1
|
Wang Y, Liu L, Deng P, Ji H. Photocatalyzed Acylation of Azauracil Derivatives with Aldehydes. J Org Chem 2024; 89:11083-11087. [PMID: 39044345 DOI: 10.1021/acs.joc.4c01320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
A novel approach for the acylation of azauracil derivatives with aldehydes has been developed utilizing sodium decatungstate (NaDT) as a photocatalyst. This method demonstrates broad substrate tolerance and yields moderate to excellent outcomes. Notably, it aligns with green chemistry principles by eliminating oxidants, utilizing eco-friendly energy sources, and offering high scalability and operational simplicity.
Collapse
Affiliation(s)
- Yi Wang
- College of Pharmacy, Shaoyang University, Shaoyang 422099, China
| | - Lianghong Liu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Peng Deng
- College of Pharmacy, Shaoyang University, Shaoyang 422099, China
| | - Hongtao Ji
- Postdoctoral Mobile Station of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| |
Collapse
|
2
|
Cao S, Chen JX, Zhang XL, Song X, Song WY, Wu YS, Zhang YH, Liu Z. Merging Quinoxalin-2(1 H)-ones Excitation with Cobaloxime Catalysis: C3 Alkylation of Quinoxalin-2(1 H)-ones with Unactivated Alkyl Iodides and Carboxylic Acids under Light. Org Lett 2024; 26:5833-5838. [PMID: 38934368 DOI: 10.1021/acs.orglett.4c02021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Reported herein is a practical, economical, and efficient construction of 3-alkylated quinoxalin-2(1H)-ones with alkyl carboxylic acids and alkyl iodides by quinoxalin-2(1H)-one excitation and cobaloxime catalysis. Primary, secondary, and tertiary alkyl iodides and carboxylic acids all could be efficiently transferred into target products with excellent functional group tolerance. Mechanism studies reveal that the quinoxalin-2(1H)-one derivatives could be directly excited and yield alkyl carbon radicals from alkyl carboxylic acids and alkyl iodides with the aid of the cobaloxime complex.
Collapse
Affiliation(s)
- Shuo Cao
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Jia-Xin Chen
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Xiu-Li Zhang
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Xian Song
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Wen-Yu Song
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Yu-Sheng Wu
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| | - Yan-Hui Zhang
- School of Medical Imaging, Shandong Second Medical University Weifang, 261053 China
| | - Zan Liu
- School of Pharmacy, Shandong Second Medical University Weifang, 261053 China
| |
Collapse
|
3
|
Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
Collapse
Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| |
Collapse
|
4
|
Chakrapani A, Ruiz‐Larrabeiti O, Pohl R, Svoboda M, Krásný L, Hocek M. Glucosylated 5‐Hydroxymethylpyrimidines as Epigenetic DNA Bases Regulating Transcription and Restriction Cleavage. Chemistry 2022; 28:e202200911. [DOI: 10.1002/chem.202200911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Olatz Ruiz‐Larrabeiti
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Svoboda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Libor Krásný
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| |
Collapse
|
5
|
Zipse H, Zott FL, Korotenko V. The pH-Dependence of the Hydration of 5-Formylcytosine - an Experimental and Theoretical Study. Chembiochem 2022; 23:e202100651. [PMID: 35084086 PMCID: PMC9304204 DOI: 10.1002/cbic.202100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/24/2022] [Indexed: 11/07/2022]
Abstract
5-Formylcytosine is an important nucleobase in epigenetic regulation, whose hydrate form has been implicated in the formation of 5-carboxycytosine as well as oligonucleotide binding events. The hydrate content of 5-formylcytosine and its uracil derivative has now been quantified using a combination of NMR and mass spectroscopic measurements as well as theoretical studies. Small amounts of hydrate can be identified for the protonated form of 5-formylcytosine and for neutral 5-formyluracil. For neutral 5-formylcytosine, however, direct detection of the hydrate was not possible due to its very low abundance. This is in full agreement with theoretical estimates.
Collapse
Affiliation(s)
- Hendrik Zipse
- Ludwig-Maximilians-Universität, Department of Chemistry, Butenandt-Str. 5-13, 81377, München, GERMANY
| | - Fabian L Zott
- LMU München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Vasily Korotenko
- LMU: Ludwig-Maximilians-Universitat Munchen, department of chemistry, GERMANY
| |
Collapse
|
6
|
Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. RSC Chem Biol 2022; 3:1069-1075. [PMID: 35975001 PMCID: PMC9347353 DOI: 10.1039/d2cb00133k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2′-deoxyribonucleosides and their corresponding 5′-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1-hydroxypropyl)pyrimidine nucleosides were separated and their absolute configuration was determined by a combination of X-ray and NMR analysis. The modified dNXTPs were used as substrates for PCR synthesis of modified DNA templates used for the study of transcription with bacterial RNA polymerase. Fundamental differences in transcription efficiency were observed, depending on the various modifications. The most notable effects included pronounced stimulation of transcription from 5-ethyluracil-bearing templates (200% transcription yield compared to natural thymine) and an enhancing effect of 5-acetylcytosine versus inhibiting effect of 5-acetyluracil. In summary, these results reveal that RNA polymerase copes with dramatically altered DNA structure and suggest that these nucleobases could potentially play roles as artificial epigenetic DNA nucleobases. Nucleotides derived from homologues of epigenetic pyrimidine bases were prepared and used for polymerase synthesis of modified DNA templates. Interesting effects of the substituents on PCR and transcription have been observed.![]()
Collapse
Affiliation(s)
- Filip Gracias
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Libor Krásný
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| |
Collapse
|
7
|
Schmidl D, Jonasson NSW, Korytiaková E, Carell T, Daumann LJ. Biomimetic Iron Complex Achieves TET Enzyme Reactivity**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David Schmidl
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Niko S. W. Jonasson
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Eva Korytiaková
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Thomas Carell
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Lena J. Daumann
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| |
Collapse
|
8
|
Schmidl D, Jonasson NSW, Korytiaková E, Carell T, Daumann LJ. Biomimetic Iron Complex Achieves TET Enzyme Reactivity*. Angew Chem Int Ed Engl 2021; 60:21457-21463. [PMID: 34181314 PMCID: PMC8518650 DOI: 10.1002/anie.202107277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/23/2021] [Indexed: 12/12/2022]
Abstract
The epigenetic marker 5-methyl-2'-deoxycytidine (5mdC) is the most prevalent modification to DNA. It is removed inter alia via an active demethylation pathway: oxidation by Ten-Eleven Translocation 5-methyl cytosine dioxygenase (TET) and subsequent removal via base excision repair or direct demodification. Recently, we have shown that the synthetic iron(IV)-oxo complex [FeIV (O)(Py5 Me2 H)]2+ (1) can serve as a biomimetic model for TET by oxidizing the nucleobase 5-methyl cytosine (5mC) to its natural metabolites. In this work, we demonstrate that nucleosides and even short oligonucleotide strands can also serve as substrates, using a range of HPLC and MS techniques. We found that the 5-position of 5mC is oxidized preferably by 1, with side reactions occurring only at the strand ends of the used oligonucleotides. A detailed study of the reactivity of 1 towards nucleosides confirms our results; that oxidation of the anomeric center (1') is the most common side reaction.
Collapse
Affiliation(s)
- David Schmidl
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Niko S. W. Jonasson
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Eva Korytiaková
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Thomas Carell
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Lena J. Daumann
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| |
Collapse
|
9
|
Feng Y, Chen JJ, Xie NB, Ding JH, You XJ, Tao WB, Zhang X, Yi C, Zhou X, Yuan BF, Feng YQ. Direct decarboxylation of ten-eleven translocation-produced 5-carboxylcytosine in mammalian genomes forms a new mechanism for active DNA demethylation. Chem Sci 2021; 12:11322-11329. [PMID: 34567494 PMCID: PMC8409474 DOI: 10.1039/d1sc02161c] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
DNA cytosine methylation (5-methylcytosine, 5mC) is the most important epigenetic mark in higher eukaryotes. 5mC in genomes is dynamically controlled by writers and erasers. DNA (cytosine-5)-methyltransferases (DNMTs) are responsible for the generation and maintenance of 5mC in genomes. Active demethylation of 5-methylcytosine (5mC) is achieved by ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are further processed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER) to restore unmodified cytosines. The TET-TDG-BER pathway could cause the production of DNA strand breaks and therefore jeopardize the integrity of genomes. Here, we investigated the direct decarboxylation of 5caC in mammalian genomes by using metabolic labeling with 2'-fluorinated 5caC (F-5caC) and mass spectrometry analysis. Our results clearly demonstrated the decarboxylation of 5caC occurring in mammalian genomes, which unveiled that, in addition to the TET-TDG-BER pathway, the direct decarboxylation of TET-produced 5caC constituted a new pathway for active demethylation of 5mC in mammalian genomes.
Collapse
Affiliation(s)
- Yang Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China .,School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Juan-Juan Chen
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Neng-Bin Xie
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Xue-Jiao You
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Wan-Bing Tao
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Xiaoxue Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University Beijing 100871 China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University Beijing 100871 China
| | - Xiang Zhou
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China .,School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China .,School of Health Sciences, Wuhan University Wuhan 430071 China
| |
Collapse
|
10
|
Zhang HY, Chen J, Lu CC, Han YP, Zhang Y, Zhao J. Visible-Light-Induced C(sp 2)-C(sp 3) Cross-Dehydrogenative-Coupling Reaction of N-Heterocycles with N-Alkyl- N-methylanilines under Mild Conditions. J Org Chem 2021; 86:11723-11735. [PMID: 34369160 DOI: 10.1021/acs.joc.1c01207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Disclosed herein is a cross-dehydrogenative-coupling reaction of N-heterocycles including 1,2,4-triazine-3,5(2H, 4H)-diones and quinoxaline-2(1H)-ones with N-methylanilines to form C(sp2)-C(sp3) under visible-light illumination and ambient air at room temperature. In this process, easily available Ru(bpy)3Cl2·6H2O serves as the catalyst, and air acts as the green oxidant. This method features high atom economy, environmental friendliness, and convenient operation and provides an efficient and practical access to aminomethyl-substituted N-heterocycles with extensive functional group compatibility in 40-86% yields.
Collapse
Affiliation(s)
- Hong-Yu Zhang
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| | - Jianjun Chen
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| | - Cong-Cong Lu
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| | - Ya-Ping Han
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| | - Yuecheng Zhang
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| | - Jiquan Zhao
- School of Chemical Engineering and Technology, Hebei Provincial Key Lab of Green Chemical Technology & High Efficient Energy Saving, Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300130, P. R. China
| |
Collapse
|
11
|
Korytiaková E, Kamińska E, Müller M, Carell T. Deformylation of 5-Formylcytidine in Different Cell Types. Angew Chem Int Ed Engl 2021; 60:16869-16873. [PMID: 34110681 PMCID: PMC8362038 DOI: 10.1002/anie.202107089] [Citation(s) in RCA: 4] [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: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Epigenetic programming of cells requires methylation of deoxycytidines (dC) to 5-methyl-dC (mdC) followed by oxidation to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). Subsequent transformation of fdC and cadC back to dC by various pathways establishes a chemical intra-genetic control circle. One of the discussed pathways involves the Tdg-independent deformylation of fdC directly to dC. Here we report the synthesis of a fluorinated fdC feeding probe (F-fdC) to study direct deformylation to F-dC. The synthesis was performed along a novel pathway that circumvents any F-dC as a reaction intermediate to avoid contamination interference. Feeding of F-fdC and observation of F-dC formation in vivo allowed us to gain insights into the Tdg-independent removal process. While deformylation was shown to occur in stem cells, we here provide data that prove deformylation also in different somatic cell types. We also investigated active demethylation in a non-dividing neurogenin-inducible system of iPS cells that differentiate into bipolar neurons.
Collapse
Affiliation(s)
- Eva Korytiaková
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Ewelina Kamińska
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| |
Collapse
|
12
|
Korytiaková E, Kamińska E, Müller M, Carell T. Deformylierung von 5‐Formylcytidin in unterschiedlichen Zelltypen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Eva Korytiaková
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Ewelina Kamińska
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Markus Müller
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Thomas Carell
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| |
Collapse
|
13
|
Schelter F, Kirchner A, Traube FR, Müller M, Steglich W, Carell T. 5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks. Chemistry 2021; 27:8100-8104. [PMID: 33769637 PMCID: PMC8252671 DOI: 10.1002/chem.202100551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 01/20/2023]
Abstract
The four non-canonical nucleotides in the human genome 5-methyl-, 5-hydroxymethyl-, 5-formyl- and 5-carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten-eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α-ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome.
Collapse
Affiliation(s)
- Florian Schelter
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Angie Kirchner
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeCB2 0REUK
| | | | - Markus Müller
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Wolfgang Steglich
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Thomas Carell
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| |
Collapse
|
14
|
Kreppel A, Ochsenfeld C. The Enzymatic Decarboxylation Mechanism of 5-Carboxy Uracil: A Comprehensive Quantum Chemical Study. J Chem Theory Comput 2021; 17:96-104. [PMID: 33356236 DOI: 10.1021/acs.jctc.0c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic regulation of DNA methylation is an important process for the control of gene expression in mammals. It is believed that in the demethylation pathway of 5-methyl cytosine, the intermediate 5-carboxy cytosine (5caC) can be actively decarboxylated alongside the substitution in the base excision repair. For the active decarboxylation of 5caC, a decarboxylase has not been identified so far. Due to the similar chemistry of the decarboxylation of 5-carboxy uracil (5caU) to uracil (U) in the pyrimidine salvage pathway catalyzed by the iso-orotate decarboxylase (IDCase), the study of this reaction might give valuable insights into the active 5caC decarboxylation process. In this work, we employ quantum chemical and molecular mechanic calculations and find that the catalytic mechanism of IDCase proceeds via a direct decarboxylation mechanism. Detailed investigations on the reaction coordinate reveal that it is a one-step mechanism with concerted proton transfer and C-C bond opening.
Collapse
Affiliation(s)
- Andrea Kreppel
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
| |
Collapse
|
15
|
Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett 2020; 22:9081-9085. [PMID: 33156631 DOI: 10.1021/acs.orglett.0c03462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2'-deoxycytidine and uridine 3'-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were used as primers for PCR to construct DNA templates modified in the promoter region that allowed switching of transcription through photochemical uncaging.
Collapse
Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| |
Collapse
|
16
|
Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
Collapse
Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| |
Collapse
|
17
|
Reversal of nucleobase methylation by dioxygenases. Nat Chem Biol 2020; 16:1160-1169. [DOI: 10.1038/s41589-020-00675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
|
18
|
Tran A, Zheng S, White DS, Curry AM, Cen Y. Retracted Article: Divergent synthesis of 5-substituted pyrimidine 2'-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases. Chem Sci 2020; 11:11818-11826. [PMID: 34123208 PMCID: PMC8162711 DOI: 10.1039/d0sc04161k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
Collapse
Affiliation(s)
- Ai Tran
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences Colchester VT 05446 USA
| | - Song Zheng
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences Colchester VT 05446 USA
| | - Dawanna S White
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Alyson M Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University Richmond VA 23219 USA
| |
Collapse
|
19
|
Abstract
DNA methylation is a key layer of epigenetic regulation. The deposition of methylation marks relies on the catalytic activity of DNA methyltransferases (DNMTs), and their active removal relies on the activity of ten-eleven translocation (TET) enzymes. Paradoxically, in important biological contexts these antagonistic factors are co-expressed and target overlapping genomic regions. The ensuing cyclic biochemistry of cytosine modifications gives rise to a continuous, out-of-thermal equilibrium transition through different methylation states. But what is the purpose of this intriguing turnover of DNA methylation? Recent evidence demonstrates that methylation turnover is enriched at gene distal regulatory elements, including enhancers, and can give rise to large-scale oscillatory dynamics. We discuss this phenomenon and propose that DNA methylation turnover might facilitate key lineage decisions.
Collapse
|
20
|
Zheng S, Tran A, Curry AM, White DS, Cen Y. Convenient synthesis of pyrimidine 2'-deoxyribonucleoside monophosphates with important epigenetic marks at the 5-position. Org Biomol Chem 2020; 18:5164-5173. [PMID: 32584362 DOI: 10.1039/d0ob00884b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methyl groups of thymine and 5-methylcytosine (5mC) bases in DNA undergo endogenous oxidation damage. Additionally, 5mC residues can be enzymatically deaminated or oxidized through either genetic alterations or the newly identified epigenetic reprogramming pathway. Several methods have been developed to measure the formation of modified DNA nucleobases including 32P-postlabeling. However, the postlabeling method is often limited by the absence of authentic chemical standards. The synthesis of monophosphate standards of nucleotide oxidation products is complicated by the presence of additional functional groups on the modified bases that require complex protection and deprotection strategies. Due to the emerging interest in the pyrimidine oxidation products, the corresponding protected 3'-phosphoramidites needed for solid-phase oligonucleotide synthesis have been reported, and several are commercially available. We report here an efficient synthesis of 3'-monophosphates from 3'-phosphoramidites and the subsequent enzymatic conversion of 3'-monophosphates to the corresponding 5'-monophosphates using commercially available enzymes.
Collapse
Affiliation(s)
- Song Zheng
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Ai Tran
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Alyson M Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Dawanna S White
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA. and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| |
Collapse
|
21
|
Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S, Carell T. Analysis of an Active Deformylation Mechanism of 5-Formyl-deoxycytidine (fdC) in Stem Cells. Angew Chem Int Ed Engl 2020; 59:5591-5594. [PMID: 31999041 PMCID: PMC7155088 DOI: 10.1002/anie.202000414] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 11/30/2022]
Abstract
The removal of 5‐methyl‐deoxycytidine (mdC) from promoter elements is associated with reactivation of the silenced corresponding genes. It takes place through an active demethylation process involving the oxidation of mdC to 5‐hydroxymethyl‐deoxycytidine (hmdC) and further on to 5‐formyl‐deoxycytidine (fdC) and 5‐carboxy‐deoxycytidine (cadC) with the help of α‐ketoglutarate‐dependent Tet oxygenases. The next step can occur through the action of a glycosylase (TDG), which cleaves fdC out of the genome for replacement by dC. A second pathway is proposed to involve C−C bond cleavage that converts fdC directly into dC. A 6‐aza‐5‐formyl‐deoxycytidine (a‐fdC) probe molecule was synthesized and fed to various somatic cell lines and induced mouse embryonic stem cells, together with a 2′‐fluorinated fdC analogue (F‐fdC). While deformylation of F‐fdC was clearly observed in vivo, it did not occur with a‐fdC, thus suggesting that the C−C bond‐cleaving deformylation is initiated by nucleophilic activation.
Collapse
Affiliation(s)
- Alexander Schön
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Ewelina Kaminska
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Florian Schelter
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Eveliina Ponkkonen
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Eva Korytiaková
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Sarah Schiffers
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| |
Collapse
|