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Kumar V N, Tamilanban T. Computational therapeutic repurposing of tavaborole targeting arginase-1 for venous leg ulcer. Comput Biol Chem 2024; 111:108112. [PMID: 38843583 DOI: 10.1016/j.compbiolchem.2024.108112] [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] [Received: 04/09/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/19/2024]
Abstract
Venous leg ulcers (VLUs) pose a growing healthcare challenge due to aging, obesity, and sedentary lifestyles. Despite various treatments available, addressing the complex nature of VLUs remains difficult. In this context, this study investigates repurposing boronated drugs to inhibit arginase 1 activity for VLU treatment. The molecular docking study conducted by Schrodinger GLIDE targeted the binuclear manganese cluster of arginase 1 enzyme (2PHO). Further, the ligand-protein complex was subjected to molecular dynamic studies at 500 ns in Gromacs-2019.4. Trajectory analysis was performed using the GROMACS simulation package of protein RMSD, RMSF, RG, SASA, and H-Bond. The docking study revealed intriguing results where the tavaborole showed a better docking score (-3.957 Kcal/mol) compared to the substrate L-arginine (-3.379 Kcal/mol) and standard L-norvaline (-3.141 Kcal/mol). Tavaborole interaction with aspartic acid ultimately suggests that the drug molecule binds to the catalytic site of arginase 1, potentially influencing the enzyme's function. The dynamics study revealed the compounds' stability and compactness of the protein throughout the simulation. The RMSD, RMSF, SASA, RG, inter and intra H-bond, PCA, FEL, and MMBSA studies affirmed the ligand-protein and protein complex flexibility, compactness, binding energy, van der waals energy, and solvation dynamics. These results revealed the stability and the interaction of the ligand with the catalytic site of arginase 1 enzyme, triggering the study towards the VLU treatment.
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Affiliation(s)
- Naveen Kumar V
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu - 603 203, India
| | - T Tamilanban
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu - 603 203, India.
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2
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Kahali S, Das SK, Kumar R, Gupta K, Kundu R, Bhattacharya B, Nath A, Venkatramani R, Datta A. A water-soluble, cell-permeable Mn(ii) sensor enables visualization of manganese dynamics in live mammalian cells. Chem Sci 2024; 15:10753-10769. [PMID: 39027293 PMCID: PMC11253179 DOI: 10.1039/d4sc00907j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Central roles of Mn2+ ions in immunity, brain function, and photosynthesis necessitate probes for tracking this essential metal ion in living systems. However, developing a cell-permeable, fluorescent sensor for selective imaging of Mn2+ ions in the aqueous cellular milieu has remained a challenge. This is because Mn2+ is a weak binder to ligand-scaffolds and Mn2+ ions quench fluorescent dyes leading to turn-off sensors that are not applicable for in vivo imaging. Sensors with a unique combination of Mn2+ selectivity, μM sensitivity, and response in aqueous media are necessary for not only visualizing labile cellular Mn2+ ions live, but also for measuring Mn2+ concentrations in living cells. No sensor has achieved this combination thus far. Here we report a novel, completely water-soluble, reversible, fluorescent turn-on, Mn2+ selective sensor, M4, with a K d of 1.4 μM for Mn2+ ions. M4 entered cells within 15 min of direct incubation and was applied to image Mn2+ ions in living mammalian cells in both confocal fluorescence intensity and lifetime-based set-ups. The probe was able to visualize Mn2+ dynamics in live cells revealing differential Mn2+ localization and uptake dynamics under pathophysiological versus physiological conditions. In a key experiment, we generated an in-cell Mn2+ response curve for the sensor which allowed the measurement of the endogenous labile Mn2+ concentration in HeLa cells as 1.14 ± 0.15 μM. Thus, our computationally designed, selective, sensitive, and cell-permeable sensor with a 620 nM limit of detection for Mn2+ in water provides the first estimate of endogenous labile Mn2+ levels in mammalian cells.
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Affiliation(s)
- Smitaroopa Kahali
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Sujit Kumar Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ravinder Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Kunika Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Rajasree Kundu
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Baivabi Bhattacharya
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Arnab Nath
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
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3
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Fernández De Santaella J, Ren J, Vanella R, Nash MA. Enzyme Cascade with Horseradish Peroxidase Readout for High-Throughput Screening and Engineering of Human Arginase-1. Anal Chem 2023; 95:7150-7157. [PMID: 37094096 DOI: 10.1021/acs.analchem.2c05429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
We report an enzyme cascade with horseradish peroxidase-based readout for screening human arginase-1 (hArg1) activity. We combined the four enzymes hArg1, ornithine decarboxylase, putrescine oxidase, and horseradish peroxidase in a reaction cascade that generated colorimetric or fluorescent signals in response to hArg1 activity and used this cascade to assay wild-type and variant hArg1 sequences as soluble enzymes and displayed on the surface of Escherichia coli. We screened a curated 13-member hArg1 library covering mutations that modified the electrostatic environment surrounding catalytic residues D128 and H141, and identified the R21E variant with a 13% enhanced catalytic turnover rate compared to wild type. Our scalable one-pot single-step arginase assay with continuous kinetic readout is amenable to high-throughput screening and directed evolution of arginase libraries and testing drug candidates for arginase inhibition.
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Affiliation(s)
- Jaime Fernández De Santaella
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
| | - Jin Ren
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Rosario Vanella
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Michael A Nash
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
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4
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Distinct binding pattern of nor-NOHA inhibitor to liver arginase in aqueous solution – Perspectives from molecular dynamics simulations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Exploring molecular structure, spectral features, electronic properties and molecular docking of a novel biologically active heterocyclic compound 4-phenylthiosemicarbazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129956] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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6
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Siddappa S, Marathe GK. What we know about plant arginases? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:600-610. [PMID: 33069114 DOI: 10.1016/j.plaphy.2020.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/01/2020] [Indexed: 05/14/2023]
Abstract
Nitrogen is one of the essential element required for plant growth and development. In plants, most of the nitrogen is stored in arginine. Hence, metabolism of arginine to urea by arginase and its further hydrolysis to ammonia by urease is involved in nitrogen recycling to meet the metabolic demands of growing plants. In this respect, plant arginases differ from that of animals. Animals excrete urea while plants recycle the urea. However, the studies on the biochemical and biophysical characteristics of plant arginase are limited when compared to animal arginase(s). In this review, the structural and biochemical characteristics of various plant arginases are discussed. Moreover, the significance of arginase in nitrogen recycling is explained and recent literature on function and activation of plant arginases in response to various environmental (biotic and abiotic) insults is also presented.
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Affiliation(s)
- Shiva Siddappa
- Department of Studies in Biochemistry, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India
| | - Gopal Kedihithlu Marathe
- Department of Studies in Biochemistry, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India; Department of Studies in Molecular Biology, University of Mysore, Manasagangothri, Mysuru, 570006, Karnataka, India.
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7
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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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8
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Oda K, Shimotani N, Kuroda T, Matoba Y. Crystal structure of an N ω-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:506-514. [PMID: 32496212 DOI: 10.1107/s2059798320004908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/06/2020] [Indexed: 11/10/2022]
Abstract
DcsB, one of the enzymes encoded in the D-cycloserine (D-CS) biosynthetic gene cluster, displays a high sequence homology to arginase, which contains two manganese ions in the active site. However, DcsB hydrolyzes Nω-hydroxy-L-arginine, but not L-arginine, to supply hydroxyurea for the biosynthesis of D-CS. Here, the crystal structure of DcsB was determined at a resolution of 1.5 Å using anomalous scattering from the manganese ions. In the crystal structure, DscB generates an artificial dimer created by the open and closed forms. Gel-filtration analysis demonstrated that DcsB is a monomeric protein, unlike arginase, which forms a trimeric structure. The active center containing the binuclear manganese cluster differs between DcsB and arginase. In DcsB, one of the ligands of the MnA ion is a cysteine, while the corresponding residue in arginase is a histidine. In addition, DcsB has no counterpart to the histidine residue that acts as a general acid/base during the catalytic reaction of arginase. The present study demonstrates that DcsB has a unique active site that differs from that of arginase.
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Affiliation(s)
- Kosuke Oda
- Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Natsuki Shimotani
- Department of Microbiology, Institute of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Teruo Kuroda
- Department of Microbiology, Institute of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Yasuyuki Matoba
- Department of Microbiology, Institute of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
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9
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Muller J, Cardey B, Zedet A, Desingle C, Grzybowski M, Pomper P, Foley S, Harakat D, Ramseyer C, Girard C, Pudlo M. Synthesis, evaluation and molecular modelling of piceatannol analogues as arginase inhibitors. RSC Med Chem 2020; 11:559-568. [PMID: 33479657 PMCID: PMC7593889 DOI: 10.1039/d0md00011f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/29/2020] [Indexed: 11/21/2022] Open
Abstract
Arginase is involved in a wide range of pathologies including cardiovascular diseases and infectious diseases whilst it is also a promising target to improve cancer immunotherapy. To date, only a limited number of inhibitors of arginase have been reported. Natural polyphenols, among them piceatannol, are moderate inhibitors of arginase. Herein, we report our efforts to investigate catechol binding by quantum chemistry and generate analogues of piceatannol. In this work, we synthesized a novel series of amino-polyphenols which were then evaluated as arginase inhibitors. Their structure-activity relationships were elucidated by deep quantum chemistry modelling. 4-((3,4-Dihydroxybenzyl)amino)benzene-1,2-diol 3t displays a mixed inhibition activity on bovine and human arginase I with IC50 (K i) values of 76 (82) μM and 89 μM, respectively.
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Affiliation(s)
- J Muller
- PEPITE EA4267 , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France . ; Tel: +(33) 381 665 542
| | - B Cardey
- Laboratoire Chrono-environnement (UMR CNRS 6249) , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France
| | - A Zedet
- PEPITE EA4267 , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France . ; Tel: +(33) 381 665 542
| | - C Desingle
- PEPITE EA4267 , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France . ; Tel: +(33) 381 665 542
| | - M Grzybowski
- OncoArendi Therapeutics , PL02089 Warsaw , Poland
| | - P Pomper
- OncoArendi Therapeutics , PL02089 Warsaw , Poland
| | - S Foley
- Laboratoire Chrono-environnement (UMR CNRS 6249) , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France
| | - D Harakat
- Institut de Chimie Moléculaire de Reims (UMR CNRS 7312) , Univ. Reims Champagne Ardenne , F-51000 Reims , France
| | - C Ramseyer
- Laboratoire Chrono-environnement (UMR CNRS 6249) , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France
| | - C Girard
- PEPITE EA4267 , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France . ; Tel: +(33) 381 665 542
| | - M Pudlo
- PEPITE EA4267 , Univ. Bourgogne Franche-Comté , F-25000 Besançon , France . ; Tel: +(33) 381 665 542
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10
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Canè S, Bronte V. Detection and functional evaluation of arginase-1 isolated from human PMNs and murine MDSC. Methods Enzymol 2020; 632:193-213. [DOI: 10.1016/bs.mie.2019.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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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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Crizanto de Lima E, Castelo-Branco FS, Maquiaveli CC, Farias AB, Rennó MN, Boechat N, Silva ER. Phenylhydrazides as inhibitors of Leishmania amazonensis arginase and antileishmanial activity. Bioorg Med Chem 2019; 27:3853-3859. [PMID: 31311700 DOI: 10.1016/j.bmc.2019.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023]
Abstract
Searching for new substances with antileishmanial activity, we synthesized and evaluated a series of α,α-difluorohydrazide and α,α-difluoramides against Leishmania amazonensis arginase (LaArg). Four α,α-difluorohydrazide derivatives showed activity against LaArg with Ki in the range of 1.3-26 μM. The study of the kinetics of LaArg inhibition showed that these substances might act via different inhibitory mechanisms or even by a combination of these. The compounds were tested against L. amazonensis promastigotes and the best result was obtained to the compound 4 (EC50 of 12.7 ± 0.3 μM). In addition, in order to obtain further insight into the binding mode of such compounds, molecular docking studies were performed to obtain additional validation of experimental results. Considering these results, it is possible to conclude that α,α-difluorohydrazide derivatives are a promising scaffold in the development of new substances against the etiological agent of leishmaniasis by targeting LaArg.
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Affiliation(s)
- Evanoel Crizanto de Lima
- Laboratório de Catálise e Síntese de Substâncias Bioativas, Universidade Federal do Rio de Janeiro Campus Macaé Professor Aloísio Teixeira, Estrada do Imburo s/n - Ajuda de Baixo, Macaé, RJ CEP 27979-000, Brazil
| | - Frederico S Castelo-Branco
- Departamento de Sintese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos - FIOCRUZ, Rio de Janeiro, RJ 21041-250, Brazil
| | - Claudia C Maquiaveli
- Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Farmacologia e Bioquímica (LFBq), Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil
| | - André B Farias
- Instituto de Biodiversidade e Sustentabilidade NUPEM/UFRJ, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Av. São José do Barreto, 764, Macaé, RJ 27965-045, Brazil
| | - Magdalena N Rennó
- Instituto de Biodiversidade e Sustentabilidade NUPEM/UFRJ, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Av. São José do Barreto, 764, Macaé, RJ 27965-045, Brazil
| | - Nubia Boechat
- Departamento de Sintese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos - FIOCRUZ, Rio de Janeiro, RJ 21041-250, Brazil.
| | - Edson R Silva
- Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Farmacologia e Bioquímica (LFBq), Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil.
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13
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Das S, Khatua K, Rakshit A, Carmona A, Sarkar A, Bakthavatsalam S, Ortega R, Datta A. Emerging chemical tools and techniques for tracking biological manganese. Dalton Trans 2019; 48:7047-7061. [DOI: 10.1039/c9dt00508k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This frontier article discusses chemical tools and techniques for tracking and imaging Mn ions in biology.
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Affiliation(s)
- Sayani Das
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Kaustav Khatua
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Ananya Rakshit
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Asuncion Carmona
- Chemical Imaging and Speciation
- CENBG
- University of Bordeaux
- UMR 5797
- 33175 Gradignan
| | - Anindita Sarkar
- Department of Biological Chemistry
- University of Michigan
- Ann Arbor
- USA
| | | | - Richard Ortega
- Chemical Imaging and Speciation
- CENBG
- University of Bordeaux
- UMR 5797
- 33175 Gradignan
| | - Ankona Datta
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
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14
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Metal ions-induced stability and function of bimetallic human arginase-I, a therapeutically important enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1153-1164. [DOI: 10.1016/j.bbapap.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/21/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022]
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15
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Abdel Wahed ASAH, Amer MAM, Abou Mohamed NM, Mobasher MI, Mamdouh H, GamalEl Din SF, ElSheemy MS. Serum Arginase II level can be a novel indicator for erectile dysfunction in patients with vasculogenic erectile dysfunction: a comparative study. Int Urol Nephrol 2018; 50:1389-1395. [DOI: 10.1007/s11255-018-1921-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
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Arginase Structure and Inhibition: Catalytic Site Plasticity Reveals New Modulation Possibilities. Sci Rep 2017; 7:13616. [PMID: 29051526 PMCID: PMC5648838 DOI: 10.1038/s41598-017-13366-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/22/2017] [Indexed: 01/23/2023] Open
Abstract
Metalloenzyme arginase is a therapeutically relevant target associated with tumor growth. To fight cancer immunosuppression, arginase activity can be modulated by small chemical inhibitors binding to its catalytic center. To better understand molecular mechanisms of arginase inhibition, a careful computer-aided mechanistic structural investigation of this enzyme was conducted. Using molecular dynamics (MD) simulations in the microsecond range, key regions of the protein active site were identified and their flexibility was evaluated and compared. A cavity opening phenomenon was observed, involving three loops directly interacting with all known ligands, while metal coordinating regions remained motionless. A novel dynamic 3D pharmacophore analysis method termed dynophores has been developed that allows for the construction of a single 3D-model comprising all ligand-enzyme interactions occurring throughout a complete MD trajectory. This new technique for the in silico study of intermolecular interactions allows for loop flexibility analysis coupled with movements and conformational changes of bound ligands. Presented MD studies highlight the plasticity of the size of the arginase active site, leading to the hypothesis that larger ligands can enter the cavity of arginase. Experimental testing of a targeted fragment library substituted by different aliphatic groups validates this hypothesis, paving the way for the design of arginase inhibitors with novel binding patterns.
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Pudlo M, Demougeot C, Girard-Thernier C. Arginase Inhibitors: A Rational Approach Over One Century. Med Res Rev 2016; 37:475-513. [DOI: 10.1002/med.21419] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/14/2016] [Accepted: 09/22/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marc Pudlo
- PEPITE - EA4267; University Bourgogne Franche-Comté; Besançon France
| | - Céline Demougeot
- PEPITE - EA4267; University Bourgogne Franche-Comté; Besançon France
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Pham TN, Bordage S, Pudlo M, Demougeot C, Thai KM, Girard-Thernier C. Cinnamide Derivatives as Mammalian Arginase Inhibitors: Synthesis, Biological Evaluation and Molecular Docking. Int J Mol Sci 2016; 17:E1656. [PMID: 27690022 PMCID: PMC5085689 DOI: 10.3390/ijms17101656] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 12/24/2022] Open
Abstract
Arginases are enzymes that are involved in many human diseases and have been targeted for new treatments. Here a series of cinnamides was designed, synthesized and evaluated in vitro and in silico for their inhibitory activity against mammalian arginase. Using a microassay on purified liver bovine arginase (b-ARG I), (E)-N-(2-phenylethyl)-3,4-dihydroxycinnamide, also named caffeic acid phenylamide (CAPA), was shown to be slightly more active than our natural reference inhibitor, chlorogenic acid (IC50 = 6.9 ± 1.3 and 10.6 ± 1.6 µM, respectively) but it remained less active that the synthetic reference inhibitor Nω-hydroxy-nor-l-arginine nor-NOHA (IC50 = 1.7 ± 0.2 µM). Enzyme kinetic studies showed that CAPA was a competitive inhibitor of arginase with Ki = 5.5 ± 1 µM. Whereas the activity of nor-NOHA was retained (IC50 = 5.7 ± 0.6 µM) using a human recombinant arginase I (h-ARG I), CAPA showed poorer activity (IC50 = 60.3 ± 7.8 µM). However, our study revealed that the cinnamoyl moiety and catechol function were important for inhibitory activity. Docking results on h-ARG I demonstrated that the caffeoyl moiety could penetrate into the active-site pocket of the enzyme, and the catechol function might interact with the cofactor Mn2+ and several crucial amino acid residues involved in the hydrolysis mechanism of arginase. The results of this study suggest that 3,4-dihydroxycinnamides are worth being considered as potential mammalian arginase inhibitors, and could be useful for further research on the development of new arginase inhibitors.
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Affiliation(s)
- Thanh-Nhat Pham
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France.
| | - Simon Bordage
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France.
- University Lille, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
| | - Marc Pudlo
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France.
| | - Céline Demougeot
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France.
| | - Khac-Minh Thai
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, 41 Dinh Tien Hoang, Dist 1, Ho Chi Minh City 700000, Vietnam.
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Grineva AA, Ageshina AA, Uvarova MA, Nefedov SE. Formation of 1-D polymer in recrystallization of the adduct Mn[(OOCC5H4)Mn(CO)3]2[O(H)Me]4 from acetonitrile. RUSS J INORG CHEM+ 2016. [DOI: 10.1134/s0036023616090060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Taslimi Y, Zahedifard F, Habibzadeh S, Taheri T, Abbaspour H, Sadeghipour A, Mohit E, Rafati S. Antitumor Effect of IP-10 by Using Two Different Approaches: Live Delivery System and Gene Therapy. J Breast Cancer 2016; 19:34-44. [PMID: 27066094 PMCID: PMC4822105 DOI: 10.4048/jbc.2016.19.1.34] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/26/2016] [Indexed: 12/11/2022] Open
Abstract
Purpose Immunotherapy is one of the treatment strategies for breast cancer, the most common cancer in women worldwide. In this approach, the patient's immune system is stimulated to attack microscopic tumors and control metastasis. Here, we used interferon γ-induced protein 10 (IP-10), which induces and strengthens antitumor immunity, as an immunotherapeutic agent. We employed Leishmania tarentolae, a nonpathogenic lizard parasite that lacks the ability to persist in mammalian macrophages, was used as a live delivery system for carrying the immunotherapeutic agent. It has been already shown that arginase activity, and consequently, polyamine production, are associated with tumor progression. Methods A live delivery system was constructed by stable transfection of pLEXSY plasmid containing the IP-10-enhanced green fluorescent protein (IP-10-egfp) fusion gene into L. tarentolae. Then, the presence of the IP-10-egfp gene and the accurate integration location into the parasite genome were confirmed. The therapeutic efficacy of IP-10 delivered via L. tarentolae and recombinant pcDNA-(IP-10-egfp) plasmid was compared by determining the arginase activity in a mouse 4T1 breast cancer model. Results The pcDNA-(IP-10-egfp) group showed a significant reduction in tumor weight and growth. Histological evaluation also revealed that only this group demonstrated inhibition of metastasis to the lung tissue. The arginase activity in the tissue of the pcDNA-(IP-10-egfp) mice significantly decreased in comparison with that in normal mice. No significant difference was observed in arginase activity in the sera of mice receiving other therapeutic strategies. Conclusion Our data indicates that IP-10 immunotherapy is a promising strategy for breast cancer treatment, as shown in the 4T1-implanted BALB/c mouse model. However, the L. tarentolae-(IP-10-EGFP) live delivery system requires dose modifications to achieve efficacy in the applied regimen (six injections in 3 weeks). Our results indicate that the arginase assay could be a good biomarker to differentiate tumoral tissues from the normal ones.
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Affiliation(s)
- Yasaman Taslimi
- Department of Biology, College of Basic Sciences, Damghan Branch, Islamic Azad University, Damghan, Iran.; Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farnaz Zahedifard
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Sima Habibzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Tahereh Taheri
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Hossain Abbaspour
- Department of Biology, College of Basic Sciences, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Alireza Sadeghipour
- Department of Pathology, Hazrat-e-Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Elham Mohit
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
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Sachs U, Schaper G, Winkler D, Kratzert D, Kurz P. Light- or oxidation-triggered CO release from [MnI(CO)3(κ3-L)] complexes: reaction intermediates and a new synthetic route to [MnIII/IV2(μ-O)2(L)2] compounds. Dalton Trans 2016; 45:17464-17473. [DOI: 10.1039/c6dt02020h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The substitution of the carbonyl ligands of [MnI(CO)3(κ3-L)] complexes can be triggered in two different ways: by near-UV irradiation or by electrochemical oxidation of MnI to MnII.
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Affiliation(s)
- Ulf Sachs
- Institut für Anorganische und Analytische Chemie
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg
- Germany
| | - Gerrit Schaper
- Institut für Anorganische und Analytische Chemie
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg
- Germany
| | - Daniela Winkler
- Institut für Anorganische und Analytische Chemie
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg
- Germany
| | - Daniel Kratzert
- Institut für Anorganische und Analytische Chemie
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg
- Germany
| | - Philipp Kurz
- Institut für Anorganische und Analytische Chemie
- Albert-Ludwigs-Universität Freiburg
- 79104 Freiburg
- Germany
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Sin YY, Baron G, Schulze A, Funk CD. Arginase-1 deficiency. J Mol Med (Berl) 2015; 93:1287-96. [PMID: 26467175 DOI: 10.1007/s00109-015-1354-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/14/2015] [Accepted: 10/01/2015] [Indexed: 12/13/2022]
Abstract
Arginase-1 (ARG1) deficiency is a rare autosomal recessive disorder that affects the liver-based urea cycle, leading to impaired ureagenesis. This genetic disorder is caused by 40+ mutations found fairly uniformly spread throughout the ARG1 gene, resulting in partial or complete loss of enzyme function, which catalyzes the hydrolysis of arginine to ornithine and urea. ARG1-deficient patients exhibit hyperargininemia with spastic paraparesis, progressive neurological and intellectual impairment, persistent growth retardation, and infrequent episodes of hyperammonemia, a clinical pattern that differs strikingly from other urea cycle disorders. This review briefly highlights the current understanding of the etiology and pathophysiology of ARG1 deficiency derived from clinical case reports and therapeutic strategies stretching over several decades and reports on several exciting new developments regarding the pathophysiology of the disorder using ARG1 global and inducible knockout mouse models. Gene transfer studies in these mice are revealing potential therapeutic options that can be exploited in the future. However, caution is advised in extrapolating results since the lethal disease phenotype in mice is much more severe than in humans indicating that the mouse models may not precisely recapitulate human disease etiology. Finally, some of the functions and implications of ARG1 in non-urea cycle activities are considered. Lingering questions and future areas to be addressed relating to the clinical manifestations of ARG1 deficiency in liver and brain are also presented. Hopefully, this review will spark invigorated research efforts that lead to treatments with better clinical outcomes.
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Affiliation(s)
- Yuan Yan Sin
- Department of Biomedical and Molecular Sciences, Queen's University, 433 Botterell Hall, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Garrett Baron
- Department of Biomedical and Molecular Sciences, Queen's University, 433 Botterell Hall, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada
| | - Andreas Schulze
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.,Genetics and Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada
| | - Colin D Funk
- Department of Biomedical and Molecular Sciences, Queen's University, 433 Botterell Hall, 18 Stuart Street, Kingston, ON, K7L 3N6, Canada.
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Winter G, Todd CD, Trovato M, Forlani G, Funck D. Physiological implications of arginine metabolism in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:534. [PMID: 26284079 PMCID: PMC4520006 DOI: 10.3389/fpls.2015.00534] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/29/2015] [Indexed: 05/18/2023]
Abstract
Nitrogen is a limiting resource for plant growth in most terrestrial habitats since large amounts of nitrogen are needed to synthesize nucleic acids and proteins. Among the 21 proteinogenic amino acids, arginine has the highest nitrogen to carbon ratio, which makes it especially suitable as a storage form of organic nitrogen. Synthesis in chloroplasts via ornithine is apparently the only operational pathway to provide arginine in plants, and the rate of arginine synthesis is tightly regulated by various feedback mechanisms in accordance with the overall nutritional status. While several steps of arginine biosynthesis still remain poorly characterized in plants, much wider attention has been paid to inter- and intracellular arginine transport as well as arginine-derived metabolites. A role of arginine as alternative source besides glutamate for proline biosynthesis is still discussed controversially and may be prevented by differential subcellular localization of enzymes. Apparently, arginine is a precursor for nitric oxide (NO), although the molecular mechanism of NO production from arginine remains unclear in higher plants. In contrast, conversion of arginine to polyamines is well documented, and in several plant species also ornithine can serve as a precursor for polyamines. Both NO and polyamines play crucial roles in regulating developmental processes as well as responses to biotic and abiotic stress. It is thus conceivable that arginine catabolism serves on the one hand to mobilize nitrogen storages, while on the other hand it may be used to fine-tune development and defense mechanisms against stress. This review summarizes the recent advances in our knowledge about arginine metabolism, with a special focus on the model plant Arabidopsis thaliana, and pinpoints still unresolved critical questions.
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Affiliation(s)
- Gudrun Winter
- Laboratory of Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Maurizio Trovato
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Forlani
- Laboratory of Plant Physiology and Biochemistry, Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dietmar Funck
- Laboratory of Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Konstanz, Germany
- *Correspondence: Dietmar Funck, Laboratory of Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany,
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Hai Y, Edwards JE, Van Zandt MC, Hoffmann KF, Christianson DW. Crystal structure of Schistosoma mansoni arginase, a potential drug target for the treatment of schistosomiasis. Biochemistry 2014; 53:4671-84. [PMID: 25007099 PMCID: PMC4138072 DOI: 10.1021/bi5004519] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The X-ray crystal structure of arginase from Schistosoma mansoni (SmARG) and the structures of its complexes with several amino acid inhibitors have been determined at atomic resolution. SmARG is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of l-arginine to form l-ornithine and urea, and this enzyme is upregulated in all forms of the parasite that interact with the human host. Current hypotheses suggest that parasitic arginases could play a role in host immune evasion by depleting pools of substrate l-arginine that would otherwise be utilized for NO biosynthesis and NO-dependent processes in the immune response. Although the amino acid sequence of SmARG is only 42% identical with that of human arginase I, residues important for substrate binding and catalysis are strictly conserved. In general, classical amino acid inhibitors such as 2(S)-amino-6-boronohexanoic acid (ABH) tend to bind more weakly to SmARG than to human arginase I despite identical inhibitor binding modes in each enzyme active site. The identification of a patch on the enzyme surface capable of accommodating the additional Cα substitutent of an α,α-disubstituted amino acid inhibitor suggests that such inhibitors could exhibit higher affinity and biological activity. The structures of SmARG complexed with two different α,α-disubstituted derivatives of ABH are presented and provide a proof of concept for this approach in the enhancement of enzyme-inhibitor affinity.
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Affiliation(s)
- Yang Hai
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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McGeary RP, Schenk G, Guddat LW. The applications of binuclear metallohydrolases in medicine: Recent advances in the design and development of novel drug leads for purple acid phosphatases, metallo-β-lactamases and arginases. Eur J Med Chem 2014; 76:132-44. [DOI: 10.1016/j.ejmech.2014.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 01/28/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Gass IA, Asadi M, Lupton DW, Moubaraki B, Bond AM, Guo SX, Murray KS. Manganese(II) Oxazolidine Nitroxide Chelates: Structure, Magnetism, and Redox Properties. Aust J Chem 2014. [DOI: 10.1071/ch14390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mononuclear oxazolidine nitroxide complex [MnII(L•)2](ClO4)2 (1) (L•, 4-dimethyl-2,2-di(2-pyridyl)oxazolidine N-oxide) has been synthesized and investigated using single-crystal X-ray diffraction, variable-temperature magnetic susceptibility measurements, and electrochemistry. The structural analysis reveals bond lengths compatible with a linear L•–MnII–L• arrangement where the ligands are in the neutral ligand form and the central MnII ion is high spin (S = 5/2). Although analysis of the variable-temperature magnetic susceptibility data suggests a strong antiferromagnetic metal–radical interaction, the radical–radical intramolecular interaction could not be determined unambiguously from such fits. The resultant isolated S = 3/2 ground state is confirmed by low-temperature magnetization versus field measurements. Electrochemical studies reveal similar square schemes and redox intermediates to the previously reported analogues [FeII(L•)2][BF4]2 and [CoII(L•)2][NO3]2.
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Hai Y, Dugery RJ, Healy D, Christianson DW. Formiminoglutamase from Trypanosoma cruzi is an arginase-like manganese metalloenzyme. Biochemistry 2013; 52:9294-309. [PMID: 24261485 DOI: 10.1021/bi401352h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The crystal structure of formiminoglutamase from Trypanosoma cruzi (TcFIGase) is reported at 1.85 Å resolution. Although the structure of this enzyme was previously determined by the Structural Genomics of Pathogenic Protozoa Consortium (PDB accession code 2A0M), this structure was determined at low pH and lacked bound metal ions; accordingly, the protein was simply annotated as "arginase superfamily protein" with undetermined function. We show that reconstitution of this protein with Mn²⁺ confers maximal catalytic activity in the hydrolysis of formiminoglutamate to yield glutamate and formamide, thereby demonstrating that this protein is a metal-dependent formiminoglutamase. Equilibration of TcFIGase crystals with MnCl₂ at higher pH yields a binuclear manganese cluster similar to that observed in arginase, except that the histidine ligand to the Mn²⁺(A) ion of arginase is an asparagine ligand (N114) to the Mn²⁺(A) ion of TcFIGase. The crystal structure of N114H TcFIGase reveals a binuclear manganese cluster essentially identical to that of arginase, but the mutant exhibits a modest 35% loss of catalytic efficiency (k(cat)/K(M)). Interestingly, when TcFIGase is prepared and crystallized in the absence of reducing agents at low pH, a disulfide linkage forms between C35 and C242 in the active site. When reconstituted with Mn²⁺ at higher pH, this oxidized enzyme exhibits a modest 33% loss of catalytic efficiency. Structure determinations of the metal-free and metal-bound forms of oxidized TcFIGase reveal that although disulfide formation constricts the main entrance to the active site, other structural changes open alternative channels to the active site that may help sustain catalytic activity.
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Affiliation(s)
- Yang Hai
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, PA 19104-6323, U.S.A
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D'Antonio EL, Ullman B, Roberts SC, Dixit UG, Wilson ME, Hai Y, Christianson DW. Crystal structure of arginase from Leishmania mexicana and implications for the inhibition of polyamine biosynthesis in parasitic infections. Arch Biochem Biophys 2013; 535:163-76. [PMID: 23583962 DOI: 10.1016/j.abb.2013.03.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 02/06/2023]
Abstract
Arginase from parasitic protozoa belonging to the genus Leishmania is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme catalyzes the first committed step in the biosynthesis of polyamines that enable cell growth and survival. The high resolution X-ray crystal structures of the unliganded form of Leishmania mexicana arginase (LmARG) and four inhibitor complexes are now reported. These complexes include the reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH) and the hydroxylated substrate analogue nor-N(ω)-hydroxy-l-arginine (nor-NOHA), which are the most potent arginase inhibitors known to date. Comparisons of the LmARG structure with that of the archetypal arginase, human arginase I, reveal that all residues important for substrate binding and catalysis are strictly conserved. However, three regions of tertiary structure differ between the parasitic enzyme and the human enzyme corresponding to the G62 - S71, L161 - C172, and I219 - V230 segments of LmARG. Additionally, variations are observed in salt link interactions that stabilize trimer assembly in LmARG. We also report biological studies in which we demonstrate that localization of LmARG to the glycosome, a unique subcellular organelle peculiar to Leishmania and related parasites, is essential for robust pathogenesis.
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Affiliation(s)
- Edward L D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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Nagagarajan S, Xue F, MacKerell AD. Impact of substrate protonation and tautomerization states on interactions with the active site of arginase I. J Chem Inf Model 2013; 53:452-60. [PMID: 23327293 DOI: 10.1021/ci300506y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human arginase is a binuclear manganese metalloenzyme that participates in the urea cycle. Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea and is linked to several disorders such as asthma and cancer. Currently, the protonation and tautomerization state of the substrate when bound to the active site, which contains two manganese ions, is not known. Knowledge of the charge-dependent behavior of arginine in the arginase I environment would be of utility toward understanding the catalytic mechanism and designing inhibitors of this enzyme. The arginine(+/0) species, including all possible neutral tautomers, were modeled using an aminoimidazole analog as template. All-atom molecular dynamics simulations were then performed on each of the charged and neutral species. In addition, a hydroxide ion was included in selected simulations to test its importance. Results show that the positively charged state of arginine is stable in the active site of arginase I, with that stabilization facilitated by the presence of hydroxide. Glu277 is indicated to play a role in stabilizing arginine in the active site and facilitating its ability to assume a catalytically competent conformation in the presence of hydroxide. The reported interactions and modeled arginine-bound arginase I structures can be used as a tool for structure-based inhibitor design, as experimental data on the structure of the substrate-enzyme complex is lacking.
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Affiliation(s)
- Shanthi Nagagarajan
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
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D'Antonio EL, Hai Y, Christianson DW. Structure and function of non-native metal clusters in human arginase I. Biochemistry 2012; 51:8399-409. [PMID: 23061982 DOI: 10.1021/bi301145n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Various binuclear metal ion clusters and complexes have been reconstituted in crystalline human arginase I by removing the Mn(2+)(2) cluster of the wild-type enzyme with metal chelators and subsequently soaking the crystalline apoenzyme in buffer solutions containing NiCl(2) or ZnCl(2). X-ray crystal structures of these metal ion variants are correlated with catalytic activity measurements that reveal differences resulting from metal ion substitution. Additionally, treatment of crystalline Mn(2+)(2)-human arginase I with Zn(2+) reveals for the first time the structural basis for inhibition by Zn(2+), which forms a carboxylate-histidine-Zn(2+) triad with H141 and E277. The imidazole side chain of H141 is known to be hyper-reactive, and its chemical modification or mutagenesis is known to similarly compromise catalysis. The reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH) binds as a tetrahedral boronate anion to Mn(2+)(2), Co(2+)(2), Ni(2+)(2), and Zn(2+)(2) clusters in human arginase I, and it can be stabilized by a third inhibitory Zn(2+) ion coordinated by H141. Because ABH binds as an analogue of the tetrahedral intermediate and its flanking transition states in catalysis, this implies that the various metallo-substituted enzymes are capable of some level of catalysis with an actual substrate. Accordingly, we establish the following trend for turnover number (k(cat)) and catalytic efficiency (k(cat)/K(M)): Mn(2+) > Ni(2+) ≈ Co(2+) ≫ Zn(2+). Therefore, Mn(2+) is required for optimal catalysis by human arginase I.
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Affiliation(s)
- Edward L D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Homology modeling, docking and molecular dynamics of the Leishmania mexicana arginase: A description of the catalytic site useful for drug design. J Mol Graph Model 2012; 38:50-9. [DOI: 10.1016/j.jmgm.2012.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/02/2012] [Accepted: 08/02/2012] [Indexed: 11/17/2022]
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D’Antonio EL, Christianson DW. Binding of the unreactive substrate analog L-2-amino-3-guanidinopropionic acid (dinor-L-arginine) to human arginase I. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:889-93. [PMID: 22869115 PMCID: PMC3412766 DOI: 10.1107/s1744309112027820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/19/2012] [Indexed: 11/11/2022]
Abstract
Human arginase I (HAI) is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea through a metal-activated hydroxide mechanism. Since HAI regulates L-Arg bioavailability for NO biosynthesis, it is a potential drug target for the treatment of cardiovascular diseases such as atherosclerosis. X-ray crystal structures are now reported of the complexes of Mn(2)(2+)-HAI and Co(2)(2+)-HAI with L-2-amino-3-guanidinopropionic acid (AGPA; also known as dinor-L-arginine), an amino acid bearing a guanidinium side chain two methylene groups shorter than that of L-arginine. Hydrogen bonds to the α-carboxylate and α-amino groups of AGPA dominate enzyme-inhibitor recognition; the guanidinium group does not interact directly with the metal ions.
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Affiliation(s)
- Edward L. D’Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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35
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D’Antonio EL, Christianson DW. Crystal structures of complexes with cobalt-reconstituted human arginase I. Biochemistry 2011; 50:8018-27. [PMID: 21870783 PMCID: PMC3172387 DOI: 10.1021/bi201101t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The binuclear manganese metalloenzyme human arginase I (HAI) is a potential protein drug for cancer chemotherapy, in that it is capable of depleting extracellular l-Arg levels in the microenvironment of tumor cells that require this nutrient to thrive. Substitution of the native Mn(2+)(2) cluster with a Co(2+)(2) cluster in the active site yields an enzyme with enhanced catalytic activity at physiological pH (∼7.4) that could serve as an improved protein drug for L-Arg depletion therapy [Stone, E. M., Glazer, E. S., Chantranupong, L., Cherukuri, P., Breece, R. M., Tierney, D. L., Curley, S. A., Iverson, B. L., and Georgiou, G. (2010) ACS Chem. Biol. 5, 333-342]. A different catalytic mechanism is proposed for Co(2+)(2)-HAI compared with that of Mn(2+)(2)-HAI, including an unusual Nε-Co(2+) coordination mode, to rationalize the lower K(M) value of L-Arg and the lower K(i) value of L-Orn. However, we now report that no unusual metal coordination modes are observed in the cobalt-reconstituted enzyme. The X-ray crystal structures of unliganded Co(2+)(2)-HAI determined at 2.10 Å resolution (pH 7.0) and 1.97 Å resolution (pH 8.5), as well as the structures of Co(2+)(2)-HAI complexed with the reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH, pH 7.0) and the catalytic product L-Orn (pH 7.0) determined at 1.85 and 1.50 Å resolution, respectively, are essentially identical to the corresponding structures of Mn(2+)(2)-HAI. Therefore, in the absence of significant structural differences between Co(2+)(2)-HAI and Mn(2+)(2)-HAI, we suggest that a higher concentration of metal-bridging hydroxide ion at physiological pH for Co(2+)(2)-HAI, a consequence of the lower pK(a) of a Co(2+)-bound water molecule compared with a Mn(2+)-bound water molecule, strengthens electrostatic interactions with cationic amino acids and accounts for enhanced affinity as reflected in the lower K(M) value of L-Arg and the lower K(i) value of L-Orn.
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Affiliation(s)
- Edward L. D’Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
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36
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Ilies M, Di Costanzo L, Dowling DP, Thorn KJ, Christianson DW. Binding of α,α-disubstituted amino acids to arginase suggests new avenues for inhibitor design. J Med Chem 2011; 54:5432-43. [PMID: 21728378 DOI: 10.1021/jm200443b] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Arginase is a binuclear manganese metalloenzyme that hydrolyzes L-arginine to form L-ornithine and urea, and aberrant arginase activity is implicated in various diseases such as erectile dysfunction, asthma, atherosclerosis, and cerebral malaria. Accordingly, arginase inhibitors may be therapeutically useful. Continuing our efforts to expand the chemical space of arginase inhibitor design and inspired by the binding of 2-(difluoromethyl)-L-ornithine to human arginase I, we now report the first study of the binding of α,α-disubstituted amino acids to arginase. Specifically, we report the design, synthesis, and assay of racemic 2-amino-6-borono-2-methylhexanoic acid and racemic 2-amino-6-borono-2-(difluoromethyl)hexanoic acid. X-ray crystal structures of human arginase I and Plasmodium falciparum arginase complexed with these inhibitors reveal the exclusive binding of the L-stereoisomer; the additional α-substituent of each inhibitor is readily accommodated and makes new intermolecular interactions in the outer active site of each enzyme. Therefore, this work highlights a new region of the protein surface that can be targeted for additional affinity interactions, as well as the first comparative structural insights on inhibitor discrimination between a human and a parasitic arginase.
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Affiliation(s)
- Monica Ilies
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104-2875, United States
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37
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Carbon paste electrode modified with a binuclear manganese complex as a sensitive voltammetric sensor for tryptophan. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0619-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Lee SJ, Kim DJ, Kim HS, Lee BI, Yoon HJ, Yoon JY, Kim KH, Jang JY, Im HN, An DR, Song JS, Kim HJ, Suh SW. Crystal structures of Pseudomonas aeruginosa guanidinobutyrase and guanidinopropionase, members of the ureohydrolase superfamily. J Struct Biol 2011; 175:329-38. [PMID: 21600989 DOI: 10.1016/j.jsb.2011.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/13/2011] [Accepted: 05/04/2011] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA) catalyze the hydrolysis of 4-guanidinobutyrate and 3-guanidinopropionate, respectively. They belong to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase. In this study, we have determined the crystal structures of GbuA and GpuA from P. aeruginosa to provide a structural insight into their substrate specificity. Although GbuA and GpuA share a common structural fold of the typical ureohydrolase superfamily, they exhibit significant variations in two active site loops. Mutagenesis of Met161 of GbuA and Tyr157 of GpuA, both of which are located in the active site loop 1 and predicted to be involved in substrate recognition, significantly affected their enzymatic properties, implying their important roles in catalysis.
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Affiliation(s)
- Sang Jae Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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39
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Newman J, Pearce L, Lesburg CA, Strickland C, Peat TS. Crystallization of an apo form of human arginase: using all the tools in the toolbox simultaneously. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:90-3. [PMID: 21206033 PMCID: PMC3079981 DOI: 10.1107/s1744309110046208] [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: 10/21/2010] [Accepted: 11/09/2010] [Indexed: 11/10/2022]
Abstract
Arginase (EC 3.5.3.1) is an aminohydrolase that acts on L-arginine to produce urea and ornithine. Two isotypes of the enzyme are found in humans. Type I is predominantly produced in the liver and is a homotrimer of 35 kDa subunits. Human arginase (hArginase) I is seen to be up-regulated in many diseases and is a potential therapeutic target for many diverse indications. Previous reports of crystallization and structure determination of hArginase have always included inhibitors of the enzyme: here, the first case of a true apo crystal form of the enzyme which is suitable for small-molecule soaking is reported. The crystals belonged to space group P2(1)2(1)2(1) and have approximate unit-cell parameters a=53, b=67.5, c=250 Å. The crystals showed slightly anisotropic diffraction to beyond 2.0 Å resolution.
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Affiliation(s)
- Janet Newman
- Materials Science and Engineering, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.
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40
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Francuski BM, Novaković SB, Bogdanović GA. Electronic features and hydrogen bonding capacity of the sulfur acceptor in thioureido-based compounds. Experimental charge density study of 4-methyl-3-thiosemicarbazide. CrystEngComm 2011. [DOI: 10.1039/c0ce00760a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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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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Di Costanzo L, Ilies M, Thorn KJ, Christianson DW. Inhibition of human arginase I by substrate and product analogues. Arch Biochem Biophys 2010; 496:101-8. [PMID: 20153713 DOI: 10.1016/j.abb.2010.02.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 02/08/2010] [Accepted: 02/09/2010] [Indexed: 11/29/2022]
Abstract
Human arginase I is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to generate L-ornithine and urea. We demonstrate that N-hydroxy-L-arginine (NOHA) binds to this enzyme with K(d)=3.6 microM, and nor-N-hydroxy-L-arginine (nor-NOHA) binds with K(d)=517 nM (surface plasmon resonance) or K(d) approximately 50 nM (isothermal titration calorimetry). Crystals of human arginase I complexed with NOHA and nor-NOHA afford 2.04 and 1.55 A resolution structures, respectively, which are significantly improved in comparison with previously-determined structures of the corresponding complexes with rat arginase I. Higher resolution structures clarify the binding interactions of the inhibitors. Finally, the crystal structure of the complex with L-lysine (K(d)=13 microM) is reported at 1.90 A resolution. This structure confirms the importance of hydrogen bond interactions with inhibitor alpha-carboxylate and alpha-amino groups as key specificity determinants of amino acid recognition in the arginase active site.
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Affiliation(s)
- Luigi Di Costanzo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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43
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Hosny NM, El-Dossoki FI, Mostafa MM. Spectral and Thermal Studies of Some New Metal Complexes Derived from N-[(Phenylamino)Thioxomethyl] Hydrazinocarbonyl Methyl Pyridinium Chloride (PTHMPC). PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500902800246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nasser M. Hosny
- a Chemistry Department, Faculty of Science , Suez-Canal University , Port-Said, Egypt
| | - Farid I. El-Dossoki
- a Chemistry Department, Faculty of Science , Suez-Canal University , Port-Said, Egypt
| | - Mohsen M. Mostafa
- b Chemistry Department, Faculty of Science , Mansoura University , Mansoura, Egypt
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44
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Kozoni C, Manolopoulou E, Siczek M, Lis T, Brechin EK, Milios CJ. Polynuclear manganese amino acid complexes. Dalton Trans 2010; 39:7943-50. [DOI: 10.1039/c0dt00192a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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45
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46
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Kozoni C, Siczek M, Lis T, Brechin EK, Milios CJ. The first amino acid manganese cluster: a [Mn(IV)2Mn(III)3] DL-valine cage. Dalton Trans 2009:9117-9. [PMID: 20449184 DOI: 10.1039/b916258p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first polymetallic Mn complex containing an amino acid (the pro-ligand DL-valine) is reported.
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Affiliation(s)
- Chrysa Kozoni
- Department of Chemistry, University of Crete, 71003 Herakleion, Greece
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47
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Shishova EY, Di Costanzo L, Emig FA, Ash DE, Christianson DW. Probing the specificity determinants of amino acid recognition by arginase. Biochemistry 2009; 48:121-31. [PMID: 19093830 DOI: 10.1021/bi801911v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the alpha-amino and alpha-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate alpha-carboxylate and T135, (2) a direct hydrogen bond between the substrate alpha-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate alpha-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased K(M) values but have less pronounced effects on catalytic function as reflected by minimal variations of k(cat). As with substrate K(M) values, inhibitor K(d) values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.
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Affiliation(s)
- Ekaterina Y Shishova
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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48
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Zakharian TY, Di Costanzo L, Christianson DW. Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I. Org Biomol Chem 2008; 6:3240-3. [PMID: 18802628 PMCID: PMC2790808 DOI: 10.1039/b811797g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid is reported along with the X-ray crystal structure of its complex with human arginase I, revealing unique coordination interactions with two manganese ions in the enzyme active site.
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Affiliation(s)
| | | | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA; Fax: 1 215 573 2201; Tel: 1 215 898 5714; E-mail:
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49
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Dowling DP, Di Costanzo L, Gennadios HA, Christianson DW. Evolution of the arginase fold and functional diversity. Cell Mol Life Sci 2008; 65:2039-55. [PMID: 18360740 PMCID: PMC2653620 DOI: 10.1007/s00018-008-7554-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein Evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique alpha/beta fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel eight-stranded beta-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core alpha/beta fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes.
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Affiliation(s)
- D. P. Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - L. Di Costanzo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - H. A. Gennadios
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - D. W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
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