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Li J, Wang X, Zhang H, Hu X, Peng X, Jiang W, Zhuo L, Peng Y, Zeng G, Wang Z. Fenamates: Forgotten treasure for cancer treatment and prevention: Mechanisms of action, structural modification, and bright future. Med Res Rev 2024. [PMID: 39171404 DOI: 10.1002/med.22079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/03/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
Fenamates as classical nonsteroidal anti-inflammatory agents are widely used for relieving pain. Preclinical studies and epidemiological data highlight their chemo-preventive and chemotherapeutic potential for cancer. However, comprehensive reviews of fenamates in cancer are limited. To accelerate the repurposing of fenamates, this review summarizes the results of fenamates alone or in combination with existing chemotherapeutic agents. This paper also explores targets of fenamates in cancer therapy, including COX, AKR family, AR, gap junction, FTO, TEAD, DHODH, TAS2R14, ion channels, and DNA. Besides, this paper discusses other mechanisms, such as regulating Wnt/β-catenin, TGF-β, p38 MAPK, and NF-κB pathway, and the regulation of the expressions of Sp, EGR-1, NAG-1, ATF-3, ErbB2, AR, as well as the modulation of the tumor immune microenvironment. Furthermore, this paper outlined the structural modifications of fenamates, highlighting their potential as promising leads for anticancer drugs.
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Affiliation(s)
- Junfang Li
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaodong Wang
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Honghua Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaoling Hu
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Xue Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weifan Jiang
- Postdoctoral Station for Basic Medicine, School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Linsheng Zhuo
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Postdoctoral Station for Basic Medicine, School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yan Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Guo Zeng
- Postdoctoral Station for Basic Medicine, School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhen Wang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Postdoctoral Station for Basic Medicine, School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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2
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Vyas VK, Shukla T, Sharma M. Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. Future Med Chem 2023; 15:1295-1321. [PMID: 37551689 DOI: 10.4155/fmc-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.
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Affiliation(s)
- Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Tanvi Shukla
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
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3
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Chaudhary D, Singh A, Marzuki M, Ghosh A, Kidwai S, Gosain TP, Chawla K, Gupta SK, Agarwal N, Saha S, Kumar Y, Thakur KG, Singhal A, Singh R. Identification of small molecules targeting homoserine acetyl transferase from Mycobacterium tuberculosis and Staphylococcus aureus. Sci Rep 2022; 12:13801. [PMID: 35963878 PMCID: PMC9376091 DOI: 10.1038/s41598-022-16468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
There is an urgent need to validate new drug targets and identify small molecules that possess activity against both drug-resistant and drug-sensitive bacteria. The enzymes belonging to amino acid biosynthesis have been shown to be essential for growth in vitro, in vivo and have not been exploited much for the development of anti-tubercular agents. Here, we have identified small molecule inhibitors targeting homoserine acetyl transferase (HSAT, MetX, Rv3341) from M. tuberculosis. MetX catalyses the first committed step in L-methionine and S-adenosyl methionine biosynthesis resulting in the formation of O-acetyl-homoserine. Using CRISPRi approach, we demonstrate that conditional repression of metX resulted in inhibition of M. tuberculosis growth in vitro. We have determined steady state kinetic parameters for the acetylation of L-homoserine by Rv3341. We show that the recombinant enzyme followed Michaelis-Menten kinetics and utilizes both acetyl-CoA and propionyl-CoA as acyl-donors. High-throughput screening of a 2443 compound library resulted in identification of small molecule inhibitors against MetX enzyme from M. tuberculosis. The identified lead compounds inhibited Rv3341 enzymatic activity in a dose dependent manner and were also active against HSAT homolog from S. aureus. Molecular docking of the identified primary hits predicted residues that are essential for their binding in HSAT homologs from M. tuberculosis and S. aureus. ThermoFluor assay demonstrated direct binding of the identified primary hits with HSAT proteins. Few of the identified small molecules were able to inhibit growth of M. tuberculosis and S. aureus in liquid cultures. Taken together, our findings validated HSAT as an attractive target for development of new broad-spectrum anti-bacterial agents that should be effective against drug-resistant bacteria.
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Affiliation(s)
- Deepika Chaudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Avantika Singh
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Mardiana Marzuki
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Saqib Kidwai
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Kiran Chawla
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.,Singapore Immunology Network (SIgN), (A*STAR), Singapore, 138648, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India. .,Tuberculosis Research Laboratory, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, PO Box # 4, Faridabad, 121001, India.
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4
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Huff SE, Winter JM, Dealwis CG. Inhibitors of the Cancer Target Ribonucleotide Reductase, Past and Present. Biomolecules 2022; 12:biom12060815. [PMID: 35740940 PMCID: PMC9221315 DOI: 10.3390/biom12060815] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/02/2023] Open
Abstract
Ribonucleotide reductase (RR) is an essential multi-subunit enzyme found in all living organisms; it catalyzes the rate-limiting step in dNTP synthesis, namely, the conversion of ribonucleoside diphosphates to deoxyribonucleoside diphosphates. As expression levels of human RR (hRR) are high during cell replication, hRR has long been considered an attractive drug target for a range of proliferative diseases, including cancer. While there are many excellent reviews regarding the structure, function, and clinical importance of hRR, recent years have seen an increase in novel approaches to inhibiting hRR that merit an updated discussion of the existing inhibitors and strategies to target this enzyme. In this review, we discuss the mechanisms and clinical applications of classic nucleoside analog inhibitors of hRRM1 (large catalytic subunit), including gemcitabine and clofarabine, as well as inhibitors of the hRRM2 (free radical housing small subunit), including triapine and hydroxyurea. Additionally, we discuss novel approaches to targeting RR and the discovery of new classes of hRR inhibitors.
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Affiliation(s)
- Sarah E. Huff
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
| | - Jordan M. Winter
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Akron, OH 44106, USA;
| | - Chris G. Dealwis
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
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5
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A comprehensive review on quinones based fluoride selective colorimetric and fluorescence chemosensors. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2021.109744] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Yamamoto M, Ichinohe T, Watanabe A, Kobayashi A, Zhang R, Song J, Kawaguchi Y, Matsuda Z, Inoue JI. The Antimalarial Compound Atovaquone Inhibits Zika and Dengue Virus Infection by Blocking E Protein-Mediated Membrane Fusion. Viruses 2020; 12:v12121475. [PMID: 33371476 PMCID: PMC7767512 DOI: 10.3390/v12121475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022] Open
Abstract
Flaviviruses bear class II fusion proteins as their envelope (E) proteins. Here, we describe the development of an in vitro quantitative mosquito-cell-based membrane-fusion assay for the E protein using dual split proteins (DSPs). The assay does not involve the use of live viruses and allows the analysis of a membrane-fusion step independent of other events in the viral lifecycle, such as endocytosis. The progress of membrane fusion can be monitored continuously by measuring the activities of Renilla luciferase derived from the reassociation of DSPs during cell fusion. We optimized the assay to screen an FDA-approved drug library for a potential membrane fusion inhibitor using the E protein of Zika virus. Screening results identified atovaquone, which was previously described as an antimalarial agent. Atovaquone potently blocked the in vitro Zika virus infection of mammalian cells with an IC90 of 2.1 µM. Furthermore, four distinct serotypes of dengue virus were also inhibited by atovaquone with IC90 values of 1.6–2.5 µM, which is a range below the average blood concentration of atovaquone after its oral administration in humans. These findings make atovaquone a likely candidate drug to treat illnesses caused by Zika as well as dengue viruses. Additionally, the DSP assay is useful to study the mechanism of membrane fusion in Flaviviruses.
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Affiliation(s)
- Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takeshi Ichinohe
- Division of Viral Infection, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Aya Watanabe
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ayako Kobayashi
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
| | - Rui Zhang
- Laboratory of Structural Virology and Immunology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100864, China;
| | - Jiping Song
- China-Japan Joint Laboratory of Molecular Immunology & Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100864, China;
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
- Division of Molecular Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Zene Matsuda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 780-8072, Japan
- Correspondence: (Z.M.); (J.-i.I.); Tel.: +81-3-6409-2204 (Z.M.); +81-3-6409-2476 (J.-i.I.)
| | - Jun-ichiro Inoue
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan; (M.Y.); (A.W.); (A.K.); (Y.K.)
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 113-0033, Japan
- Senior Professor Office, The University of Tokyo, Tokyo 113-0033, Japan
- Correspondence: (Z.M.); (J.-i.I.); Tel.: +81-3-6409-2204 (Z.M.); +81-3-6409-2476 (J.-i.I.)
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Song J, Malwal SR, Baig N, Schurig-Briccio LA, Gao Z, Vaidya GS, Yang K, Abutaleb NS, Seleem MN, Gennis RB, Pogorelov TV, Oldfield E, Feng X. Discovery of Prenyltransferase Inhibitors with In Vitro and In Vivo Antibacterial Activity. ACS Infect Dis 2020; 6:2979-2993. [PMID: 33085463 DOI: 10.1021/acsinfecdis.0c00472] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cis-prenyltransferases such as undecaprenyl diphosphate synthase (UPPS) and decaprenyl diphosphate synthase (DPPS) are essential enzymes in bacteria and are involved in cell wall biosynthesis. UPPS and DPPS are absent in the human genome, so they are of interest as targets for antibiotic development. Here, we screened a library of 750 compounds from National Cancer Institute Diversity Set V for the inhibition of Mycobacterium tuberculosis DPPS and found 17 hits, and then IC50s were determined using dose-response curves. Compounds were tested for growth inhibition against a panel of bacteria, for in vivo activity in a Staphylococcus aureus/Caenorhabditis elegans model, and for mammalian cell toxicity. The most active DPPS inhibitor was the dicarboxylic acid redoxal (compound 10), which also inhibited undecaprenyl diphosphate synthase (UPPS) as well as farnesyl diphosphate synthase. 10 was active against S. aureus, Clostridiodes difficile, Bacillus anthracis Sterne, and Bacillus subtilis, and there was a 3.4-fold increase in IC50 on addition of a rescue agent, undecaprenyl monophosphate. We found that 10 was also a weak protonophore uncoupler, leading to the idea that it targets both isoprenoid biosynthesis and the proton motive force. In an S. aureus/C. elegans in vivo model, 10 reduced the S. aureus burden 3 times more effectively than did ampicillin.
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Affiliation(s)
- Junfeng Song
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | | | | | | | | | | | - Kailing Yang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Nader S. Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohamed N. Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | | | | | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
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8
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Löffler M, Carrey EA, Knecht W. The pathway to pyrimidines: The essential focus on dihydroorotate dehydrogenase, the mitochondrial enzyme coupled to the respiratory chain. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1281-1305. [PMID: 32043431 DOI: 10.1080/15257770.2020.1723625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper is based on the Anne Simmonds Memorial Lecture, given by Monika Löffler at the International Symposium on Purine and Pyrimidine Metabolism in Man, Lyon 2019. It is dedicated to H. Anne Simmonds (died 2010) - a founding member of the ESSPPMM, since 2003 Purine and Pyrimidine Society - and her outstanding contributions to the identification and study of inborn errors of purine and pyrimidine metabolism. The distinctive intracellular arrangement of pyrimidine de novo synthesis in higher eukaryotes is important to cells with a high demand for nucleic acid synthesis. The proximity of the enzyme active sites and the resulting channeling in CAD and UMP synthase is of kinetic benefit. The intervening enzyme dihydroorotate dehydrogenase (DHODH) is located in the mitochondrion with access to the ubiquinone pool, thus ensuring efficient removal of redox equivalents through the constitutive activity of the respiratory chain, also a mechanism through which the input of 2 ATP for carbamylphosphate synthesis is balanced by Oxphos. The obligatory contribution of O2 to de novo UMP synthesis means that DHODH has a pivotal role in adapting the proliferative capacity of cells to different conditions of oxygenation, such as hypoxia in growing tumors. DHODH also is a validated drug target in inflammatory diseases. This survey of selected topics of personal interest and reflection spans some 40 years of our studies from tumor cell cultures under hypoxia to in vitro assays including purification from mitochondria, localization, cloning, expression, biochemical characterization, crystallisation, kinetics and inhibition patterns of eukaryotic DHODH enzymes.
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Affiliation(s)
- Monika Löffler
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps-University Marburg, Marburg, Germany
| | | | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University, Lund, Sweden
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9
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Meekrathok P, Thongsom S, Aunkham A, Kaewmaneewat A, Kitaoku Y, Choowongkomon K, Suginta W. Novel GH-20 β-N-acetylglucosaminidase inhibitors: Virtual screening, molecular docking, binding affinity, and anti-tumor activity. Int J Biol Macromol 2020; 142:503-512. [DOI: 10.1016/j.ijbiomac.2019.09.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023]
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10
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Garavito MF, Narvaez-Ortiz HY, Pulido DC, Löffler M, Judelson HS, Restrepo S, Zimmermann BH. Phytophthora infestans Dihydroorotate Dehydrogenase Is a Potential Target for Chemical Control - A Comparison With the Enzyme From Solanum tuberosum. Front Microbiol 2019; 10:1479. [PMID: 31316493 PMCID: PMC6611227 DOI: 10.3389/fmicb.2019.01479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/13/2019] [Indexed: 01/04/2023] Open
Abstract
The oomycete Phytophthora infestans is the causal agent of tomato and potato late blight, a disease that causes tremendous economic losses in the production of solanaceous crops. The similarities between oomycetes and the apicomplexa led us to hypothesize that dihydroorotate dehydrogenase (DHODH), the enzyme catalyzing the fourth step in pyrimidine biosynthetic pathway, and a validated drug target in treatment of malaria, could be a potential target for controlling P. infestans growth. In eukaryotes, class 2 DHODHs are mitochondrially associated ubiquinone-linked enzymes that catalyze the fourth, and only redox step of de novo pyrimidine biosynthesis. We characterized the enzymes from both the pathogen and a host, Solanum tuberosum. Plant DHODHs are known to be class 2 enzymes. Sequence analysis suggested that the pathogen enzyme (PiDHODHs) also belongs to this class. We confirmed the mitochondrial localization of GFP-PiDHODH showing colocalization with mCherry-labeled ATPase in a transgenic pathogen. N-terminally truncated versions of the two DHODHs were overproduced in E. coli, purified, and kinetically characterized. StDHODH exhibited a apparent specific activity of 41 ± 1 μmol min-1 mg-1, a kcatapp of 30 ± 1 s-1, and a Kmapp of 20 ± 1 μM for L-dihydroorotate, and a Kmapp= 30 ± 3 μM for decylubiquinone (Qd). PiDHODH exhibited an apparent specific activity of 104 ± 1 μmol min-1 mg-1, a kcatapp of 75 ± 1 s-1, and a Kmapp of 57 ± 3 μM for L-dihydroorotate, and a Kmapp of 15 ± 1 μM for Qd. The two enzymes exhibited different activities with different quinones and napthoquinone derivatives, and different sensitivities to compounds known to cause inhibition of DHODHs from other organisms. The IC50 for A77 1726, a nanomolar inhibitor of human DHODH, was 2.9 ± 0.6 mM for StDHODH, and 79 ± 1 μM for PiDHODH. In vivo, 0.5 mM A77 1726 decreased mycelial growth by approximately 50%, after 92 h. Collectively, our findings suggest that the PiDHODH could be a target for selective inhibitors and we provide a biochemical background for the development of compounds that could be helpful for the control of the pathogen, opening the way to protein crystallization.
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Affiliation(s)
- Manuel F Garavito
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.,Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | | | - Dania Camila Pulido
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Monika Löffler
- Faculty of Medicine, Department of Biology, University of Marburg, Marburg, Germany
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
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11
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Ivanov S, Semin M, Lagunin A, Filimonov D, Poroikov V. In Silico Identification of Proteins Associated with Drug-induced Liver Injury Based on the Prediction of Drug-target Interactions. Mol Inform 2017; 36. [PMID: 28145637 DOI: 10.1002/minf.201600142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022]
Abstract
Drug-induced liver injury (DILI) is the leading cause of acute liver failure as well as one of the major reasons for drug withdrawal from clinical trials and the market. Elucidation of molecular interactions associated with DILI may help to detect potentially hazardous pharmacological agents at the early stages of drug development. The purpose of our study is to investigate which interactions with specific human protein targets may cause DILI. Prediction of interactions with 1534 human proteins was performed for the dataset with information about 699 drugs, which were divided into three categories of DILI: severe (178 drugs), moderate (310 drugs) and without DILI (211 drugs). Based on the comparison of drug-target interactions predicted for different drugs' categories and interpretation of those results using clustering, Gene Ontology, pathway and gene expression analysis, we identified 61 protein targets associated with DILI. Most of the revealed proteins were linked with hepatocytes' death caused by disruption of vital cellular processes, as well as the emergence of inflammation in the liver. It was found that interaction of a drug with the identified targets is the essential molecular mechanism of the severe DILI for the most of the considered pharmaceuticals. Thus, pharmaceutical agents interacting with many of the identified targets may be considered as candidates for filtering out at the early stages of drug research.
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Affiliation(s)
- Sergey Ivanov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Maxim Semin
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Alexey Lagunin
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Dmitry Filimonov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia
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12
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Crona M, Codó P, Jonna VR, Hofer A, Fernandes AP, Tholander F. A ribonucleotide reductase inhibitor with deoxyribonucleoside-reversible cytotoxicity. Mol Oncol 2016; 10:1375-1386. [PMID: 27511871 DOI: 10.1016/j.molonc.2016.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Ribonucleotide Reductase (RNR) is the sole enzyme that catalyzes the reduction of ribonucleotides into deoxyribonucleotides. Even though RNR is a recognized target for antiproliferative molecules, and the main target of the approved drug hydroxyurea, few new leads targeted to this enzyme have been developed. We have evaluated a recently identified set of RNR inhibitors with respect to inhibition of the human enzyme and cellular toxicity. One compound, NSC73735, is particularly interesting; it is specific for leukemia cells and is the first identified compound that hinders oligomerization of the mammalian large RNR subunit. Similar to hydroxyurea, it caused a disruption of the cell cycle distribution of cultured HL-60 cells. In contrast to hydroxyurea, the disruption was reversible, indicating higher specificity. NSC73735 thus defines a potential lead candidate for RNR-targeted anticancer drugs, as well as a chemical probe with better selectivity for RNR inhibition than hydroxyurea.
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Affiliation(s)
- Mikael Crona
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Paula Codó
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | | | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Aristi P Fernandes
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Fredrik Tholander
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.
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13
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Pery E, Sheehy A, Miranda Nebane N, Misra V, Mankowski MK, Rasmussen L, Lucile White E, Ptak RG, Gabuzda D. Redoxal, an inhibitor of de novo pyrimidine biosynthesis, augments APOBEC3G antiviral activity against human immunodeficiency virus type 1. Virology 2015; 484:276-287. [PMID: 26141568 DOI: 10.1016/j.virol.2015.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3G (A3G) is a cytidine deaminase that restricts HIV-1 replication by inducing G-to-A hypermutation in viral DNA; deamination-independent mechanisms are also implicated. HIV-1 Vif protein counteracts A3G by inducing its proteasomal degradation. Thus, the Vif-A3G axis is a potential therapeutic target. To identify compounds that inhibit Vif:A3G interaction, a 307,520 compound library was tested in a TR-FRET screen. Two identified compounds, redoxal and lomofungin, inhibited HIV-1 replication in peripheral blood mononuclear cells. Lomofungin activity was linked to A3G, but not pursued further due to cytotoxicity. Redoxal displayed A3G-dependent restriction, inhibiting viral replication by stabilizing A3G protein levels and increasing A3G in virions. A3G-independent activity was also detected. Treatment with uridine or orotate, intermediates of pyrimidine synthesis, diminished redoxal-induced stabilization of A3G and antiviral activity. These results identify redoxal as an inhibitor of HIV-1 replication and suggest its ability to inhibit pyrimidine biosynthesis suppresses viral replication by augmenting A3G antiviral activity.
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Affiliation(s)
- Erez Pery
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States; Department of Pathology, Harvard Medical School, Boston, MA 02115, United States
| | - Ann Sheehy
- Department of Biology, College of the Holy Cross, Worcester, MA 01610, United States
| | - N Miranda Nebane
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - Vikas Misra
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States
| | - Marie K Mankowski
- Southern Research Institute, Department of Infectious Disease Research, Frederick, MD 21701, United States
| | - Lynn Rasmussen
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - E Lucile White
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - Roger G Ptak
- Southern Research Institute, Department of Infectious Disease Research, Frederick, MD 21701, United States
| | - Dana Gabuzda
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States; Department of Neurology (Microbiology), Harvard Medical School, Boston, MA 02115, United States.
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14
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Pery E, Sheehy A, Nebane NM, Brazier AJ, Misra V, Rajendran KS, Buhrlage SJ, Mankowski MK, Rasmussen L, White EL, Ptak RG, Gabuzda D. Identification of a novel HIV-1 inhibitor targeting Vif-dependent degradation of human APOBEC3G protein. J Biol Chem 2015; 290:10504-17. [PMID: 25724652 DOI: 10.1074/jbc.m114.626903] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 11/06/2022] Open
Abstract
APOBEC3G (A3G) is a cellular cytidine deaminase that restricts HIV-1 replication by inducing G-to-A hypermutation in viral DNA and by deamination-independent mechanisms. HIV-1 Vif binds to A3G, resulting in its degradation via the 26 S proteasome. Therefore, this interaction represents a potential therapeutic target. To identify compounds that inhibit interaction between A3G and HIV-1 Vif in a high throughput format, we developed a homogeneous time-resolved fluorescence resonance energy transfer assay. A 307,520 compound library from the NIH Molecular Libraries Small Molecule Repository was screened. Secondary screens to evaluate dose-response performance and off-target effects, cell-based assays to identify compounds that attenuate Vif-dependent degradation of A3G, and assays testing antiviral activity in peripheral blood mononuclear cells and T cells were employed. One compound, N.41, showed potent antiviral activity in A3G(+) but not in A3G(-) T cells and had an IC50 as low as 8.4 μM and a TC50 of >100 μM when tested against HIV-1Ba-L replication in peripheral blood mononuclear cells. N.41 inhibited the Vif-A3G interaction and increased cellular A3G levels and incorporation of A3G into virions, thereby attenuating virus infectivity in a Vif-dependent manner. N.41 activity was also species- and Vif-dependent. Preliminary structure-activity relationship studies suggest that a hydroxyl moiety located at a phenylamino group is critical for N.41 anti-HIV activity and identified N.41 analogs with better potency (IC50 as low as 4.2 μM). These findings identify a new lead compound that attenuates HIV replication by liberating A3G from Vif regulation and increasing its innate antiviral activity.
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Affiliation(s)
- Erez Pery
- From the Departments of Cancer Immunology and AIDS and Departments of Pathology and
| | - Ann Sheehy
- Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610
| | - N Miranda Nebane
- Southern Research Institute High Throughput Screening Center, Birmingham, Alabama 35205, and
| | | | - Vikas Misra
- From the Departments of Cancer Immunology and AIDS and
| | | | | | - Marie K Mankowski
- Southern Research Institute, Department of Infectious Disease Research, Frederick, Maryland 21701
| | - Lynn Rasmussen
- Southern Research Institute High Throughput Screening Center, Birmingham, Alabama 35205, and
| | - E Lucile White
- Southern Research Institute High Throughput Screening Center, Birmingham, Alabama 35205, and
| | - Roger G Ptak
- Southern Research Institute, Department of Infectious Disease Research, Frederick, Maryland 21701
| | - Dana Gabuzda
- From the Departments of Cancer Immunology and AIDS and Neurology (Microbiology), Harvard Medical School, Boston, Massachusetts 02115,
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15
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Jali BR, Kuang Y, Neamati N, Baruah JB. Selective binding of naphthoquinone derivatives to serum albumin proteins and their effects on cytotoxicity. Chem Biol Interact 2014; 214:10-7. [DOI: 10.1016/j.cbi.2014.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/10/2013] [Accepted: 01/23/2014] [Indexed: 01/05/2023]
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16
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Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
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Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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17
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Manerba M, Vettraino M, Fiume L, Di Stefano G, Sartini A, Giacomini E, Buonfiglio R, Roberti M, Recanatini M. Galloflavin (CAS 568-80-9): a novel inhibitor of lactate dehydrogenase. ChemMedChem 2011; 7:311-7. [PMID: 22052811 DOI: 10.1002/cmdc.201100471] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 10/10/2011] [Indexed: 11/10/2022]
Abstract
One of the most prominent alterations in cancer cells is their strict dependence on the glycolytic pathway for ATP generation. This observation led to the evaluation of glycolysis inhibitors as potential anticancer agents. The inhibition of lactate dehydrogenase (LDH) is a promising way to inhibit tumor cell glucose metabolism without affecting the energetic balance of normal tissues. However, the success of this approach depends chiefly on the availability of inhibitors that display good selectivity. We identified a compound (galloflavin, CAS 568-80-9) which, in contrast to other inhibitors of human LDH, hinders both the A and B isoforms of the enzyme. To determine the mechanism of action, we collected LDH-A and -B inhibition data in competition reactions with pyruvate or NADH and evaluated the results using software for enzyme kinetics analysis. We found that galloflavin inhibits both human LDH isoforms by preferentially binding the free enzyme, without competing with the substrate or cofactor. The calculated Ki values for pyruvate were 5.46 μM (LDH-A) and 15.06 μM (LDH-B). In cultured tumor cells, galloflavin blocked aerobic glycolysis at micromolar concentrations, did not interfere with cell respiration, and induced cell death by triggering apoptosis. To our knowledge, the inhibition of LDH is, to date, the only biochemical effect described for galloflavin. Because galloflavin is not commercially available, we also describe herein a procedure for its synthesis and report its first full chemical characterization.
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Affiliation(s)
- Marcella Manerba
- Department of Experimental Pathology, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
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18
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Kumagai Y, Shinkai Y, Miura T, Cho AK. The chemical biology of naphthoquinones and its environmental implications. Annu Rev Pharmacol Toxicol 2011; 52:221-47. [PMID: 21942631 DOI: 10.1146/annurev-pharmtox-010611-134517] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quinones are a group of highly reactive organic chemical species that interact with biological systems to promote inflammatory, anti-inflammatory, and anticancer actions and to induce toxicities. This review describes the chemistry, biochemistry, and cellular effects of 1,2- and 1,4-naphthoquinones and their derivatives. The naphthoquinones are of particular interest because of their prevalence as natural products and as environmental chemicals, present in the atmosphere as products of fuel and tobacco combustion. 1,2- and 1,4-naphthoquinones are also toxic metabolites of naphthalene, the major polynuclear aromatic hydrocarbon present in ambient air. Quinones exert their actions through two reactions: as prooxidants, reducing oxygen to reactive oxygen species; and as electrophiles, forming covalent bonds with tissue nucleophiles. The targets for these reactions include regulatory proteins such as protein tyrosine phosphatases; Kelch-like ECH-associated protein 1, the regulatory protein for NF-E2-related factor 2; and the glycolysis enzyme glyceraldehyde-3-phosphate dehydrogenase. Through their actions on regulatory proteins, quinones affect various cell signaling pathways that promote and protect against inflammatory responses and cell damage. These actions vary with the specific quinone and its concentration. Effects of exposure to naphthoquinones as environmental chemicals can vary with the physical state, i.e., whether the quinone is particle bound or is in the vapor state. The exacerbation of pulmonary diseases by air pollutants can, in part, be attributed to quinone action.
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Affiliation(s)
- Yoshito Kumagai
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575, Japan
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19
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Fritzson I, Svensson B, Al-Karadaghi S, Walse B, Wellmar U, Nilsson UJ, da Graça Thrige D, Jönsson S. Inhibition of human DHODH by 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids identified by structure-guided fragment selection. ChemMedChem 2010; 5:608-17. [PMID: 20183850 DOI: 10.1002/cmdc.200900454] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A strategy that combines virtual screening and structure-guided selection of fragments was used to identify three unexplored classes of human DHODH inhibitor compounds: 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids. Structure-guided selection of fragments targeting the inner subsite of the DHODH ubiquinone binding site made these findings possible with screening of fewer than 300 fragments in a DHODH assay. Fragments from the three inhibitor classes identified were subsequently chemically expanded to target an additional subsite of hydrophobic character. All three classes were found to exhibit distinct structure-activity relationships upon expansion. The novel N-(alkylcarbonyl)anthranilic acid class shows the most promising potency against human DHODH, with IC(50) values in the low nanomolar range. The structure of human DHODH in complex with an inhibitor of this class is presented.
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20
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Setzer B, Lebrecht D, Walker UA. Pyrimidine nucleoside depletion sensitizes to the mitochondrial hepatotoxicity of the reverse transcriptase inhibitor stavudine. THE AMERICAN JOURNAL OF PATHOLOGY 2008; 172:681-90. [PMID: 18276780 DOI: 10.2353/ajpath.2008.070613] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Stavudine is a hepatotoxic antiretroviral nucleoside analogue that also inhibits the replication of mitochondrial DNA (mtDNA). To elucidate the mechanism and consequences of mtDNA depletion, we treated HepG2 cells with stavudine and either redoxal, an inhibitor of de novo pyrimidine synthesis, or uridine, from which pyrimidine pools are salvaged. Compared with treatment with stavudine alone, co-treatment with redoxal accelerated mtDNA depletion, impaired cell division, and activated caspase 3. These adverse effects were completely abrogated by uridine. Intracellular ATP levels were unaffected. Transcriptosome profiling demonstrated that redoxal and stavudine acted synergistically to induce CDKN2A and p21, indicating cell cycle arrest in G1, as well as genes involved in intrinsic and extrinsic apoptosis. Moreover, redoxal and stavudine showed synergistic interaction in the up-regulation of transcripts encoded by mtDNA and the induction of nuclear transcripts participating in energy metabolism, mitochondrial biogenesis, oxidative stress, and DNA repair. Genes involved in nucleotide metabolism were also synergistically up-regulated by both agents; this effect was completely antagonized by uridine. Thus, pyrimidine depletion sensitizes cells to stavudine-mediated mtDNA depletion and enhances secondary cell toxicity. Our results indicate that drugs that diminish pyrimidine pools should be avoided in stavudine-treated human immunodeficiency virus patients. Uridine supplementation reverses this toxicity and, because of its good tolerability, has potential clinical value for the treatment of side effects associated with pyrimidine depletion.
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Affiliation(s)
- Bernhard Setzer
- Department of Rheumatology and Clinical Immunology,Medizinische Universitätsklinik, Hugstetterstr. 55, D-79106 Freiburg, Germany
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21
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Malmquist NA, Gujjar R, Rathod PK, Phillips MA. Analysis of flavin oxidation and electron-transfer inhibition in Plasmodium falciparum dihydroorotate dehydrogenase. Biochemistry 2008; 47:2466-75. [PMID: 18225919 DOI: 10.1021/bi702218c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH) is a flavin-dependent mitochondrial enzyme that provides the only route to pyrimidine biosynthesis in the parasite. Clinically significant inhibitors of human DHODH (e.g., A77 1726) bind to a pocket on the opposite face of the flavin cofactor from dihydroorotate (DHO). This pocket demonstrates considerable sequence variability, which has allowed species-specific inhibitors of the malarial enzyme to be identified. Ubiquinone (CoQ), the physiological oxidant in the reaction, has been postulated to bind this site despite a lack of structural evidence. To more clearly define the residues involved in CoQ binding and catalysis, we undertook site-directed mutagenesis of seven residues in the structurally defined A77 1726 binding site, which we term the species-selective inhibitor site. Mutation of several of these residues (H185, F188, and F227) to Ala substantially decreased the affinity of pfDHODH-specific inhibitors (40-240-fold). In contrast, only a modest increase in the Kmapp for CoQ was observed, although mutation of Y528 in particular caused a substantial reduction in kcat (40-100-fold decrease). Pre-steady-state kinetic analysis by single wavelength stopped-flow spectroscopy showed that the mutations had no effect on the rate of the DHO-dependent reductive half-reaction, but most reduced the rate of the CoQ-dependent flavin oxidation step (3-20-fold decrease), while not significantly altering the Kdox for CoQ. As with the mutants, inhibitors that bind this site block the CoQ-dependent oxidative half-reaction without affecting the DHO-dependent step. These results identify residues involved in inhibitor binding and electron transfer to CoQ. Importantly, the data provide compelling evidence that the binding sites for CoQ and species-selective site inhibitors do not overlap, and they suggest instead that inhibitors act either by blocking the electron path between flavin and CoQ or by stabilizing a conformation that excludes CoQ binding.
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Affiliation(s)
- Nicholas A Malmquist
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, USA
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22
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Zameitat E, Gojković Z, Knecht W, Piskur J, Löffler M. Biochemical characterization of recombinant dihydroorotate dehydrogenase from the opportunistic pathogenic yeast Candida albicans. FEBS J 2006; 273:3183-91. [PMID: 16774642 DOI: 10.1111/j.1742-4658.2006.05327.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Candida albicans is the most prevalent yeast pathogen in humans, and recently it has become increasingly resistant to the current antifungal agents. In this study we investigated C. albicans dihydroorotate dehydrogenase (DHODH, EC 1.3.99.11), which catalyzes the fourth step of de novo pyrimidine synthesis, as a new target for controlling infection. We propose that the enzyme is a member of the DHODH family 2, which comprises mitochondrially bound enzymes, with quinone as the direct electron acceptor and oxygen as the final electron acceptor. Full-length DHODH and N-terminally truncated DHODH, which lacks the targeting sequence and the transmembrane domain, were subcloned from C. albicans, recombinantly expressed in Escherichia coli, purified, and characterized for their kinetics and substrate specificity. An inhibitor screening with 28 selected compounds was performed. Only the dianisidine derivative, redoxal, and the biphenyl quinoline-carboxylic acid derivative, brequinar sodium, which are known to be potent inhibitors of mammalian DHODH, markedly reduced C. albicans DHODH activity. This study provides a background for the development of antipyrimidines with high efficacy for decreasing in situ pyrimidine nucleotide pools in C. albicans.
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Affiliation(s)
- Elke Zameitat
- Institute for Physiological Chemistry, Philipps-University, Marburg, Germany.
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23
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de Witte NV, Stoppani AOM, Dubin M. 2-Phenyl-β-lapachone can affect mitochondrial function by redox cycling mediated oxidation. Arch Biochem Biophys 2004; 432:129-35. [PMID: 15542051 DOI: 10.1016/j.abb.2004.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 09/13/2004] [Indexed: 11/16/2022]
Abstract
2-Phenyl-beta-lapachone (3,4-dihydro-2-methyl-2-phenyl-2H-naphtho[1,2b]pyran-5,6-dione) (2PBL) is a o-naphthoquinone synthesized as a possible antitumoral agent. The addition of micromolar concentrations of 2PBL to rat liver mitochondria (in the presence of malate-glutamate or succinate, as respiratory substrates): (1) stimulated O(2) consumption in state 4 and inhibited O(2) consumption in state 3, thus decreasing respiratory control index (RCI); and (2) collapsed the mitochondrial membrane potential. The addition of 2PBL to rat liver submitochondrial particles: (1) stimulated NADH oxidation in the presence of rotenone, antimycin, myxothiazol or cyanide; (2) stimulated (.-)O(2)(-) production in the presence of NADH and antimycin; and (3) led to 2PBL semiquinone radical production. Control studies carried out with two p-naphthoquinones, menadione and atovaquone, did not produced equivalent effects. These findings support the hypothesis that 2PBL, undergoes redox cycling and affects mitochondrial function. The 2PBL effect is complex, involving inhibition of electron transfer, uncoupling of oxidative phosphorylation, collapse of mitochondrial membrane potential and (.-)O(2)(-) production by redox cycling. The mitochondrion could be a target organelle for 2PBL cytotoxicity.
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Affiliation(s)
- Natacha V de Witte
- Bioenergetics Research Center, School of Medicine, University of Buenos Aires, Paraguay 2155, 1121 Buenos Aires, Argentina
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24
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Zameitat E, Knecht W, Piskur J, Löffler M. Two different dihydroorotate dehydrogenases from yeast Saccharomyces kluyveri. FEBS Lett 2004; 568:129-34. [PMID: 15196933 DOI: 10.1016/j.febslet.2004.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 04/30/2004] [Accepted: 05/13/2004] [Indexed: 11/29/2022]
Abstract
Genes for two structurally and functionally different dihydroorotate dehydrogenases (DHODHs, EC 1.3.99.11), catalyzing the fourth step of pyrimidine biosynthesis, have been previously found in yeast Saccharomyces kluyveri. One is closely related to the Schizosaccharomyces pombe mitochondrial family 2 enzymes, which use quinones as direct and oxygen as the final electron acceptor. The other one resembles the Saccharomyces cerevisiae cytosolic family 1A fumarate-utilizing DHODH. The DHODHs from S. kluyveri, Sch. pombe and S. cerevisiae, were expressed in Escherichia coli and compared for their biochemical properties and interaction with inhibitors. Benzoates as pyrimidine ring analogs were shown to be selective inhibitors of cytosolic DHODs. This unique property of Saccharomyces DHODHs could appoint DHODH as a species-specific target for novel anti-fungal therapeutics.
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Affiliation(s)
- Elke Zameitat
- Institute for Physiological Chemistry, Philipps-University, Karl-von-Frisch-Strasse 1, D-35033 Marburg, Germany.
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25
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Leban J, Saeb W, Garcia G, Baumgartner R, Kramer B. Discovery of a novel series of DHODH inhibitors by a docking procedure and QSAR refinement. Bioorg Med Chem Lett 2004; 14:55-8. [PMID: 14684297 DOI: 10.1016/j.bmcl.2003.10.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel series of DHODH inhibitors was developed based on a lead which was obtained by a docking procedure and a medicinal chemistry exploration. The activity of the initial lead was improved by a QSAR method to yield low nanomolar inhibitors.
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Affiliation(s)
- Johann Leban
- 4SC AG, Am Klopferspitz 19a, 82152 Martinsried, Germany.
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26
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Ullrich A, Knecht W, Fries M, Löffler M. Recombinant expression of N-terminal truncated mutants of the membrane bound mouse, rat and human flavoenzyme dihydroorotate dehydrogenase. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1432-1327.2001.02061.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Nørager S, Arent S, Björnberg O, Ottosen M, Lo Leggio L, Jensen KF, Larsen S. Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function. J Biol Chem 2003; 278:28812-22. [PMID: 12732650 DOI: 10.1074/jbc.m303767200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroorotate dehydrogenases (DHODs) are flavoenzymes catalyzing the oxidation of (S)-dihydroorotate to orotate in the biosynthesis of UMP, the precursor of all other pyrimidine nucleotides. On the basis of sequence, DHODs can be divided into two classes, class 1, further divided in subclasses 1A and 1B, and class 2. This division corresponds to differences in cellular location and the nature of the electron acceptor. Herein we report a study of Lactococcus lactis DHODA, a representative of the class 1A enzymes. Based on the DHODA structure we selected seven residues that are highly conserved between both main classes of DHODs as well as three residues representing surface charges close to the active site for site-directed mutagenesis. The availability of both kinetic and structural data on the mutant enzymes allowed us to define the roles individual structural segments play in catalysis. We have also structurally proven the presence of an open active site loop in DHODA and obtained information about the interactions that control movements of loops around the active site. Furthermore, in one mutant structure we observed differences between the two monomers of the dimer, confirming an apparent asymmetry between the two substrate binding sites that was indicated by the kinetic results.
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Affiliation(s)
- Sofie Nørager
- Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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28
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Baldwin J, Farajallah AM, Malmquist NA, Rathod PK, Phillips MA. Malarial dihydroorotate dehydrogenase. Substrate and inhibitor specificity. J Biol Chem 2002; 277:41827-34. [PMID: 12189151 DOI: 10.1074/jbc.m206854200] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The malarial parasite relies on de novo pyrimidine biosynthesis to maintain its pyrimidine pools, and unlike the human host cell it is unable to scavenge preformed pyrimidines. Dihydroorotate dehydrogenase (DHODH) catalyzes the oxidation of dihydroorotate (DHO) to produce orotate, a key step in pyrimidine biosynthesis. The enzyme is located in the outer membrane of the mitochondria of the malarial parasite. To characterize the biochemical properties of the malarial enzyme, an N-terminally truncated version of P. falciparum DHODH has been expressed as a soluble, active enzyme in E. coli. The recombinant enzyme binds 0.9 molar equivalents of the cofactor FMN and it has a pH maximum of 8.0 (k(cat) 8 s(-1), K(m)(app) DHO (40-80 microm)). The substrate specificity of the ubiquinone cofactor (CoQ(n)) that is required for the oxidation of FMN in the second step of the reaction was also determined. The isoprenoid (n) length of CoQ(n) was a determinant of reaction efficiency; CoQ(4), CoQ(6) and decylubiquinone (CoQ(D)) were efficiently utilized in the reaction, however cofactors lacking an isoprenoid tail (CoQ(0) and vitamin K(3)) showed decreased catalytic efficiency resulting from a 4 to 7-fold increase in K(m)(app). Five potent inhibitors of mammalian DHODH, Redoxal, dichloroallyl lawsone (DCL), and three analogs of A77 1726 were tested as inhibitors of the malarial enzyme. All five compounds were poor inhibitors of the malarial enzyme, with IC(50)'s ranging from 0.1-1.0 mm. The IC(50) values for inhibition of the malarial enzyme are 10(2)-10(4)-fold higher than the values reported for the mammalian enzyme, demonstrating that inhibitor binding to DHODH is species specific. These studies provide direct evidence that the malarial DHODH active site is different from the host enzyme, and that it is an attractive target for the development of new anti-malarial agents.
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Affiliation(s)
- Jeffrey Baldwin
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas, 75390-9041, USA
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Ullrich A, Knecht W, Piskur J, Löffler M. Plant dihydroorotate dehydrogenase differs significantly in substrate specificity and inhibition from the animal enzymes. FEBS Lett 2002; 529:346-50. [PMID: 12372626 DOI: 10.1016/s0014-5793(02)03425-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The mitochondrial membrane bound dihydroorotate dehydrogenase (DHODH; EC 1.3.99.11) catalyzes the fourth step of pyrimidine biosynthesis. By the present correction of a known cDNA sequence for Arabidopsis thaliana DHODH we revealed the importance of the very C-terminal part for its catalytic activity and the reason why--in contrast to mammalian and insect species--the recombinant plant flavoenzyme was unaccessible to date for in vitro characterization. Structure-activity relationship studies explained that potent inhibitors of animal DHODH do not significantly affect the plant enzyme. These difference could be exploited for a novel approach to herb or pest growth control by limitation of pyrimidine nucleotide pools.
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Affiliation(s)
- Alexandra Ullrich
- Institute for Physiological Chemistry, Philipps-University, Karl-von-Frisch-Strasse 1, D-35033 Marburg, Germany.
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Löffler M, Knecht W, Rawls J, Ullrich A, Dietz C. Drosophila melanogaster dihydroorotate dehydrogenase: the N-terminus is important for biological function in vivo but not for catalytic properties in vitro. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2002; 32:1159-1169. [PMID: 12213251 DOI: 10.1016/s0965-1748(02)00052-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Dihydroorotate dehydrogenase (DHODH, EC 1.3.99.11), the fourth enzyme of pyrimidine de novo synthesis, is an integral flavoprotein of the inner mitchondrial membrane and is functionally connected to the respiratory chain. Here, experiments have been directed toward determining the roles of the N-terminal sequence motifs both in enzymatic properties of insect DHODH produced in vitro and the in vivo function of the protein. Full-length and three N-terminal truncated derivatives of the Drosophila melanogaster enzyme were expressed in Escherichia coli and purified. For identification on Western blots of recombinant DHODH as well as the native enzyme from flies polyclonal anti-DHODH immunoglobulins were generated and affinity-purified. The enzymatic characteristics of the four versions of DHODH were very similar, indicating that the N-terminus of the enzyme does not influence its catalytic function or its susceptibility to prominent DHODH inhibitors: A77-1726, brequinar, dichloroallyl-lawsone and redoxal. Whereas the efficacy of A77-1726 and dichloroallyl-lawsone were similar with Drosophila and human DHODH, that of brequinar and redoxal differed significantly. The differences in responses of insect DHODH and the enzyme from other species may allow the design of new agents that will selectively control insect growth, due to pyrimidine nucleotide limitation. In vivo expression of the full-length and N-truncated DHODHs from engineered transgenes revealed that the truncated proteins could not support normal de novo pyrimidine biosynthesis during development of the fly (i.e., failure to complement dhod-null mutations), apparently due to instability of the truncated proteins. It is concluded that the proper intracellular localization, directed by the N-terminal targeting and transmembrane motifs, is required for stability and subsequent proper biological function in vivo.
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Affiliation(s)
- Monika Löffler
- Institute for Physiological Chemistry, Philipps-University Marburg, Karl-von-Frisch-Str. 1, D-35033 Marburg, Germany.
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Knecht W, Loffler M. Inhibition and localization of human and rat dihydroorotate dehydrogenase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2002; 486:267-70. [PMID: 11783497 DOI: 10.1007/0-306-46843-3_52] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- W Knecht
- Department of Microbiology, Technical University of Denmark, Lyngby
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Dietz C, Hinsch E, Löffler M. Immunocytochemical detection of mitochondrial dihydroorotate dehydrogenase in human spermatozoa. INTERNATIONAL JOURNAL OF ANDROLOGY 2000; 23:294-9. [PMID: 11012787 DOI: 10.1046/j.1365-2605.2000.00246.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In mammalian cells the requirement for pyrimidines is met by uridine phosphate (UMP) de novo synthesis and, to a greater or lesser extent, by salvage of free nucleosides. The fourth enzyme of the de novo synthesis, the mitochondrially bound dihydroorotate dehydrogenase (DHODH) was the focus of the present study. Rabbit anti-DHODH IgG, which was generated using an immunization protocol with truncated recombinant human DHODH protein and purified by an immunosorbent method, was used for immunocytochemical detection and localization of this enzyme in ejaculated human spermatozoa. The presence of DHODH protein was demonstrated by Western blotting of solubilized membrane fractions with peroxidase conjugated anti-rabbit IgG in combination with chemiluminescence detection. Indirect immunofluorescence microscopy, using Cy3-conjugated anti-rabbit IgG, revealed specific binding in the midpiece of spermatozoa. As these cells no longer have a demand for de novo biosynthesis of pyrimidines, we hypothesize that the pathway could serve a specialized function in nitrogen or zinc metabolism during the process of spermiogenesis and/or epididymal maturation.
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Affiliation(s)
- C Dietz
- Institute for Physiological Chemistry, School of Medicine, Philipps-University, Marburg, Germany
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