models. The concept of deuteration has gained attention due to its advantages in the study of clinical pharmacokinetics and metabolic profiles. Herein we built a library of deuterated atorvastatins using combinatorial chemistry, and all 16 D-compounds were characterized by 1H NMR, 13C NMR, MS, and elemental analysis.
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Affiliation(s)
- Feng Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Marine Biomedical Research Institute, Qingdao, 266071, China
| | - Wenfeng Jiang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Marine Biomedical Research Institute, Qingdao, 266071, China
| | - Anthony W Czarnik
- Department of Chemistry, University of Nevada, Reno, Reno, 89557-0216, USA.
| | - Wenbao Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China. .,Marine Biomedical Research Institute, Qingdao, 266071, China.
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Abstract
The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.
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Affiliation(s)
- Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, 2, Asashironishi, Kumatori, Osaka, 590-0494, Japan,
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31
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Golden E, Attwood PV, Duff AP, Meilleur F, Vrielink A. Production and characterization of recombinant perdeuterated cholesterol oxidase. Anal Biochem 2015; 485:102-8. [PMID: 26073659 DOI: 10.1016/j.ab.2015.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
Cholesterol oxidase (CO) is a FAD (flavin adenine dinucleotide) containing enzyme that catalyzes the oxidization and isomerization of cholesterol. Studies directed toward elucidating the catalytic mechanism of CO will provide an important general understanding of Flavin-assisted redox catalysis. Hydrogen atoms play an important role in enzyme catalysis; however, they are not readily visualized in protein X-ray diffraction structures. Neutron crystallography is an ideal method for directly visualizing hydrogen positions at moderate resolutions because hydrogen and deuterium have comparable neutron scattering lengths to other heavy atoms present in proteins. The negative coherent and large incoherent scattering lengths of hydrogen atoms in neutron diffraction experiments can be circumvented by replacing hydrogen atoms with its isotope, deuterium. The perdeuterated form of CO was successfully expressed from minimal medium, purified, and crystallized. X-ray crystallographic structures of the enzyme in the perdeuterated and hydrogenated states confirm that there are no apparent structural differences between the two enzyme forms. Kinetic assays demonstrate that perdeuterated and hydrogenated enzymes are functionally identical. Together, structural and functional studies indicate that the perdeuterated protein is suitable for structural studies by neutron crystallography directed at understanding the role of hydrogen atoms in enzyme catalysis.
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Affiliation(s)
- Emily Golden
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - Paul V Attwood
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - Anthony P Duff
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia.
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33
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Uttamsingh V, Gallegos R, Liu JF, Harbeson SL, Bridson GW, Cheng C, Wells DS, Graham PB, Zelle R, Tung R. Altering metabolic profiles of drugs by precision deuteration: reducing mechanism-based inhibition of CYP2D6 by paroxetine. J Pharmacol Exp Ther 2015; 354:43-54. [PMID: 25943764 DOI: 10.1124/jpet.115.223768] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/15/2015] [Indexed: 01/24/2023] Open
Abstract
Selective deuterium substitution as a means of ameliorating clinically relevant pharmacokinetic drug interactions is demonstrated in this study. Carbon-deuterium bonds are more stable than corresponding carbon-hydrogen bonds. Using a precision deuteration platform, the two hydrogen atoms at the methylenedioxy carbon of paroxetine were substituted with deuterium. The new chemical entity, CTP-347 [(3S,4R)-3-((2,2-dideuterobenzo[d][1,3]dioxol-5-yloxy)methyl)-4-(4-fluorophenyl)piperidine], demonstrated similar selectivity for the serotonin receptor, as well as similar neurotransmitter uptake inhibition in an in vitro rat synaptosome model, as unmodified paroxetine. However, human liver microsomes cleared CTP-347 faster than paroxetine as a result of decreased inactivation of CYP2D6. In phase 1 studies, CTP-347 was metabolized more rapidly in humans and exhibited a lower pharmacokinetic accumulation index than paroxetine. These alterations in the metabolism profile resulted in significantly reduced drug-drug interactions between CTP-347 and two other CYP2D6-metabolized drugs: tamoxifen (in vitro) and dextromethorphan (in humans). Our results show that precision deuteration can improve the metabolism profiles of existing pharmacotherapies without affecting their intrinsic pharmacologies.
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Affiliation(s)
| | | | - Julie F Liu
- Concert Pharmaceuticals, Inc., Lexington, Massachusetts
| | | | | | - Changfu Cheng
- Concert Pharmaceuticals, Inc., Lexington, Massachusetts
| | - David S Wells
- Concert Pharmaceuticals, Inc., Lexington, Massachusetts
| | | | - Robert Zelle
- Concert Pharmaceuticals, Inc., Lexington, Massachusetts
| | - Roger Tung
- Concert Pharmaceuticals, Inc., Lexington, Massachusetts
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34
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Wright TG, Pasch H. A simple route to deuterated polystyrene block copolymers by reverse iodine transfer polymerisation. Polym Chem 2015. [DOI: 10.1039/c5py00278h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the first time, deuterated polystyrene block copolymers were synthesized by RITP and analysed by advanced fractionation and spectroscopic methods.
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Affiliation(s)
- Trevor Gavin Wright
- Department of Chemistry and Polymer Science
- University of Stellenbosch
- Matieland 7602
- South Africa
| | - Harald Pasch
- Department of Chemistry and Polymer Science
- University of Stellenbosch
- Matieland 7602
- South Africa
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35
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Swiderek K, Ruiz-Pernía JJ, Moliner V, Tuñón I. Heavy enzymes--experimental and computational insights in enzyme dynamics. Curr Opin Chem Biol 2014; 21:11-8. [PMID: 24709164 DOI: 10.1016/j.cbpa.2014.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/14/2014] [Indexed: 11/18/2022]
Abstract
The role of protein motions in the chemical step of enzyme-catalyzed reactions is the subject of an open debate in the scientific literature. The systematic use of isotopically substituted enzymes has been revealed as a useful tool to quantify the role of these motions. According to the Born-Oppenheimer approximation, changing the mass of the protein does not change the forces acting on the system but alters the frequencies of the protein motions, which in turn can affect the rate constant. Experimental and theoretical studies carried out in this field are presented in this article and discussed in the framework of Transition State Theory.
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Affiliation(s)
- Katarzyna Swiderek
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - J Javier Ruiz-Pernía
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain.
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36
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Jäger K, Kielstein H, Dunse M, Nass N, Paulsen F, Sel S. Enzymes of urea synthesis are expressed at the ocular surface, and decreased urea in the tear fluid is associated with dry-eye syndrome. Graefes Arch Clin Exp Ophthalmol 2013; 251:1995-2002. [PMID: 23740519 DOI: 10.1007/s00417-013-2391-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022] Open
Abstract
PURPOSE The present study aims at determining whether enzymes of urea synthesis are expressed in the human lacrimal gland and in tissues of ocular surface (conjunctiva, cornea), to give evidence for the hypothesis that urea can be locally formed from ocular tissues and is important for the composition of the tear fluid. METHODS The presences of enzymes (arginase 1, 2 and agmatinase) that directly contribute to the formation of urea were investigated in the lacrimal gland and tissues of ocular surface by RT-PCR and immunohistochemistry. We collected tear fluid, aqueous humour, and blood samples from a total of 38 subjects, and tear fluid samples from a total of 78 subjects, with and without dry-eye syndrome (DES, keratoconjunctivitis sicca), and determined the urea concentration. RESULTS The enzymes arginase 1, 2 and agmatinase were expressed in all tissues examined except for arginase 1, which was not expressed in the cornea. There was no correlation of urea concentration in tear fluid with aqueous humour and blood plasma (r = 0.13, p = 0.58 and r = 0.45, p = 0.05 respectively). However, correlation of urea concentration between aqueous humour and blood plasma was highly significant (r = 0.7, p = 0.0001). The concentration of urea in the tear fluid of patients with DES compared to healthy control group was significantly reduced (p < 0.0001). CONCLUSION Enzymes that are directly involved in the formation of urea are expressed in ocular tissues. This may imply that in the ocular surface is a well-coordinated system of enzymes that can produce urea which might be independent of external urea supply.
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Affiliation(s)
- Kristin Jäger
- Department of Anatomy and Cell Biology, Martin Luther University of Halle-Wittenberg, Große Steinstraße, Halle/Saale, Germany.
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37
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Overexpression of (His) 6 -tagged human arginase I in Saccharomyces cerevisiae and enzyme purification using metal affinity chromatography. Protein Expr Purif 2012; 81:63-68. [DOI: 10.1016/j.pep.2011.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 08/21/2011] [Accepted: 09/07/2011] [Indexed: 11/20/2022]
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38
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Chatake T, Ishikawa T, Yanagisawa Y, Yamada T, Tanaka I, Fujiwara S, Morimoro Y. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1334-8. [PMID: 22102227 PMCID: PMC3212446 DOI: 10.1107/s1744309111031903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 08/06/2011] [Indexed: 11/11/2022]
Abstract
Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.
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Affiliation(s)
- Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, Ashashironishi 2, Kumatori, Osaka, Japan.
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39
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Piszczek G, Lee JC, Tjandra N, Lee CR, Seok YJ, Levine RL, Peterkofsky A. Deuteration of Escherichia coli enzyme I(Ntr) alters its stability. Arch Biochem Biophys 2011; 507:332-42. [PMID: 21185804 PMCID: PMC3058872 DOI: 10.1016/j.abb.2010.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/18/2010] [Indexed: 11/21/2022]
Abstract
Enzyme I(Ntr) is the first protein in the nitrogen phosphotransferase pathway. Using an array of biochemical and biophysical tools, we characterized the protein, compared its properties to that of EI of the carbohydrate PTS and, in addition, examined the effect of substitution of all nonexchangeable protons by deuterium (perdeuteration) on the properties of EI(Ntr). Notably, we find that the catalytic function (autophosphorylation and phosphotransfer to NPr) remains unperturbed while its stability is modulated by deuteration. In particular, the deuterated form exhibits a reduction of approximately 4°C in thermal stability, enhanced oligomerization propensity, as well as increased sensitivity to proteolysis in vitro. We investigated tertiary, secondary, and local structural changes, both in the absence and presence of PEP, using near- and far-UV circular dichroism and Trp fluorescence spectroscopy. Our data demonstrate that the aromatic residues are particularly sensitive probes for detecting effects of deuteration with an enhanced quantum yield upon PEP binding and apparent decreases in tertiary contacts for Tyr and Trp side chains. Trp mutagenesis studies showed that the region around Trp522 responds to binding of both PEP and NPr. The significance of these results in the context of structural analysis of EI(Ntr) are evaluated.
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Affiliation(s)
- Grzegorz Piszczek
- The National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Jennifer C. Lee
- The National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Nico Tjandra
- The National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Chang-Ro Lee
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742
| | - Rodney L. Levine
- The National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Alan Peterkofsky
- The National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
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40
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Riley E, Roberts SC, Ullman B. Inhibition profile of Leishmania mexicana arginase reveals differences with human arginase I. Int J Parasitol 2011; 41:545-52. [PMID: 21232540 DOI: 10.1016/j.ijpara.2010.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 12/09/2010] [Indexed: 12/25/2022]
Abstract
Arginase (ARG), the enzyme that catalyzes the conversion of arginine to ornithine and urea, is the first and committed step in polyamine biosynthesis in Leishmania. The creation of a conditionally lethal Δarg null mutant in Leishmania mexicana has established that ARG is an essential enzyme for the promastigote form of the parasite and that the enzyme provides an important defense mechanism for parasite survival in the eukaryotic host. Furthermore, human ARGI (HsARGI) has also been implicated as a key factor in parasite proliferation. Thus, inhibitors of ARG offer a rational paradigm for drug design. To initiate a search for inhibitors of the L. mexicana ARG (LmARG), recombinant LmARG and HsARGI enzymes were purified from Escherichia coli. Both LmARG and HsARGI were specific for l-arginine and exhibited no activity with either d-arginine or agmatine as possible substrates. LmARG exhibited a K(m) of 25±4mM for l-arginine, a pH optimum ∼9.0, and was dependent upon the presence of a divalent cation, preferentially manganese. A K(m) of 13.5 ± 2mM for l-arginine was calculated for the HsARGI. A collection of 37 compounds was evaluated against both enzymes. Twelve of these compounds were identified as being either strong inhibitors of both LmARG and HsARGI or differential inhibitors between the two enzymes. Of the 12 compounds, six were selected for further analysis and the type and extent of inhibition determined.
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Affiliation(s)
- Eric Riley
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239-3098, USA
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41
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42
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Synthesis of cobalt(III) complexes with novel open chain oxime ligands and metal–ligand coordination in aqueous solution. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Ilies M, Di Costanzo L, North ML, Scott JA, Christianson DW. 2-aminoimidazole amino acids as inhibitors of the binuclear manganese metalloenzyme human arginase I. J Med Chem 2010; 53:4266-76. [PMID: 20441173 DOI: 10.1021/jm100306a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Arginase, a key metalloenzyme of the urea cycle that converts L-arginine into L-ornithine and urea, is presently considered a pharmaceutical target for the management of diseases associated with aberrant l-arginine homeostasis, such as asthma, cardiovascular diseases, and erectile dysfunction. We now report the design, synthesis, and evaluation of a series of 2-aminoimidazole amino acid inhibitors in which the 2-aminoimidazole moiety serves as a guanidine mimetic. These compounds represent a new class of arginase inhibitors. The most potent inhibitor identified in this study, 2-(S)-amino-5-(2-aminoimidazol-1-yl)pentanoic acid (A1P, 10), binds to human arginase I with K(d) = 2 microM and significantly attenuates airways hyperresponsiveness in a murine model of allergic airways inflammation. These findings suggest that 2-aminoimidazole amino acids represent new leads for the development of arginase inhibitors with promising pharmacological profiles.
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Affiliation(s)
- Monica Ilies
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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44
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Zhu X, Ng SY, Gupta AN, Feng YP, Ho B, Lapp A, Egelhaaf SU, Forsyth VT, Haertlein M, Moulin M, Schweins R, van der Maarel JRC. Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061905. [PMID: 20866438 DOI: 10.1103/physreve.81.061905] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 03/18/2010] [Indexed: 05/29/2023]
Abstract
With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.
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Affiliation(s)
- Xiaoying Zhu
- Department of Physics, National University of Singapore, Singapore
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45
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Gardberg AS, Del Castillo AR, Weiss KL, Meilleur F, Blakeley MP, Myles DAA. Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:558-67. [PMID: 20445231 DOI: 10.1107/s0907444910005494] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 02/09/2010] [Indexed: 11/10/2022]
Abstract
The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.
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46
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Zhao X, Pan F, Lu JR. Interfacial assembly of proteins and peptides: recent examples studied by neutron reflection. J R Soc Interface 2009; 6 Suppl 5:S659-70. [PMID: 19656822 PMCID: PMC2843974 DOI: 10.1098/rsif.2009.0168.focus] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 07/08/2009] [Indexed: 01/31/2023] Open
Abstract
Through reviewing a number of recent neutron reflection studies of interfacial adsorption of peptides and proteins, this paper aims to demonstrate the significance of this technique in studying interfacial biomolecular processes by illustrating the typical structural details that can be derived. The review will start with the introduction of relevant theoretical background, followed by an outline of representative biomolecular systems that have recently been studied to indicate the technical strengths of neutron reflection.
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Affiliation(s)
| | | | - Jian R. Lu
- Biological Physics Group, University of Manchester, Schuster Building, Oxford Road, Manchester M13 9PL, UK
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47
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48
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Wells GA, Müller IB, Wrenger C, Louw AI. The activity of Plasmodium falciparum arginase is mediated by a novel inter-monomer salt-bridge between Glu295-Arg404. FEBS J 2009; 276:3517-30. [PMID: 19456858 DOI: 10.1111/j.1742-4658.2009.07073.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recent study implicated a role for Plasmodium falciparum arginase in the systemic depletion of arginine levels, which in turn has been associated with human cerebral malaria pathogenesis. Arginase (EC 3.5.3.1) is a multimeric metallo-protein that catalyses the hydrolysis of arginine to ornithine and urea by means of a binuclear spin-coupled Mn(2+) cluster in the active site. A previous report indicated that P. falciparum arginase has a strong dependency between trimer formation, enzyme activity and metal co-ordination. Mutations that abolished Mn(2+) binding also caused dissociation of the trimer; conversely, mutations that abolished trimer formation resulted in inactive monomers. By contrast, the monomers of mammalian (and therefore host) arginase are also active. P. falciparum arginase thus appears to be an obligate trimer and interfering with trimer formation may therefore serve as an alternative route to enzyme inhibition. In the present study, the mechanism of the metal dependency was explored by means of homology modelling and molecular dynamics. When the active site metals are removed, loss of structural integrity is observed. This is reflected by a larger equilibration rmsd for the protein when the active site metal is removed and some loss of secondary structure. Furthermore, modelling revealed the existence of a novel inter-monomer salt-bridge between Glu295 and Arg404, which was shown to be associated with the metal dependency. Mutational studies not only confirmed the importance of this salt-bridge in trimer formation, but also provided evidence for the independence of P. falciparum arginase activity on trimer formation.
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Affiliation(s)
- Gordon A Wells
- Department of Biochemistry, University of Pretoria, South Africa
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49
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Petit-Haertlein I, Blakeley MP, Howard E, Hazemann I, Mitschler A, Haertlein M, Podjarny A. Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:406-9. [PMID: 19342793 PMCID: PMC2664773 DOI: 10.1107/s1744309109008574] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/09/2009] [Indexed: 11/10/2022]
Abstract
The highly homologous type III antifreeze protein (AFP) subfamily share the capability to inhibit ice growth at subzero temperatures. Extensive studies by X-ray crystallography have been conducted, mostly on AFPs from polar fishes. Although interactions between a defined flat ice-binding surface and a particular lattice plane of an ice crystal have now been identified, the fine structural features underlying the antifreeze mechanism still remain unclear owing to the intrinsic difficulty in identifying H atoms using X-ray diffraction data alone. Here, successful perdeuteration (i.e. complete deuteration) for neutron crystallographic studies of the North Atlantic ocean pout (Macrozoarces americanus) AFP in Escherichia coli high-density cell cultures is reported. The perdeuterated protein (AFP D) was expressed in inclusion bodies, refolded in deuterated buffer and purified by cation-exchange chromatography. Well shaped perdeuterated AFP D crystals have been grown in D(2)O by the sitting-drop method. Preliminary neutron Laue diffraction at 293 K using LADI-III at ILL showed that with a few exposures of 24 h a very low background and clear small spots up to a resolution of 1.85 A were obtained using a ;radically small' perdeuterated AFP D crystal of dimensions 0.70 x 0.55 x 0.35 mm, corresponding to a volume of 0.13 mm(3).
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Affiliation(s)
- Isabelle Petit-Haertlein
- ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | | | | | - Andre Mitschler
- IGBMC, CNRS, INSERM, UdS, 1 Rue Laurent Fries, Illkirch, France
| | - Michael Haertlein
- ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
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Holt SA, Le Brun AP, Majkrzak CF, McGillivray DJ, Heinrich F, Lösche M, Lakey JH. An ion-channel-containing model membrane: structural determination by magnetic contrast neutron reflectometry. SOFT MATTER 2009; 5:2576-2586. [PMID: 21311730 PMCID: PMC3035324 DOI: 10.1039/b822411k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To many biophysical characterisation techniques, biological membranes appear as two-dimensional structures with details of their third dimension hidden within a 5 nm profile. Probing this structure requires methods able to discriminate multiple layers a few Ångströms thick. Given sufficient resolution, neutron methods can provide the required discrimination between different biochemical components, especially when selective deuteration is employed. We have used state-of-the-art neutron reflection methods, with resolution enhancement via magnetic contrast variation to study an oriented model membrane system. The model is based on the Escherichia coli outer membrane protein OmpF fixed to a gold surface via an engineered cysteine residue. Below the gold is buried a magnetic metal layer which, in a magnetic field, displays different scattering strengths to spin-up and spin-down neutrons. This provides two independent datasets from a single biological sample. Simultaneous fitting of the two datasets significantly refines the resulting model. A β-mercaptoethanol (βME) passivating surface, applied to the gold to prevent protein denaturation, is resolved for the first time as an 8.2 ± 0.6 Å thick layer, demonstrating the improved resolution and confirming that this layer remains after OmpF assembly. The thiolipid monolayer (35.3 ± 0.5 Å), assembled around the OmpF is determined and finally a fluid DMPC layer is added (total lipid thickness 58.7 ± 0.9 Å). The dimensions of trimeric OmpF in isolation (53.6 ± 2.5 Å), after assembly of lipid monolayer (57.5 ± 0.9 Å) and lipid bilayer (58.7 ± 0.9 Å), are precisely determined and show little variation.
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Affiliation(s)
- Stephen A. Holt
- ISIS, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, OX11 0QX, UK
| | - Anton P. Le Brun
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Charles F. Majkrzak
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-6102, USA
| | - Duncan J. McGillivray
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-6102, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-6102, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213-3890, USA
| | - Mathias Lösche
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-6102, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213-3890, USA
| | - Jeremy H. Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
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