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Sun D, Liu X, Zhu M, Chen Y, Li C, Cheng X, Zhu Z, Lu F, Qin HM. Efficient Biosynthesis of High-Value Succinic Acid and 5-Hydroxyleucine Using a Multienzyme Cascade and Whole-Cell Catalysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12502-12510. [PMID: 31623431 DOI: 10.1021/acs.jafc.9b05529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Succinic acid (SA) is applied in the food, chemical, and pharmaceutical industries. 5-Hydroxyleucine (5-HLeu) is a promising precursor for the biosynthesis of antituberculosis drugs. Here, we designed a promising synthetic route for the simultaneous production of SA and 5-HLeu by combining l-leucine dioxygenase (NpLDO), l-glutamate oxidase (LGOX), and catalase (CAT). Two bioconversion systems: "a multienzyme cascade catalysis in vitro" (MECCS) and "whole-cell catalysis system" (WCCS) were constructed. A high-activity NpLDO mutant was screened by error-prone polymerase chain reaction (PCR) and showed 6.1-fold improvement of catalytic activity. After optimization of reaction conditions, MECSS yielded 3.15 g/L SA and 3.92 g/L 5-HLeu, while the production of SA and 5-HLeu by the most effective WCSS reached 15.12 and 18.83 g/L, respectively. This is the first attempt to use ferrous iron/α-ketoglutarate-dependent dioxygenases for the simultaneous production of SA and hydroxy-amino-acid. This research provides a tool for industrial production of food of high-value products from low-cost raw materials.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
| | - Xin Liu
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Menglu Zhu
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Ying Chen
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Chao Li
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Xiaotao Cheng
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
- National Engineering Laboratory for Industrial Enzymes , Tianjin 300457 , People's Republic of China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology , Ministry of Education , Tianjin 300457 , People's Republic of China
- College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
- Tianjin Key Laboratory of Industrial Microbiology , Tianjin 300457 , People's Republic of China
- National Engineering Laboratory for Industrial Enzymes , Tianjin 300457 , People's Republic of China
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102
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Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Münzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ. Aspartate/asparagine-β-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern. Nat Commun 2019; 10:4910. [PMID: 31659163 PMCID: PMC6817910 DOI: 10.1038/s41467-019-12711-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/26/2019] [Indexed: 01/18/2023] Open
Abstract
AspH is an endoplasmic reticulum (ER) membrane-anchored 2-oxoglutarate oxygenase whose C-terminal oxygenase and tetratricopeptide repeat (TPR) domains present in the ER lumen. AspH catalyses hydroxylation of asparaginyl- and aspartyl-residues in epidermal growth factor-like domains (EGFDs). Here we report crystal structures of human AspH, with and without substrate, that reveal substantial conformational changes of the oxygenase and TPR domains during substrate binding. Fe(II)-binding by AspH is unusual, employing only two Fe(II)-binding ligands (His679/His725). Most EGFD structures adopt an established fold with a conserved Cys1–3, 2–4, 5–6 disulfide bonding pattern; an unexpected Cys3–4 disulfide bonding pattern is observed in AspH-EGFD substrate complexes, the catalytic relevance of which is supported by studies involving stable cyclic peptide substrate analogues and by effects of Ca(II) ions on activity. The results have implications for EGFD disulfide pattern processing in the ER and will enable medicinal chemistry efforts targeting human 2OG oxygenases. AspH catalyses hydroxylation of asparagine and aspartate residues in epidermal growth factor-like domains (EGFDs). Here, the authors present crystal structures of AspH with and without substrates and show that AspH uses EFGD substrates with a non-canonical disulfide pattern.
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Affiliation(s)
- Inga Pfeffer
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Sacha A Jensen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Grazyna T Kochan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Nadia J Kershaw
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsty S Hewitson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Luke A McNeill
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Holger Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Martin Münzel
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.,NDORMS, Botnar Research Centre, University of Oxford, Old Road, Oxford, OX3 7LD, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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103
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Martin CB, Chaplin VD, Eyles SJ, Knapp MJ. Protein Flexibility of the α-Ketoglutarate-Dependent Oxygenase Factor-Inhibiting HIF-1: Implications for Substrate Binding, Catalysis, and Regulation. Biochemistry 2019; 58:4047-4057. [PMID: 31499004 DOI: 10.1021/acs.biochem.9b00619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein dynamics are crucial for the mechanistically ordered enzymes to bind to their substrate in the correct sequence and perform catalysis. Factor-inhibiting HIF-1 (FIH) is a nonheme Fe(II) α-ketoglutarate-dependent oxygenase that is a key hypoxia (low pO2) sensor in humans. As these hypoxia-sensing enzymes follow a multistep chemical mechanism consuming α-ketoglutarate, a protein substrate that is hydroxylated, and O2, understanding protein flexibility and the order of substrate binding may aid in the development of strategies for selective targeting. The primary substrate of FIH is the C-terminal transactivation domain (CTAD) of hypoxia-inducible factor 1α (HIF) that is hydroxylated on the side chain of Asn803. We assessed changes in protein flexibility connected to metal and αKG binding, finding that (M+αKG) binding significantly stabilized the cupin barrel core of FIH as evidenced by enhanced thermal stability and decreased protein dynamics as assessed by global amide hydrogen/deuterium exchange mass spectrometry and limited proteolysis. Confirming predictions of the consensus mechanism, (M+αKG) increased the affinity of FIH for CTAD as measured by titrations monitoring intrinsic tryptophan fluorescence. The decreased protein dynamics caused by (M+αKG) enforces a sequentially ordered substrate binding sequence in which αKG binds before CTAD, suggesting that selective inhibition may require inhibitors that target the binding sites of both αKG and the prime substrate. A consequence of the correlation between dynamics and αKG binding is that all relevant ligands must be included in binding-based inhibitor screens, as shown by testing permutations of M, αKG, and inhibitor.
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Affiliation(s)
- Cristina B Martin
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Vanessa D Chaplin
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Michael J Knapp
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
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104
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Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
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Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
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105
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Liu YT, Hsiao CH, Tzang BS, Hsu TC. In vitro and in vivo effects of traditional Chinese medicine formula T33 in human breast cancer cells. Altern Ther Health Med 2019; 19:211. [PMID: 31409331 PMCID: PMC6693224 DOI: 10.1186/s12906-019-2630-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023]
Abstract
Background Breast cancer is the leading cause of cancer-related death in women worldwide. Although traditional Chinese medicine (TCM) is commonly used by patients with breast cancer, little is known about TCM prescriptions for breast cancer. This study investigated the effects of a new TCM formula, T33, comprising Radix Kansui, Rheum rhabarbarum, Paeonia lactiflora, Jiangbanxia, and Zhigancao on breast cancer cells in vitro and in vivo. Methods To evaluate the effects of T33 on human breast cancer, HMEpiC, MDA-MB231 and MCF-7 cells were treated with different concentrations of T33 and then analyzed using MTT and Transwell migration assays. To elucidate the involvement of autophagy in the T33-induced death of MDA-MB231 and MCF-7 cells, immunofluorescence staining with LC3-II-specific antibodies was performed. Tumor xenografts were generated by subcutaneously injecting either MDA-MB231 or MCF-7 cells into BALB/c nude mice to determine the effects of T33 on these cell lines in vivo. Results The experimental results revealed that 0.1 mg/mL, 0.5 mg/mL, 2.5 mg/mL, 5 mg/mL and 10 mg/mL T33 significantly inhibited the proliferation and invasion of MDA-MB231 and MCF-7 cells. Moreover, significant autophagy was observed in MDA-MB231 and MCF-7 cells in the presence of 2.5 mg/mL, 5 mg/mL and 10 mg/mL T33. An animal study further revealed that both low (200 mg/kg) and high (600 mg/kg) doses of T33 inhibited the proliferation of xenografted breast cancer cells in BALB/c nude mice. Conclusion These findings demonstrate for the first time that T33 has potential in the treatment of breast cancer owing to its antiproliferative effects and induction of autophagy.
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106
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Islam MS, McDonough MA, Chowdhury R, Gault J, Khan A, Pires E, Schofield CJ. Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J Biol Chem 2019; 294:11637-11652. [PMID: 31147442 PMCID: PMC6663879 DOI: 10.1074/jbc.ra119.008693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
JmjC domain-containing protein 6 (JMJD6) is a 2-oxoglutarate (2OG)-dependent oxygenase linked to various cellular processes, including splicing regulation, histone modification, transcriptional pause release, hypoxia sensing, and cancer. JMJD6 is reported to catalyze hydroxylation of lysine residue(s) of histones, the tumor-suppressor protein p53, and splicing regulatory proteins, including u2 small nuclear ribonucleoprotein auxiliary factor 65-kDa subunit (U2AF65). JMJD6 is also reported to catalyze N-demethylation of N-methylated (both mono- and di-methylated) arginine residues of histones and other proteins, including HSP70 (heat-shock protein 70), estrogen receptor α, and RNA helicase A. Here, we report MS- and NMR-based kinetic assays employing purified JMJD6 and multiple substrate fragment sequences, the results of which support the assignment of purified JMJD6 as a lysyl hydroxylase. By contrast, we did not observe N-methyl arginyl N-demethylation with purified JMJD6. Biophysical analyses, including crystallographic analyses of JMJD6Δ344-403 in complex with iron and 2OG, supported its assignment as a lysyl hydroxylase rather than an N-methyl arginyl-demethylase. The screening results supported some, but not all, of the assigned JMJD6 substrates and identified other potential JMJD6 substrates. We envision these results will be useful in cellular and biological work on the substrates and functions of JMJD6 and in the development of selective inhibitors of human 2OG oxygenases.
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Affiliation(s)
- Md Saiful Islam
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph Gault
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Amjad Khan
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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107
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Zheng H, Tie Y, Fang Z, Wu X, Yi T, Huang S, Liang X, Qian Y, Wang X, Pi R, Chen S, Peng Y, Yang S, Zhao X, Wei X. Jumonji domain-containing 6 (JMJD6) identified as a potential therapeutic target in ovarian cancer. Signal Transduct Target Ther 2019; 4:24. [PMID: 31637004 PMCID: PMC6799828 DOI: 10.1038/s41392-019-0055-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 02/05/2023] Open
Abstract
Jumonji domain-containing 6 (JMJD6) is a candidate gene associated with tumorigenesis, and JMJD6 overexpression predicts poor differentiation and unfavorable survival in some cancers. However, there are no studies reporting the expression of JMJD6 in ovarian cancer, and no JMJD6 inhibitors have been developed and applied to targeted cancer therapy research. In the present study, we found that the high expression of JMJD6 in ovarian cancer was correlated with poor prognosis in ovarian cancer. A potential inhibitor (SKLB325) was designed based on the crystal structure of the jmjC domain of JMJD6. This molecule significantly suppressed proliferation and induced apoptosis in a dose-dependent manner in SKOV3 cell lines as detected by CCK-8 cell proliferation assays and flow cytometry. A Matrigel endothelial tube formation assay showed that SKLB325 inhibited capillary tube organization and migration in HUVECs in vitro. We also observed that JMJD6 colocalized with p53 protein in the nucleus, with mRNA and protein expression of p53 as well as its downstream effectors significantly increasing both in vitro and in intraperitoneal tumor tissues treated with SKLB325. In addition, SKLB325 significantly reduced the intraperitoneal tumor weight and markedly prolonged the survival of tumor-bearing mice. Taken together, our findings suggest that JMJD6 may be a marker of poor prognosis in ovarian cancer and that SKLB325 may be a potential candidate drug for the treatment of ovarian cancer.
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Affiliation(s)
- Heng Zheng
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Yan Tie
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Zhen Fang
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Xiaoai Wu
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Tao Yi
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Shuang Huang
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Xiao Liang
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Yanping Qian
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Xi Wang
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Ruyu Pi
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Siyuan Chen
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Yong Peng
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Shengyong Yang
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second Hospital, Sichuan University, 610041 Chengdu, P. R. China
| | - Xiawei Wei
- Lab of Aging Research and Cancer Drug Targets, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan P. R. China
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108
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Langley GW, Abboud MI, Lohans CT, Schofield CJ. Inhibition of a viral prolyl hydroxylase. Bioorg Med Chem 2019; 27:2405-2412. [PMID: 30737136 DOI: 10.1016/j.bmc.2019.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
The hydroxylation of prolyl-residues in eukaryotes is important in collagen biosynthesis and in hypoxic signalling. The hypoxia inducible factor (HIF) prolyl hydroxylases (PHDs) are drug targets for the treatment of anaemia, while the procollagen prolyl hydroxylases and other 2-oxoglutarate dependent oxygenases are potential therapeutic targets for treatment of cancer, fibrotic disease, and infection. We describe assay development and inhibition studies for a procollagen prolyl hydroxylase from Paramecium bursaria chlorella virus 1 (vCPH). The results reveal HIF PHD inhibitors in clinical trials also inhibit vCPH. Implications for the targeting of the human PHDs and microbial prolyl hydroxylases are discussed.
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Affiliation(s)
- Gareth W Langley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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109
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Chen D, Teng JM, North PE, Lapinski PE, King PD. RASA1-dependent cellular export of collagen IV controls blood and lymphatic vascular development. J Clin Invest 2019; 129:3545-3561. [PMID: 31185000 DOI: 10.1172/jci124917] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Combined germline and somatic second hit inactivating mutations of the RASA1 gene, which encodes a negative regulator of the Ras signaling pathway, cause blood and lymphatic vascular lesions in the human autosomal dominant vascular disorder capillary malformation-arteriovenous malformation (CM-AVM). How RASA1 mutations in endothelial cells (EC) result in vascular lesions in CM-AVM is unknown. Here, using different murine models of RASA1-deficiency, we found that RASA1 was essential for the survival of EC during developmental angiogenesis in which primitive vascular plexuses are remodeled into hierarchical vascular networks. RASA1 was required for EC survival during developmental angiogenesis because it was necessary for export of collagen IV from EC and deposition in vascular basement membranes. In the absence of RASA1, dysregulated Ras mitogen-activated protein kinase (MAPK) signal transduction in EC resulted in impaired folding of collagen IV and its retention in the endoplasmic reticulum (ER) leading to EC death. Remarkably, the chemical chaperone, 4-phenylbutyric acid, and small molecule inhibitors of MAPK and 2-oxoglutarate dependent collagen IV modifying enzymes rescued ER retention of collagen IV and EC apoptosis and resulted in normal developmental angiogenesis. These findings have important implications with regards an understanding of the molecular pathogenesis of CM-AVM and possible means of treatment.
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Affiliation(s)
- Di Chen
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Joyce M Teng
- Department of Dermatology, Stanford University, Stanford, California, USA
| | - Paula E North
- Department of Pathology, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Philip E Lapinski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Philip D King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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110
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Jing X, Wang X, Zhang W, An J, Luo P, Nie Y, Xu Y. Highly Regioselective and Stereoselective Hydroxylation of Free Amino Acids by a 2-Oxoglutarate-Dependent Dioxygenase from Kutzneria albida. ACS OMEGA 2019; 4:8350-8358. [PMID: 31459923 PMCID: PMC6648376 DOI: 10.1021/acsomega.9b00983] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 04/30/2019] [Indexed: 05/13/2023]
Abstract
Hydroxyl amino acids have tremendous potential applications in food and pharmaceutical industries. However, available dioxygenases are limited for selective and efficient hydroxylation of free amino acids. Here, we identified a 2-oxoglutarate-dependent dioxygenase from Kutzneria albida by gene mining and characterized the encoded protein (KaPH1). KaPH1 was estimated to have a molecular weight of 29 kDa. The optimal pH and temperature for its l-proline hydroxylation activity were 6.5 and 30 °C, respectively. The K m and k cat values of KaPH1 were 1.07 mM and 0.54 s-1, respectively, for this reaction by which 120 mM l-proline was converted to trans-4-hydroxy-l-proline with 92.8% yield (3.93 g·L-1·h-1). EDTA, [1,10-phenanthroline], Cu2+, Zn2+, Co2+, and Ni2+ inhibited this reaction. KaPH1 was also active toward l-isoleucine for 4-hydroxyisoleucine synthesis. Additionally, the unique biophysical features of KaPH1 were predicted by molecular modeling whereby this study also contributes to our understanding of the catalytic mechanisms of 2-oxoglutarate-dependent dioxygenases.
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Affiliation(s)
- Xiaoran Jing
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xinye Wang
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Wenli Zhang
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jianhong An
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pengjie Luo
- China
National Center for Food Safety Risk Assessment, NHC Key Laboratory of Food Safety Risk Assessment, 37 Guangqu Road, Beijing 100022, China
- E-mail: (P.L.)
| | - Yao Nie
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- E-mail: (Y.N.)
| | - Yan Xu
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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111
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Stoehr A, Kennedy L, Yang Y, Patel S, Lin Y, Linask KL, Fergusson M, Zhu J, Gucek M, Zou J, Murphy E. The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing. JCI Insight 2019; 5:128496. [PMID: 31112528 DOI: 10.1172/jci.insight.128496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mechanisms regulating translation and splicing are not well understood. We provide insight into a new regulator of translation, OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain-containing protein 1), which is a prolyl-hydroxylase that catalyzes the posttranslational hydroxylation of Pro-62 in the small ribosomal protein S23. We show that deletion of OGFOD1 in an in vitro model of human cardiomyocytes decreases translation of specific proteins (e.g., RNA-binding proteins) and alters splicing. RNA sequencing showed poor correlation between changes in mRNA and protein synthesis, suggesting that posttranscriptional regulation was the primary cause for the observed differences. We found that loss of OGFOD1 and the resultant alterations in protein translation modulates the cardiac proteome, shifting it towards higher protein amounts of sarcomeric proteins such as cardiac troponins, titin and cardiac myosin binding protein C. Furthermore, we found a decrease of OGFOD1 during cardiomyocyte differentiation. These results suggest that loss of OGFOD1 modulates protein translation and splicing, thereby leading to alterations in the cardiac proteome and highlight the role of altered translation and splicing in regulating the proteome..
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Affiliation(s)
| | | | | | | | - Yongshun Lin
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Kaari L Linask
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | | | - Jun Zhu
- DNA Sequencing and Genomics Core
| | | | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
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112
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Wohlrab C, Kuiper C, Vissers MC, Phillips E, Robinson BA, Dachs GU. Ascorbate modulates the hypoxic pathway by increasing intracellular activity of the HIF hydroxylases in renal cell carcinoma cells. HYPOXIA 2019; 7:17-31. [PMID: 31192266 PMCID: PMC6527796 DOI: 10.2147/hp.s201643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
Abstract
Purpose: Protein levels and activity of the hypoxia-inducible transcription factors HIF-1 and HIF-2 are controlled by hydroxylation of the regulatory alpha chains. Proline hydroxylases (PHDs) target the protein for degradation via the von-Hippel-Lindau (VHL)-ubiquitin-ligase complex, and asparagine hydroxylation by Factor Inhibiting HIF (FIH) leads to transcriptional inactivation. In cell-free systems, these enzymes require ascorbate as a cofactor, and this is also inferred to be an intracellular requirement for effective hydroxylation. However, how intracellular concentrations of ascorbate affect hydroxylase activity is unknown. In this study, we investigated the modulation of the regulatory hydroxylases in cancer cells by intracellular ascorbate. Materials and methods: To facilitate this investigation, we used clear cell renal carcinoma cell lines that were VHL-proficient (Caki-1), with a normal hypoxic response, or VHL-defective (Caki-2 and 786-0), with uncontrolled accumulation of HIF-α chains. We monitored the effect of intracellular ascorbate on the hypoxia-induced accumulation of HIF-1α, HIF-2α and the expression of downstream HIF targets BNIP3, cyclin D1 and GLUT1. Changes in hydroxylation of the HIF-1α protein in response to ascorbate were also investigated in 786-0 cells gene-modified to express full-length HIF-1α (786-HIF1). Results: In VHL-proficient cells, hypoxia induced accumulation of HIF-1α and BNIP3 which was dampened in mild hypoxia by elevated intracellular ascorbate. Increased HIF-2α accumulation occurred only under severe hypoxia and this was not modified by ascorbate availability. In VHL-defective cells, ascorbate supplementation induced additional accumulation of HIF under hypoxic conditions and HIF pathway proteins were unchanged by oxygen supply. In 786-HIF1 cells, levels of hydroxylated HIF-1α were elevated in response to increasing intracellular ascorbate levels. Conclusion: Our data provide evidence that the hypoxic pathway can be modulated by increasing HIF hydroxylase activity via intracellular ascorbate availability. In VHL-defective cells, accumulation of HIF-alpha proteins is independent of hydroxylation and is unaffected by intracellular ascorbate levels.
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Affiliation(s)
- Christina Wohlrab
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Caroline Kuiper
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Margreet Cm Vissers
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Elisabeth Phillips
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Bridget A Robinson
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Canterbury Regional Cancer and Hematology Service, Canterbury District Health Board, Christchurch, New Zealand
| | - Gabi U Dachs
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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113
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Huang Y, Su R, Sheng Y, Dong L, Dong Z, Xu H, Ni T, Zhang ZS, Zhang T, Li C, Han L, Zhu Z, Lian F, Wei J, Deng Q, Wang Y, Wunderlich M, Gao Z, Pan G, Zhong D, Zhou H, Zhang N, Gan J, Jiang H, Mulloy JC, Qian Z, Chen J, Yang CG. Small-Molecule Targeting of Oncogenic FTO Demethylase in Acute Myeloid Leukemia. Cancer Cell 2019; 35:677-691.e10. [PMID: 30991027 PMCID: PMC6812656 DOI: 10.1016/j.ccell.2019.03.006] [Citation(s) in RCA: 528] [Impact Index Per Article: 105.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 01/08/2019] [Accepted: 03/16/2019] [Indexed: 11/24/2022]
Abstract
FTO, an mRNA N6-methyladenosine (m6A) demethylase, was reported to promote leukemogenesis. Using structure-based rational design, we have developed two promising FTO inhibitors, namely FB23 and FB23-2, which directly bind to FTO and selectively inhibit FTO's m6A demethylase activity. Mimicking FTO depletion, FB23-2 dramatically suppresses proliferation and promotes the differentiation/apoptosis of human acute myeloid leukemia (AML) cell line cells and primary blast AML cells in vitro. Moreover, FB23-2 significantly inhibits the progression of human AML cell lines and primary cells in xeno-transplanted mice. Collectively, our data suggest that FTO is a druggable target and that targeting FTO by small-molecule inhibitors holds potential to treat AML.
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MESH Headings
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacokinetics
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Cell Cycle Checkpoints/drug effects
- Cell Differentiation/drug effects
- Cell Proliferation/drug effects
- Dose-Response Relationship, Drug
- Enzyme Inhibitors/chemistry
- Enzyme Inhibitors/pharmacokinetics
- Enzyme Inhibitors/pharmacology
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/enzymology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Methylation
- Mice, Inbred BALB C
- Mice, Inbred NOD
- Mice, Transgenic
- Molecular Targeted Therapy
- Protein Conformation
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats, Sprague-Dawley
- Signal Transduction
- Structure-Activity Relationship
- U937 Cells
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Su
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Yue Sheng
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lei Dong
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Ze Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongjiao Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tengfeng Ni
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zijie Scott Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Tao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenying Li
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Li Han
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Zhenyun Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fulin Lian
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiangbo Wei
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Qiangqiang Deng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yungui Wang
- Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zhiwei Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guoyu Pan
- University of the Chinese Academy of Sciences, Beijing 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dafang Zhong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Zhou
- University of the Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Naixia Zhang
- University of the Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zhijian Qian
- Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Jianjun Chen
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA.
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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114
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Holt-Martyn JP, Tumber A, Rahman MZ, Lippl K, Figg W, McDonough MA, Chowdhury R, Schofield CJ. Studies on spiro[4.5]decanone prolyl hydroxylase domain inhibitors. MEDCHEMCOMM 2019; 10:500-504. [PMID: 31057728 PMCID: PMC6482412 DOI: 10.1039/c8md00548f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/09/2019] [Indexed: 12/12/2022]
Abstract
The 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (PHDs) are targets for treatment of anaemia and other ischaemia related diseases. PHD inhibitors are in clinical trials; however, the number of reported templates for PHD inhibition is limited. We report structure-activity relationship and crystallographic studies on spiro[4.5]decanone containing PHD inhibitors. Together with other studies, our results reveal spiro[4.5]decanones as useful templates for generation of potent and selective 2OG oxygenase inhibitors.
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Affiliation(s)
- James P Holt-Martyn
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Anthony Tumber
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Mohammed Z Rahman
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Kerstin Lippl
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - William Figg
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Rasheduzzaman Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
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115
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Hydroxylation of protein constituents of the human translation system: structural aspects and functional assignments. Future Med Chem 2019; 11:357-369. [PMID: 30802140 DOI: 10.4155/fmc-2018-0317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During the current decade, data on the post-translational hydroxylation of specific amino acid residues of some ribosomal proteins and translation factors in both eukaryotes and eubacteria have accumulated. The reaction is catalyzed by dedicated oxygenases (so-called ribosomal oxygenases), whose action is impaired under hypoxia conditions. The modification occurs at amino acid residues directly involved in the formation of the main functional sites of ribosomes and factors. This review summarizes currently available data on the specific hydroxylation of protein constituents of eukaryotic and eubacterial translation systems with a special emphasis on the human system, as well as on the links between hypoxia impacts on the operation of ribosomal oxygenases, the functioning of the translational apparatus and human health problems.
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116
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Waheed SO, Ramanan R, Chaturvedi SS, Ainsley J, Evison M, Ames JM, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Conformational flexibility influences structure-function relationships in nucleic acid N-methyl demethylases. Org Biomol Chem 2019; 17:2223-2231. [PMID: 30720838 DOI: 10.1039/c9ob00162j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
N-Methylation of DNA/RNA bases can be regulatory or damaging and is linked to diseases including cancer and genetic disorders. Bacterial AlkB and human FTO are DNA/RNA demethylases belonging to the Fe(ii) and 2-oxoglutarate oxygenase superfamily. Modelling studies reveal conformational dynamics influence structure-function relationships of AlkB and FTO, e.g. why 1-methyladenine is a better substrate for AlkB than 6-methyladenine. Simulations show that the flexibility of the double stranded DNA substrate in AlkB influences correlated motions, including between the core jelly-roll fold and an active site loop involved in substrate binding. The FTO N- and C-terminal domains move in respect to one another in a manner likely important for substrate binding. Substitutions, including clinically observed ones, influencing catalysis contribute to the network of correlated motions in AlkB and FTO. Overall, the calculations highlight the importance of the overall protein environment and its flexibility to the geometry of the reactant complexes.
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Affiliation(s)
- Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, USA.
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117
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Janssen JJE, Grefte S, Keijer J, de Boer VCJ. Mito-Nuclear Communication by Mitochondrial Metabolites and Its Regulation by B-Vitamins. Front Physiol 2019; 10:78. [PMID: 30809153 PMCID: PMC6379835 DOI: 10.3389/fphys.2019.00078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are cellular organelles that control metabolic homeostasis and ATP generation, but also play an important role in other processes, like cell death decisions and immune signaling. Mitochondria produce a diverse array of metabolites that act in the mitochondria itself, but also function as signaling molecules to other parts of the cell. Communication of mitochondria with the nucleus by metabolites that are produced by the mitochondria provides the cells with a dynamic regulatory system that is able to respond to changing metabolic conditions. Dysregulation of the interplay between mitochondrial metabolites and the nucleus has been shown to play a role in disease etiology, such as cancer and type II diabetes. Multiple recent studies emphasize the crucial role of nutritional cofactors in regulating these metabolic networks. Since B-vitamins directly regulate mitochondrial metabolism, understanding the role of B-vitamins in mito-nuclear communication is relevant for therapeutic applications and optimal dietary lifestyle. In this review, we will highlight emerging concepts in mito-nuclear communication and will describe the role of B-vitamins in mitochondrial metabolite-mediated nuclear signaling.
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Affiliation(s)
| | | | | | - Vincent C. J. de Boer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
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118
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Wilson C, Krieg AJ. KDM4B: A Nail for Every Hammer? Genes (Basel) 2019; 10:E134. [PMID: 30759871 PMCID: PMC6410163 DOI: 10.3390/genes10020134] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
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Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
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119
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Thinnes CC, Lohans CT, Abboud MI, Yeh T, Tumber A, Nowak RP, Attwood M, Cockman ME, Oppermann U, Loenarz C, Schofield CJ. Selective Inhibitors of a Human Prolyl Hydroxylase (OGFOD1) Involved in Ribosomal Decoding. Chemistry 2019; 25:2019-2024. [PMID: 30427558 PMCID: PMC6471485 DOI: 10.1002/chem.201804790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 12/12/2022]
Abstract
Human prolyl hydroxylases are involved in the modification of transcription factors, procollagen, and ribosomal proteins, and are current medicinal chemistry targets. To date, there are few reports on inhibitors selective for the different types of prolyl hydroxylases. We report a structurally informed template-based strategy for the development of inhibitors selective for the human ribosomal prolyl hydroxylase OGFOD1. These inhibitors did not target the other human oxygenases tested, including the structurally similar hypoxia-inducible transcription factor prolyl hydroxylase, PHD2.
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Affiliation(s)
| | | | | | - Tzu‐Lan Yeh
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Radosław P. Nowak
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
- Department of Cancer BiologyDana-Farber Cancer InstituteBoston, MA02215USA
| | - Martin Attwood
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Matthew E. Cockman
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Udo Oppermann
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Christoph Loenarz
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität Freiburg79104FreiburgGermany
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120
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Lamadema N, Burr S, Brewer AC. Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox. Free Radic Biol Med 2019; 131:282-298. [PMID: 30572012 DOI: 10.1016/j.freeradbiomed.2018.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
The chromatin structure of the mammalian genome must facilitate both precisely-controlled DNA replication together with tightly-regulated gene transcription. This necessarily involves complex mechanisms and processes which remain poorly understood. It has long been recognised that the epigenetic landscape becomes established during embryonic development and acts to specify and determine cell fate. In addition, the chromatin structure is highly dynamic and allows for both cellular reprogramming and homeostatic modulation of cell function. In this respect, the functions of epigenetic "erasers", which act to remove covalently-linked epigenetic modifications from DNA and histones are critical. The enzymatic activities of the TET and JmjC protein families have been identified as demethylases which act to remove methyl groups from DNA and histones, respectively. Further, they are characterised as members of the Fe(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. This provides the intriguing possibility that their enzymatic activities may be modulated by cellular metabolism, oxygen availability and redox-based mechanisms, all of which are likely to display dynamic cell- and tissue-specific patterns of flux. Here we discuss the current evidence for such [O2]- and redox-dependent regulation of the TET and Jmjc demethylases and the potential physiological and pathophysiological functional consequences of such regulation.
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Affiliation(s)
- Nermina Lamadema
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Simon Burr
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Alison C Brewer
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom.
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121
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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122
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Bush JT, Leśniak RK, Yeh TL, Belle R, Kramer H, Tumber A, Chowdhury R, Flashman E, Mecinović J, Schofield CJ. Small-molecules that covalently react with a human prolyl hydroxylase - towards activity modulation and substrate capture. Chem Commun (Camb) 2019; 55:1020-1023. [PMID: 30452037 PMCID: PMC6350621 DOI: 10.1039/c8cc07706a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/01/2018] [Indexed: 12/13/2022]
Abstract
We describe covalently binding modulators of the activity of human prolyl hydroxylase domain 2 (PHD2) and studies towards a strategy for photocapture of PHD2 substrates. Reversible active site binding of electrophile bearing compounds enables susbsequent covalent reaction with a lysine residue (K408) in the flexible C-terminal region of PHD2 to give a modified protein that retains catalytic activity.
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Affiliation(s)
- Jacob T. Bush
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Robert K. Leśniak
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Roman Belle
- Institute for Molecules and Materials
, Radboud University
,
Heyendaalseweg 135
, 6525 AJ Nijmegen
, The Netherlands
| | - Holger Kramer
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Anthony Tumber
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Emily Flashman
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
| | - Jasmin Mecinović
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
- Institute for Molecules and Materials
, Radboud University
,
Heyendaalseweg 135
, 6525 AJ Nijmegen
, The Netherlands
- Department of Physics, Chemistry and Pharmacy
, University of Southern Denmark
,
Campusvej 55
, 5230 Odense
, Denmark
.
| | - Christopher J. Schofield
- Chemistry Research Laboratory
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
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123
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Leon KE, Aird KM. Jumonji C Demethylases in Cellular Senescence. Genes (Basel) 2019; 10:genes10010033. [PMID: 30634491 PMCID: PMC6356615 DOI: 10.3390/genes10010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
Abstract
Senescence is a stable cell cycle arrest that is either tumor suppressive or tumor promoting depending on context. Epigenetic changes such as histone methylation are known to affect both the induction and suppression of senescence by altering expression of genes that regulate the cell cycle and the senescence-associated secretory phenotype. A conserved group of proteins containing a Jumonji C (JmjC) domain alter chromatin state, and therefore gene expression, by demethylating histones. Here, we will discuss what is currently known about JmjC demethylases in the induction of senescence, and how these enzymes suppress senescence to contribute to tumorigenesis.
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Affiliation(s)
- Kelly E Leon
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| | - Katherine M Aird
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
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124
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Sun D, Gao D, Liu X, Zhu M, Li C, Chen Y, Zhu Z, Lu F, Qin HM. Redesign and engineering of a dioxygenase targeting biocatalytic synthesis of 5-hydroxyl leucine. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00110g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The protein engineering and metabolic engineering strategies are performed to solve rate-limiting steps in the biosynthesis of 5-HLeu.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Dengke Gao
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Xin Liu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Menglu Zhu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Chao Li
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Ying Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
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125
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Bundred JR, Hendrix E, Coleman ML. The emerging roles of ribosomal histidyl hydroxylases in cell biology, physiology and disease. Cell Mol Life Sci 2018; 75:4093-4105. [PMID: 30151692 PMCID: PMC6182338 DOI: 10.1007/s00018-018-2903-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/27/2022]
Abstract
Hydroxylation is a novel protein modification catalyzed by a family of oxygenases that depend on fundamental nutrients and metabolites for activity. Protein hydroxylases have been implicated in a variety of key cellular processes that play important roles in both normal homeostasis and pathogenesis. Here, in this review, we summarize the current literature on a highly conserved sub-family of oxygenases that catalyze protein histidyl hydroxylation. We discuss the evidence supporting the biochemical assignment of these emerging enzymes as ribosomal protein hydroxylases, and provide an overview of their role in immunology, bone development, and cancer.
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Affiliation(s)
- James R Bundred
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eline Hendrix
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mathew L Coleman
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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126
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Fets L, Driscoll PC, Grimm F, Jain A, Nunes PM, Gounis M, Doglioni G, Papageorgiou G, Ragan TJ, Campos S, Silva Dos Santos M, MacRae JI, O'Reilly N, Wright AJ, Benes CH, Courtney KD, House D, Anastasiou D. MCT2 mediates concentration-dependent inhibition of glutamine metabolism by MOG. Nat Chem Biol 2018; 14:1032-1042. [PMID: 30297875 PMCID: PMC6298574 DOI: 10.1038/s41589-018-0136-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
α-Ketoglutarate (αKG) is a key node in many important metabolic pathways. The αKG analog N-oxalylglycine (NOG) and its cell-permeable prodrug dimethyloxalylglycine (DMOG) are extensively used to inhibit αKG-dependent dioxygenases. However, whether NOG interference with other αKG-dependent processes contributes to its mode of action remains poorly understood. Here we show that, in aqueous solutions, DMOG is rapidly hydrolyzed, yielding methyloxalylglycine (MOG). MOG elicits cytotoxicity in a manner that depends on its transport by monocarboxylate transporter 2 (MCT2) and is associated with decreased glutamine-derived tricarboxylic acid-cycle flux, suppressed mitochondrial respiration and decreased ATP production. MCT2-facilitated entry of MOG into cells leads to sufficiently high concentrations of NOG to inhibit multiple enzymes in glutamine metabolism, including glutamate dehydrogenase. These findings reveal that MCT2 dictates the mode of action of NOG by determining its intracellular concentration and have important implications for the use of (D)MOG in studying αKG-dependent signaling and metabolism.
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Affiliation(s)
- Louise Fets
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Paul C Driscoll
- Metabolomics Science Technology Platform, Francis Crick Institute, London, UK
| | - Fiona Grimm
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Aakriti Jain
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Patrícia M Nunes
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Michalis Gounis
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Ginevra Doglioni
- Cancer Metabolism Laboratory, Francis Crick Institute, London, UK
| | - George Papageorgiou
- Peptide Chemistry Science Technology Platform, Francis Crick Institute, London, UK
| | | | - Sebastien Campos
- Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
| | | | - James I MacRae
- Metabolomics Science Technology Platform, Francis Crick Institute, London, UK
| | - Nicola O'Reilly
- Peptide Chemistry Science Technology Platform, Francis Crick Institute, London, UK
| | - Alan J Wright
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center & Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kevin D Courtney
- Department of Internal Medicine, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David House
- Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
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127
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Niu Y, Wan A, Lin Z, Lu X, Wan G. N 6-Methyladenosine modification: a novel pharmacological target for anti-cancer drug development. Acta Pharm Sin B 2018; 8:833-843. [PMID: 30505654 PMCID: PMC6251950 DOI: 10.1016/j.apsb.2018.06.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 12/11/2022] Open
Abstract
N6-Methyladenosine (m6A) modification is the most pervasive modification of human mRNA molecules. It is reversible via regulation of m6A modification methyltransferase, demethylase and proteins that preferentially recognize m6A modification as “writers”, “erasers” and “readers”, respectively. Altered expression levels of the m6A modification key regulators substantially affect their function, leading to significant phenotype changes in the cell and organism. Recent studies have proved that the m6A modification plays significant roles in regulation of metabolism, stem cell self-renewal, and metastasis in a variety of human cancers. In this review, we describe the potential roles of m6A modification in human cancers and summarize their underlying molecular mechanisms. Moreover, we will highlight potential therapeutic approaches by targeting the key m6A modification regulators for cancer drug development.
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128
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Guillade L, Sarno F, Tarhonskaya H, Nebbioso A, Alvarez S, Kawamura A, Schofield CJ, Altucci L, de Lera ÁR. Synthesis and Biological Evaluation of Tripartin, a Putative KDM4 Natural Product Inhibitor, and 1-Dichloromethylinden-1-ol Analogues. ChemMedChem 2018; 13:1949-1956. [PMID: 30047603 DOI: 10.1002/cmdc.201800377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Indexed: 12/17/2022]
Abstract
The natural product tripartin has been reported to inhibit the N-methyl-lysine histone demethylase KDM4A. A synthesis of tripartin starting from 3,5-dimethoxyphenylacrylic acid was developed, and the enantiomers were separated by chiral HPLC. We observed that both tripartin enantiomers manifested an apparent increase in H3K9me3 levels when dosed in cells, as measured by western blot analysis. Thus, there is no enantiomeric discrimination toward this natural product in terms of its effects on cellular histone methylation status. Interestingly, tripartin did not inhibit isolated KDM4A-E under our assay conditions (IC50 >100 μm). Tripartin analogues with a dichloromethylcarbinol group derived from the indanone scaffold were synthesized and found to be inactive against isolated recombinant KDM4 enzymes and in cell-based assays. Although the precise cellular mode of action of tripartin is unclear, our evidence suggests that it may affect histone methylation status via a mechanism other than direct inhibition of the KDM4 histone demethylases.
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Affiliation(s)
- Lucía Guillade
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Federica Sarno
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Angela Nebbioso
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Susana Alvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lucia Altucci
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Ángel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
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129
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Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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130
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Jones SE, Olsen L, Dorosz J, Seger ST, Andersson JL, Kristensen LH, Gajhede M. Peptides Derived from Histone 3 and Modified at Position 18 Inhibit Histone Demethylase KDM6 Enzymes. Chembiochem 2018; 19:1817-1822. [PMID: 29878441 DOI: 10.1002/cbic.201800185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/12/2022]
Abstract
The KDM6 subfamily of histone lysine demethylases has recently been implicated as a putative target in the treatment of a number of diseases; this makes the availability of potent and selective inhibitors important. Due to high sequence similarity of the catalytic domain of Jumonji C histone demethylases, the development of small-molecule, family-specific inhibitors has, however, proven challenging. One approach to achieve the selective inhibition of these enzymes is the use of peptides derived from the substrate, the histone 3 C terminus. Here we used computational methods to optimize such inhibitors of the KDM6 family. Through natural amino acid substitution, it is shown that a K18I variant of a histone H3 derived peptide significantly increases affinity towards the KDM6 enzymes. The crystal structure of KDM6B in complex with a histone 3 derived K18I peptide reveals a tighter fit of the isoleucine side chain, compared with that of the arginine. As a consequence, the peptide R17 residue also has increased hydrophilic interactions. These interactions of the optimized peptide are likely to be responsible for the increased affinity to the KDM6 enzymes.
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Affiliation(s)
- Sarah E Jones
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Lars Olsen
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Signe T Seger
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
| | - Jan L Andersson
- Nuevolution AB (publ.), Rønnegade 8, 2100, Copenhagen, Denmark
| | | | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
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131
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Sun D, Gao D, Xu P, Guo Q, Zhu Z, Cheng X, Bai S, Qin HM, Lu F. A novel l -leucine 5-hydroxylase from Nostoc piscinale unravels unexpected sulfoxidation activity toward l -methionine. Protein Expr Purif 2018; 149:1-6. [DOI: 10.1016/j.pep.2018.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/13/2018] [Indexed: 01/21/2023]
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132
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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133
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Heuser M, Yun H, Thol F. Epigenetics in myelodysplastic syndromes. Semin Cancer Biol 2018; 51:170-179. [PMID: 28778402 PMCID: PMC7116652 DOI: 10.1016/j.semcancer.2017.07.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 12/20/2022]
Abstract
Epigenetic regulators are the largest group of genes mutated in MDS patients. Most mutated genes belong to one of three groups of genes with normal functions in DNA methylation, in H3K27 methylation/acetylation or in H3K4 methylation. Mutations in the majority of epigenetic regulators disrupt their normal function and induce a loss-of-function phenotype. The transcriptional consequences are often failure to repress differentiation programs and upregulation of self-renewal pathways. However, the mechanisms how different epigenetic regulators result in similar transcriptional consequences are not well understood. Hypomethylating agents are active in higher risk MDS patients, but their efficacy does not correlate with mutations in epigenetic regulators and the median duration of hematologic response is limited to 10-13 months. Inhibitors of histone deacetylases (HDAC) yielded disappointing results so far, questioning this approach in MDS patients. We review the clinical relevance of epigenetic mutations in MDS, discuss their functional consequences and highlight the role of epigenetic therapies in this difficult to treat disease.
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Affiliation(s)
- Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany.
| | - Haiyang Yun
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, UK; Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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134
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Abstract
Collagen is the dominant protein of the extracellular matrix. Its distinguishing feature is a three-stranded helix of great tensile strength. (2 S,4 R)-4-Hydroxyproline residues are essential for the stability of this triple helix. These residues arise from the post-translational modification of (2 S)-proline residues by collagen prolyl 4-hydroxylases (CP4Hs), which are members of the Fe(II)- and α-ketoglutarate (AKG)-dependent dioxygenase family. Here, we provide a framework for the inhibition of CP4Hs as the basis for treating fibrotic diseases and cancer metastasis. We begin with a summary of the structure and enzymatic reaction mechanism of CP4Hs. Then, we review the metal ions, metal chelators, mimetics of AKG and collagen strands, and natural products that are known to inhibit CP4Hs. Our focus is on inhibitors with potential utility in the clinic. We conclude with a prospectus for more effective inhibitors.
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Affiliation(s)
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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135
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Markolovic S, Zhuang Q, Wilkins SE, Eaton CD, Abboud MI, Katz MJ, McNeil HE, Leśniak RK, Hall C, Struwe WB, Konietzny R, Davis S, Yang M, Ge W, Benesch JLP, Kessler BM, Ratcliffe PJ, Cockman ME, Fischer R, Wappner P, Chowdhury R, Coleman ML, Schofield CJ. The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases. Nat Chem Biol 2018; 14:688-695. [PMID: 29915238 PMCID: PMC6027965 DOI: 10.1038/s41589-018-0071-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/03/2018] [Indexed: 11/14/2022]
Abstract
Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(II)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.
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Affiliation(s)
- Suzana Markolovic
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Qinqin Zhuang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah E Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte D Eaton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Helen E McNeil
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Robert K Leśniak
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte Hall
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Simon Davis
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ming Yang
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Peter J Ratcliffe
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Matthew E Cockman
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Clark Center, Stanford, CA, USA.
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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136
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Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain – A fragment based approach. Bioorg Med Chem Lett 2018; 28:1708-1713. [DOI: 10.1016/j.bmcl.2018.04.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
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137
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Bowkett D, Talon R, Tallant C, Schofield C, von Delft F, Knapp S, Bruton G, Brennan PE. Identifying Small-Molecule Binding Sites for Epigenetic Proteins at Domain-Domain Interfaces. ChemMedChem 2018; 13:1051-1057. [PMID: 29578648 PMCID: PMC6001751 DOI: 10.1002/cmdc.201800030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/16/2018] [Indexed: 12/27/2022]
Abstract
Epigenetics is a rapidly growing field in drug discovery. Of particular interest is the role of post-translational modifications to histones and the proteins that read, write, and erase such modifications. The development of inhibitors for reader domains has focused on single domains. One of the major difficulties of designing inhibitors for reader domains is that, with the notable exception of bromodomains, they tend not to possess a well-enclosed binding site amenable to small-molecule inhibition. As many of the proteins in epigenetic regulation have multiple domains, there are opportunities for designing inhibitors that bind at a domain-domain interface which provide a more suitable interaction pocket. Examination of X-ray structures of multiple domains involved in recognising and modifying post-translational histone marks using the SiteMap algorithm identified potential binding sites at domain-domain interfaces. For the tandem plant homeodomain-bromodomain of SP100C, a potential inter-domain site identified computationally was validated experimentally by the discovery of ligands by X-ray crystallographic fragment screening.
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Affiliation(s)
- David Bowkett
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Romain Talon
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Cynthia Tallant
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Chris Schofield
- Chemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Frank von Delft
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Stefan Knapp
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe University60438Frankfurt am MainGermany
| | - Gordon Bruton
- GlaxoSmithKlineMedicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
| | - Paul E. Brennan
- Structural Genomics Consortium (SGC) & Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford, NDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
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138
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Beck H, Jeske M, Thede K, Stoll F, Flamme I, Akbaba M, Ergüden J, Karig G, Keldenich J, Oehme F, Militzer H, Hartung IV, Thuss U. Discovery of Molidustat (BAY 85-3934): A Small-Molecule Oral HIF-Prolyl Hydroxylase (HIF-PH) Inhibitor for the Treatment of Renal Anemia. ChemMedChem 2018; 13:988-1003. [PMID: 29485740 PMCID: PMC6001664 DOI: 10.1002/cmdc.201700783] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/20/2018] [Indexed: 12/17/2022]
Abstract
Small-molecule inhibitors of hypoxia-inducible factor prolyl hydroxylases (HIF-PHs) are currently under clinical development as novel treatment options for chronic kidney disease (CKD) associated anemia. Inhibition of HIF-PH mimics hypoxia and leads to increased erythropoietin (EPO) expression and subsequently increased erythropoiesis. Herein we describe the discovery, synthesis, structure-activity relationship (SAR), and proposed binding mode of novel 2,4-diheteroaryl-1,2-dihydro-3H-pyrazol-3-ones as orally bioavailable HIF-PH inhibitors for the treatment of anemia. High-throughput screening of our corporate compound library identified BAY-908 as a promising hit. The lead optimization program then resulted in the identification of molidustat (BAY 85-3934), a novel small-molecule oral HIF-PH inhibitor. Molidustat is currently being investigated in clinical phase III trials as molidustat sodium for the treatment of anemia in patients with CKD.
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Affiliation(s)
- Hartmut Beck
- Medicinal Chemistry WuppertalBayer AG42096WuppertalGermany
| | - Mario Jeske
- Medicinal Chemistry WuppertalBayer AG42096WuppertalGermany
| | - Kai Thede
- Medicinal Chemistry BerlinBayer AG13342BerlinGermany
| | | | - Ingo Flamme
- Cardiology Research WuppertalBayer AG42096WuppertalGermany
| | - Metin Akbaba
- Medicinal Chemistry WuppertalBayer AG42096WuppertalGermany
| | | | - Gunter Karig
- Medicinal Chemistry WuppertalBayer AG42096WuppertalGermany
| | | | - Felix Oehme
- Cardiology Research WuppertalBayer AG42096WuppertalGermany
| | | | | | - Uwe Thuss
- DMPK WuppertalBayer AG42096WuppertalGermany
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139
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Boriack-Sjodin PA, Ribich S, Copeland RA. RNA-modifying proteins as anticancer drug targets. Nat Rev Drug Discov 2018; 17:435-453. [PMID: 29773918 DOI: 10.1038/nrd.2018.71] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.
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140
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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141
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Herr CQ, Hausinger RP. Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases. Trends Biochem Sci 2018; 43:517-532. [PMID: 29709390 DOI: 10.1016/j.tibs.2018.04.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/21/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
Since their discovery in the 1960s, the family of Fe(II)/2-oxoglutarate-dependent oxygenases has undergone a tremendous expansion to include enzymes catalyzing a vast diversity of biologically important reactions. Recent examples highlight roles in controlling chromatin modification, transcription, mRNA demethylation, and mRNA splicing. Others generate modifications in tRNA, translation factors, ribosomes, and other proteins. Thus, oxygenases affect all components of molecular biology's central dogma, in which information flows from DNA to RNA to proteins. These enzymes also function in biosynthesis and catabolism of cellular metabolites, including antibiotics and signaling molecules. Due to their critical importance, ongoing efforts have targeted family members for the development of specific therapeutics. This review provides a general overview of recently characterized oxygenase reactions and their key biological roles.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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142
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Huang J, Yin P. Structural Insights into N 6-methyladenosine (m 6A) Modification in the Transcriptome. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:85-98. [PMID: 29709557 PMCID: PMC6112310 DOI: 10.1016/j.gpb.2018.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 01/04/2023]
Abstract
More than 100 types of chemical modifications in RNA have been well documented. Recently, several modifications, such as N6-methyladenosine (m6A), have been detected in mRNA, opening the window into the realm of epitranscriptomics. The m6A modification is the most abundant modification in mRNA and non-coding RNA (ncRNA). At the molecular level, m6A affects almost all aspects of mRNA metabolism, including splicing, translation, and stability, as well as microRNA (miRNA) maturation, playing essential roles in a range of cellular processes. The m6A modification is regulated by three classes of proteins generally referred to as the “writer” (adenosine methyltransferase), “eraser” (m6A demethylating enzyme), and “reader” (m6A-binding protein). The m6A modification is reversibly installed and removed by writers and erasers, respectively. Readers, which are members of the YT521-B homology (YTH) family proteins, selectively bind to RNA and affect its fate in an m6A-dependent manner. In this review, we summarize the structures of the functional proteins that modulate the m6A modification, and provide our insights into the m6A-mediated gene regulation.
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Affiliation(s)
- Jinbo Huang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
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143
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Nishio K, Belle R, Katoh T, Kawamura A, Sengoku T, Hanada K, Ohsawa N, Shirouzu M, Yokoyama S, Suga H. Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity. Chembiochem 2018; 19:979-985. [PMID: 29665240 DOI: 10.1002/cbic.201800047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Indexed: 12/29/2022]
Abstract
The ten-eleven translocation (TET) protein family, consisting of three isoforms (TET1/2/3), have been found in mammalian cells and have a crucial role in 5-methylcytosine demethylation in genomic DNA through the catalysis of oxidation reactions assisted by 2-oxoglutarate (2OG). DNA methylation/demethylation contributes to the regulation of gene expression at the transcriptional level, and recent studies have revealed that TET1 is highly elevated in malignant cells of various diseases and related to malignant alteration. TET1 inhibitors based on a scaffold of thioether macrocyclic peptides, which have been discovered by the random nonstandard peptide integrated discovery (RaPID) system, are reported. The affinity-based selection was performed against the TET1 compact catalytic domain (TET1CCD) to yield thioether macrocyclic peptides. These peptides exhibited inhibitory activity of the TET1 catalytic domain (TET1CD), with an IC50 value as low as 1.1 μm. One of the peptides, TiP1, was also able to inhibit TET1CD over TET2CD with tenfold selectivity, although it was likely to target the 2OG binding site; this provides a good starting point to develop more selective inhibitors.
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Affiliation(s)
- Kosuke Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Roman Belle
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Welcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Toru Sengoku
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kazuharu Hanada
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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144
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Furan- and Thiophene-2-Carbonyl Amino Acid Derivatives Activate Hypoxia-Inducible Factor via Inhibition of Factor Inhibiting Hypoxia-Inducible Factor-1. Molecules 2018; 23:molecules23040885. [PMID: 29641495 PMCID: PMC6017830 DOI: 10.3390/molecules23040885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 11/17/2022] Open
Abstract
Induction of a series of anti-hypoxic proteins protects cells during exposure to hypoxic conditions. Hypoxia-inducible factor-α (HIF-α) is a major transcription factor that orchestrates this protective effect. To activate HIF exogenously, without exposing cells to hypoxic conditions, many small-molecule inhibitors targeting prolyl hydroxylase domain-containing protein have been developed. In addition, suppression of factor inhibiting HIF-1 (FIH-1) has also been shown to have the potential to activate HIF-α. However, few small-molecule inhibitors of FIH-1 have been developed. In this study, we synthesized a series of furan- and thiophene-2-carbonyl amino acid derivatives having the potential to inhibit FIH-1. The inhibitory activities of these compounds were evaluated in SK-N-BE(2)c cells by measuring HIF response element (HRE) promoter activity. Several furan- and thiophene-2-carbonyl amino acid derivatives inhibited FIH-1 based on correlations among the docking score of the FIH-1 active site, the chemical structure of the compounds, and biological HIF-α/HRE transcriptional activity.
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145
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Association between mutant IDHs and tumorigenesis in gliomas. Med Mol Morphol 2018; 51:194-198. [PMID: 29633022 DOI: 10.1007/s00795-018-0189-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 04/02/2018] [Indexed: 01/14/2023]
Abstract
To become immortalized, cells need to maintain the telomere length via the activation of telomerase or alternative lengthening of telomere. Mutations in IDH1/2 are strongly associated with the early stage of gliomagenesis. Previous work has shown that the accumulation of 2-HG, which is induced by mutant IDH1/2, inhibits α-KG-dependent deoxygenase and leads to genome-wide histone and DNA methylation alterations. These alterations are believed to contribute to tumorigenesis. H-Ras can transform human astrocytes with the inactivation of p53/pRb and expression of hTERT; however, mutant IDH1 can also transform cells. Moreover, mutant IDH1 can drive the immortalization and transformation of p53-/pRb-deficient astrocytes by reactivating telomerase and stabilizing telomeres in combination with increased histone lysine methylation and c-Myc/Max binding at the TERT promoter. It remains unclear whether mutant IDH1/2 acts only as the initial driver of gliomagenesis or it maintains transformed cells. Clinical studies are being performed to assess the use of mutant IDH1/2 inhibitors for treating gliomas.
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146
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Koivunen P, Laukka T. The TET enzymes. Cell Mol Life Sci 2018; 75:1339-1348. [PMID: 29184981 PMCID: PMC11105636 DOI: 10.1007/s00018-017-2721-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 12/19/2022]
Abstract
During the past decade, we have learnt that the most common DNA modification, 5-methylcytosine (5mC), playing crucial roles in development and disease, is not stable but can be actively reversed to its unmodified form via enzymatic catalysis involving the TET enzymes. These ground-breaking discoveries have been achieved thanks to technological advances in the detection of the oxidized forms of 5mC and to the boldness of individual scientists. The TET enzymes require molecular oxygen for their catalysis, making them important targets for hypoxia research. They also require special cofactors which enable additional levels of regulation. Moreover, mutations and other genetic alterations in TETs are found, especially in myeloid malignances. This review focuses on the kinetic and inhibitory properties of the TET enzymes and the role of TETs in cellular differentiation and transformation and in cancer.
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Affiliation(s)
- Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, 90014, Oulu, Finland.
| | - Tuomas Laukka
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, 90014, Oulu, Finland
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147
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Abstract
2-Oxoglutarate (2OG)-dependent oxygenases (2OGXs) catalyze a remarkably diverse range of oxidative reactions. In animals, these comprise hydroxylations and N-demethylations proceeding via hydroxylation; in plants and microbes, they catalyze a wider range including ring formations, rearrangements, desaturations, and halogenations. The catalytic flexibility of 2OGXs is reflected in their biological functions. After pioneering work identified the roles of 2OGXs in collagen biosynthesis, research revealed they also function in plant and animal development, transcriptional regulation, nucleic acid modification/repair, fatty acid metabolism, and secondary metabolite biosynthesis, including of medicinally important antibiotics. In plants, 2OGXs are important agrochemical targets and catalyze herbicide degradation. Human 2OGXs, particularly those regulating transcription, are current therapeutic targets for anemia and cancer. Here, we give an overview of the biochemistry of 2OGXs, providing examples linking to biological function, and outline how knowledge of their enzymology is being exploited in medicine, agrochemistry, and biocatalysis.
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Affiliation(s)
- Md Saiful Islam
- The Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;
| | - Thomas M Leissing
- The Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;
| | - Rasheduzzaman Chowdhury
- The Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;
| | - Richard J Hopkinson
- The Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom; .,Current affiliation for Richard J. Hopkinson: Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom;
| | - Christopher J Schofield
- The Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;
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148
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Matre P, Velez J, Jacamo R, Qi Y, Su X, Cai T, Chan SM, Lodi A, Sweeney SR, Ma H, Davis RE, Baran N, Haferlach T, Su X, Flores ER, Gonzalez D, Konoplev S, Samudio I, DiNardo C, Majeti R, Schimmer AD, Li W, Wang T, Tiziani S, Konopleva M. Inhibiting glutaminase in acute myeloid leukemia: metabolic dependency of selected AML subtypes. Oncotarget 2018; 7:79722-79735. [PMID: 27806325 PMCID: PMC5340236 DOI: 10.18632/oncotarget.12944] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023] Open
Abstract
Metabolic reprogramming has been described as a hallmark of transformed cancer cells. In this study, we examined the role of the glutamine (Gln) utilization pathway in acute myeloid leukemia (AML) cell lines and primary AML samples. Our results indicate that a subset of AML cell lines is sensitive to Gln deprivation. Glutaminase (GLS) is a mitochondrial enzyme that catalyzes the conversion of Gln to glutamate. One of the two GLS isoenzymes, GLS1 is highly expressed in cancer and encodes two different isoforms: kidney (KGA) and glutaminase C (GAC). We analyzed mRNA expression of GLS1 splicing variants, GAC and KGA, in several large AML datasets and identified increased levels of expression in AML patients with complex cytogenetics and within specific molecular subsets. Inhibition of glutaminase by allosteric GLS inhibitor bis-2-(5-phenylacetamido-1, 2, 4-thiadiazol-2-yl) ethyl sulfide or by novel, potent, orally bioavailable GLS inhibitor CB-839 reduced intracellular glutamate levels and inhibited growth of AML cells. In cell lines and patient samples harboring IDH1/IDH2 (Isocitrate dehydrogenase 1 and 2) mutations, CB-839 reduced production of oncometabolite 2-hydroxyglutarate, inducing differentiation. These findings indicate potential utility of glutaminase inhibitors in AML therapy, which can inhibit cell growth, induce apoptosis and/or differentiation in specific leukemia subtypes.
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Affiliation(s)
- Polina Matre
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Juliana Velez
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rodrigo Jacamo
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuan Qi
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoping Su
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tianyu Cai
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Chan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Shannon R Sweeney
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Helen Ma
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Eric Davis
- Lymphoma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Xiaohua Su
- Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa Renee Flores
- Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Doriann Gonzalez
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej Konoplev
- Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ismael Samudio
- The Centre for Drug Research and Development Biologics, Vancouver, British Columbia, Canada
| | - Courtney DiNardo
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravi Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D Schimmer
- Medical Biophysics, Princess Margaret Hospital / Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Weiqun Li
- Analytical Chemistry, Pharmacology, Spectroscopy, Calithera Biosciences, South San Francisco, CA, USA
| | - Taotao Wang
- Analytical Chemistry, Pharmacology, Spectroscopy, Calithera Biosciences, South San Francisco, CA, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Marina Konopleva
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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149
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Ye D, Guan KL, Xiong Y. Metabolism, Activity, and Targeting of D- and L-2-Hydroxyglutarates. Trends Cancer 2018; 4:151-165. [PMID: 29458964 PMCID: PMC5884165 DOI: 10.1016/j.trecan.2017.12.005] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022]
Abstract
Isocitrate dehydrogenases (IDH1/2) are frequently mutated in multiple types of human cancer, resulting in neomorphic enzymes that convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG). The current view on the mechanism of IDH mutation holds that 2-HG acts as an antagonist of α-KG to competitively inhibit the activity of α-KG-dependent dioxygenases, including those involved in histone and DNA demethylation. Recent studies have implicated 2-HG in activities beyond epigenetic modification. Multiple enzymes have been discovered that lack mutations but that can nevertheless produce 2-HG promiscuously under hypoxic or acidic conditions. Therapies are being developed to treat IDH-mutant cancers by targeting either the mutant IDH enzymes directly or the pathways sensitized by 2-HG.
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Affiliation(s)
- Dan Ye
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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150
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Lee J, Perez L, Liu Y, Wang H, Hooley RJ, Zhong W. Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis. Anal Chem 2018; 90:1881-1888. [PMID: 29286640 DOI: 10.1021/acs.analchem.7b03969] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.
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Affiliation(s)
| | | | | | - Hua Wang
- Instrument Analysis Center, Yancheng Teachers University , Yancheng, Jiangsu 224007, China
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