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Witek W, Sliwiak J, Rawski M, Ruszkowski M. Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. FRONTIERS IN PLANT SCIENCE 2024; 15:1343980. [PMID: 38559763 PMCID: PMC10978614 DOI: 10.3389/fpls.2024.1343980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of Medicago truncatula HISN5 (MtHISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. MtHISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure MtHISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
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Affiliation(s)
- Wojciech Witek
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Sliwiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Michal Rawski
- Cryo-EM Facility, SOLARIS National Synchrotron Radiation Centre, Krakow, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Wang L, Liu R, Li F, Meng Y, Lu H. Unveiling the novel characteristics of IGPD polymer and inhibitors binding affinities using 12-6-4 LJ-type nonbonded Mn2+ model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pozdnyakov IP, Sherin PS, Salomatova VA, Parkhats MV, Grivin VP, Dzhagarov BM, Bazhin NM, Plyusnin VF. Photooxidation of herbicide amitrole in the presence of fulvic acid. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:20320-20327. [PMID: 28233210 DOI: 10.1007/s11356-017-8580-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Fulvic acid (Henan ChangSheng Corporation) photoinduced degradation of non-UVA-absorbing herbicide amitrole (3-amino-1,2,4-triazole, AMT) as a way for its removal from polluted water was investigated in details. It was shown that the main primary species generated by fulvic acid under UVA radiation, triplet state and hydrated electron, are not directly involved in the herbicide degradation. AMT decays in reactions with secondary intermediates, reactive oxygen species, formed in reactions of the primary ones with dissolved oxygen. Singlet oxygen is responsible for 80% of herbicide oxidation, and •OH and O2-• radicals-for the remaining 20% of AMT. It was found that quantum yield of AMT photodegradation (ϕ 365nm) decreases linearly from 2.2 × 10-3 to 1.2 × 10-3 with the increase of fulvic acid concentration from 1.1 to 30 mg L-1. On the contrary, the increase of AMT concentration from 0.8 to 25 mg L-1 leads to practically linear growth of ϕ 365nm value from 1.8 × 10-4 to 4 × 10-3. Thus, the fulvic acid exhibits a good potential as UVA photooxidizer of organic pollutants sensitive to the singlet oxygen (ϕ 532nm(1O2) = 0.025 at pH 6.5).
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Affiliation(s)
- Ivan P Pozdnyakov
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya str, Novosibirsk, Russian Federation, 630090.
- Novosibirsk State University, 2 Pirogova St., Novosibirsk, Russian Federation, 630090.
| | - Peter S Sherin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk, Russian Federation, 630090
- International Tomography Center, 3a Institutskaya str, Novosibirsk, Russian Federation, 630090
| | - Victoria A Salomatova
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya str, Novosibirsk, Russian Federation, 630090
| | - Marina V Parkhats
- B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 220072, Minsk, Belarus
| | - Vjacheslav P Grivin
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya str, Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, 2 Pirogova St., Novosibirsk, Russian Federation, 630090
| | - Boris M Dzhagarov
- B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 220072, Minsk, Belarus
| | - Nikolai M Bazhin
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya str, Novosibirsk, Russian Federation, 630090
| | - Victor F Plyusnin
- V.V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya str, Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, 2 Pirogova St., Novosibirsk, Russian Federation, 630090
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Fujii N, Yano S, Takeshita K. Selective enhancing effect of metal ions on mutagenicity. Genes Environ 2016; 38:21. [PMID: 27822322 PMCID: PMC5088689 DOI: 10.1186/s41021-016-0049-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND We investigated the enhancing effect of metal ions on several mutagens and examined their mechanism of action. We performed the Ames tests on six mutagens, i.e., 2-(2-furyl)-3-(5-nitro-2-furyl)acrylamide, 4-nitroquinoline 1-oxide (4NQO), quercetin, 2-aminoanthracene (2-AA), benzo[a]pyrene, and 3-amino-1,4-dimethyl-5H-pyrido-[4,3-b]indole, in the presence of five metal ions: Ca(II), Mg(II), Mn(II), Cu(II), and Zn(II). RESULTS Cu(II) enhanced the mutagenicity of only 4NQO and reduced the mutagenicity of the other mutagens. Zn (II) enhanced the mutagenicity of only 2-AA. To clarify the mechanism underlying the enhancing effects of Cu(II), we examined the production of reactive oxygen species (ROS) and 8-oxoguanine (8-oxoG), a DNA damage marker, in human lung carcinoma A549 cells. Cu(II) induced a remarkable increase in intracellular ROS and 8-oxoG production in the presence of 4NQO. CONCLUSIONS Our results suggest that the enhancing effect of Cu(II) and Zn(II) on the mutagenicity of specific mutagens is caused by an increase in ROS.
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Affiliation(s)
- Nobuyoshi Fujii
- Safety Evaluation Laboratory, UBE Scientific Analysis Laboratory, Inc., 1978-6, Aza-okinoyama Oaza-kogushi, Ube-shi, Yamaguchi-pref. Japan
| | - Shigemitsu Yano
- Safety Evaluation Laboratory, UBE Scientific Analysis Laboratory, Inc., 1978-6, Aza-okinoyama Oaza-kogushi, Ube-shi, Yamaguchi-pref. Japan
| | - Kenji Takeshita
- Safety Evaluation Laboratory, UBE Scientific Analysis Laboratory, Inc., 1978-6, Aza-okinoyama Oaza-kogushi, Ube-shi, Yamaguchi-pref. Japan
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Dietl AM, Amich J, Leal S, Beckmann N, Binder U, Beilhack A, Pearlman E, Haas H. Histidine biosynthesis plays a crucial role in metal homeostasis and virulence of Aspergillus fumigatus. Virulence 2016; 7:465-76. [PMID: 26854126 PMCID: PMC4871644 DOI: 10.1080/21505594.2016.1146848] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aspergillus fumigatus is the most prevalent airborne fungal pathogen causing invasive fungal infections in immunosuppressed individuals. The histidine biosynthetic pathway is found in bacteria, archaebacteria, lower eukaryotes, and plants, but is absent in mammals. Here we demonstrate that deletion of the gene encoding imidazoleglycerol-phosphate dehydratase (HisB) in A. fumigatus causes (i) histidine auxotrophy, (ii) decreased resistance to both starvation and excess of various heavy metals, including iron, copper and zinc, which play a pivotal role in antimicrobial host defense, (iii) attenuation of pathogenicity in 4 virulence models: murine pulmonary infection, murine systemic infection, murine corneal infection, and wax moth larvae. In agreement with the in vivo importance of histidine biosynthesis, the HisB inhibitor 3-amino-1,2,4-triazole reduced the virulence of the A. fumigatus wild type and histidine supplementation partially rescued virulence of the histidine-auxotrophic mutant in the wax moth model. Taken together, this study reveals limited histidine availability in diverse A. fumigatus host niches, a crucial role for histidine in metal homeostasis, and the histidine biosynthetic pathway as being an attractive target for development of novel antifungal therapy approaches.
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Affiliation(s)
- Anna-Maria Dietl
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Jorge Amich
- b IZKF Forschergruppe für Experimentelle Stammzelltransplantation, Medizinische Klinik und Poliklinik II & Universitäts-Kinderklinik , Würzburg , Germany
| | - Sixto Leal
- c Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Nicola Beckmann
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Ulrike Binder
- d Division of Hygiene & Medical Microbiology, Medical University of Innsbruck , Innsbruck , Austria
| | - Andreas Beilhack
- b IZKF Forschergruppe für Experimentelle Stammzelltransplantation, Medizinische Klinik und Poliklinik II & Universitäts-Kinderklinik , Würzburg , Germany
| | - Eric Pearlman
- c Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Hubertus Haas
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
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Nikoloff N, Larramendy ML, Soloneski S. Comparative evaluation in vitro of the herbicide flurochloridone by cytokinesis-block micronucleus cytome and comet assays. ENVIRONMENTAL TOXICOLOGY 2014; 29:884-892. [PMID: 22987626 DOI: 10.1002/tox.21816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/13/2012] [Accepted: 08/18/2012] [Indexed: 06/01/2023]
Abstract
The in-vitro effects of flurochloridone and its formulations Twin Pack Gold® (25% a.i.) and Rainbow® (25% a.i.) were evaluated in Chinese Hamster Ovary K1 (CHO-K1) cells. The cytokinesis-block micronucleus cytome (CBMN-cyt) and single-cell gel electrophoresis (SCGE) assays were used. The activities were tested within the range of final concentrations of 0.25-15 μg flurochloridone/mL. The results demonstrated that both the flurochloridone and Rainbow® were not able to induce micronuclei (MN). On the other hand, Twin Pack Gold® only increased the frequency of MN at 5 μg/mL. Furthermore, 10 and 15 μg/mL of both formulations resulted in a cellular cytotoxicity demonstrated by alterations in the nuclear division index and cellular death. SCGE assay appeared to be a more sensitive bioassay for detecting primary DNA strand breaks at lower concentrations of flurochloridone than MN did. A marked increase in the genetic damage index was observed when 5 and 15 μg/mL of both flurochloridone and Rainbow® but only when 15 μg/mL of Twin Pack Gold® were used. This is the first report demonstrating that flurochloridone and its two commercial formulations are able to induce single-strand DNA breaks in vitro on mammalian cells.
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Affiliation(s)
- Noelia Nikoloff
- Cátedra de Citología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Calle 64 N° 3, B1904AMA La Plata, Argentina
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Nikoloff N, Larramendy ML, Soloneski S. Assessment of DNA damage, cytotoxicity, and apoptosis in human hepatoma (HepG2) cells after flurochloridone herbicide exposure. Food Chem Toxicol 2014; 65:233-41. [DOI: 10.1016/j.fct.2013.12.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/23/2013] [Accepted: 12/27/2013] [Indexed: 12/20/2022]
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