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Kvach MV, Harjes S, Kurup HM, Jameson GB, Harjes E, Filichev VV. Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A. Beilstein J Org Chem 2024; 20:1088-1098. [PMID: 38774272 PMCID: PMC11106675 DOI: 10.3762/bjoc.20.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/26/2024] [Indexed: 05/24/2024] Open
Abstract
Nucleoside and polynucleotide cytidine deaminases (CDAs), such as CDA and APOBEC3, share a similar mechanism of cytosine to uracil conversion. In 1984, phosphapyrimidine riboside was characterised as the most potent inhibitor of human CDA, but the quick degradation in water limited the applicability as a potential therapeutic. To improve stability in water, we synthesised derivatives of phosphapyrimidine nucleoside having a CH2 group instead of the N3 atom in the nucleobase. A charge-neutral phosphinamide and a negatively charged phosphinic acid derivative had excellent stability in water at pH 7.4, but only the charge-neutral compound inhibited human CDA, similar to previously described 2'-deoxyzebularine (Ki = 8.0 ± 1.9 and 10.7 ± 0.5 µM, respectively). However, under basic conditions, the charge-neutral phosphinamide was unstable, which prevented the incorporation into DNA using conventional DNA chemistry. In contrast, the negatively charged phosphinic acid derivative was incorporated into DNA instead of the target 2'-deoxycytidine using an automated DNA synthesiser, but no inhibition of APOBEC3A was observed for modified DNAs. Although this shows that the negative charge is poorly accommodated in the active site of CDA and APOBEC3, the synthetic route reported here provides opportunities for the synthesis of other derivatives of phosphapyrimidine riboside for potential development of more potent CDA and APOBEC3 inhibitors.
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Affiliation(s)
- Maksim V Kvach
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Harikrishnan M Kurup
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Geoffrey B Jameson
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
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2
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Kurup HM, Kvach MV, Harjes S, Jameson GB, Harjes E, Filichev VV. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A. Org Biomol Chem 2023; 21:5117-5128. [PMID: 37282621 PMCID: PMC10282898 DOI: 10.1039/d3ob00392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.
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Affiliation(s)
- Harikrishnan M Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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3
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Ludford PT, Li Y, Yang S, Tor Y. Cytidine deaminase can deaminate fused pyrimidine ribonucleosides. Org Biomol Chem 2021; 19:6237-6243. [PMID: 34019616 PMCID: PMC8295196 DOI: 10.1039/d1ob00705j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tolerance of cytidine deaminase (CDA) to expanded heterocycles is explored via three fluorescent cytidine analogues, where the pyrimidine core is fused to three distinct five-membered heterocycles at the 5/6 positions. The reaction between CDA and each analogue is followed by absorption and emission spectroscopy, revealing shorter reaction times for all analogues than the native substrate. Pseudo-first order and Michaelis-Menten kinetic analyses provide insight into the enzymatic deamination reactions and assist in drawing comparison to established structure activity relationships. Finally, inhibitor screening modalities are created for each analogue and validated with zebularine and tetrahydrouridine, two known CDA inhibitors.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Shenghua Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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4
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Malki Y, Martinez J, Masurier N. 1,3-Diazepine: A privileged scaffold in medicinal chemistry. Med Res Rev 2021; 41:2247-2315. [PMID: 33645848 DOI: 10.1002/med.21795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/20/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Privileged structures have been widely used as effective templates for drug discovery. While benzo-1,4-diazepine constitutes the first historical example of such a structure, the 1,3 analogue is just as rich in terms of applications in medicinal chemistry. The 1,3-diazepine moiety is present in numerous biological active compounds including natural products, and is used to design compounds displaying a large range of biological activities. It is present in the clinically used anticancer compound pentostatin, in several recent FDA approved β-lactamase inhibitors (e.g., avibactam) and also in coformycin, a natural product known as a ring-expanded purine analogue displaying antiviral and anticancer activities. Several other 1,3-diazepine containing compounds have entered into clinical trials. This heterocyclic structure has been and is still widely used in medicinal chemistry to design enzyme inhibitors, GPCR ligands, and so forth. This review endeavours to highlight the main use of the 1,3-diazepine scaffold and its derivatives, and their applications in medicinal chemistry, drug design, and therapy. We will focus more particularly on the development of enzyme inhibitors incorporating this scaffold, with a strong emphasis on the molecular interactions involved in the inhibition mechanism.
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Affiliation(s)
- Yohan Malki
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean Martinez
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nicolas Masurier
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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5
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Nakamura K, Aizawa K, Aung KH, Yamauchi J, Tanoue A. Zebularine upregulates expression of CYP genes through inhibition of DNMT1 and PKR in HepG2 cells. Sci Rep 2017; 7:41093. [PMID: 28112215 PMCID: PMC5253741 DOI: 10.1038/srep41093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/14/2016] [Indexed: 01/22/2023] Open
Abstract
Drug-induced hepatotoxicity is one of the major reasons cited for drug withdrawal. Therefore, it is of extreme importance to detect human hepatotoxic candidates as early as possible during the drug development process. In this study, we aimed to enhance hepatocyte functions such as CYP gene expression in HepG2 cells, one of the most extensively used cell lines in evaluating hepatotoxicity of chemicals and drugs. We found that zebularine, a potent inhibitor of DNA methylation, remarkably upregulates the expression of CYP genes in HepG2 cells. In addition, we revealed that the upregulation of CYP gene expression by zebularine was mediated through the inhibition of both DNA methyltransferase 1 (DNMT1) and double-stranded RNA-dependent protein kinase (PKR). Furthermore, HepG2 cells treated with zebularine were more sensitive than control cells to drug toxicity. Taken together, our results show that zebularine may make HepG2 cells high-functioning and thus could be useful for evaluating the hepatotoxicity of chemicals and drugs speedily and accurately in in-vitro systems. The finding that zebularine upregulates CYP gene expression through DNMT1 and PKR modulation sheds light on the mechanisms controlling hepatocyte function and thus may aid in the development of new in-vitro systems using high-functioning hepatocytes.
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Affiliation(s)
- Kazuaki Nakamura
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kazuko Aizawa
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kyaw Htet Aung
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Junji Yamauchi
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Akito Tanoue
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
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6
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van Bemmel DM, Brank AS, Eritja R, Marquez VE, Christman JK. DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site. Biochem Pharmacol 2009; 78:633-41. [PMID: 19467223 DOI: 10.1016/j.bcp.2009.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022]
Abstract
Aberrant cytosine methylation in promoter regions leads to gene silencing associated with cancer progression. A number of DNA methyltransferase inhibitors are known to reactivate silenced genes; including 5-azacytidine and 2-(1H)-pyrimidinone riboside (zebularine). Zebularine is a more stable, less cytotoxic inhibitor compared to 5-azacytidine. To determine the mechanistic basis for this difference, we carried out a detailed comparisons of the interaction between purified DNA methyltransferases and oligodeoxyribonucleotides (ODNs) containing either 5-azacytosine or 2-(1H)-pyrimidinone in place of the cytosine targeted for methylation. When incorporated into small ODNs, the rate of C5 DNA methyltransferase inhibition by both nucleosides is essentially identical. However, the stability and reversibility of the enzyme complex in the absence and presence of cofactor differs. 5-Azacytosine ODNs form complexes with C5 DNA methyltransferases that are irreversible when the 5-azacytosine ring is intact. ODNs containing 2-(1H)-pyrimidinone at the enzymatic target site are competitive inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases. We determined that the ternary complexes between the enzymes, 2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl methionine are maintained through the formation of a reversible covalent interaction. The differing stability and reversibility of the covalent bonds may partially account for the observed differences in cytotoxicity between zebularine and 5-azacytidine inhibitors.
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Affiliation(s)
- Dana M van Bemmel
- Department of Biochemistry and Molecular Biology, Omaha, NE 68198-5870, USA.
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7
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Effects of a novel DNA methyltransferase inhibitor zebularine on human breast cancer cells. Breast Cancer Res Treat 2009; 120:581-92. [PMID: 19459041 DOI: 10.1007/s10549-009-0420-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/04/2009] [Indexed: 12/13/2022]
Abstract
Because DNA methyltransferase (DNMT) inhibitors like azacytidine and decitabine are known to be effective in the clinic for diseases like myelodysplastic syndromes that may result in part from transcriptional dysregulation due to epigenetic changes, there is interest in developing novel DNMT inhibitors that would be more effective and less toxic. The effects of one such agent, zebularine, which inhibits DNMT and cytidine deaminase, were assessed in two human breast cancer cell lines, MDA-MB-231 and MCF-7. Zebularine treatment inhibited cell growth in a dose and time dependent manner with an IC-50 of approximately 100 microM and 150 microM in MDA-MB-231 and MCF-7 cells, respectively, on 96 h exposure. This was associated with increased expression of p21, decreased expression of cyclin-D, and induction of S-phase arrest. At high doses zebularine induced changes in apoptotic proteins in a cell line specific manner manifested by alteration in caspase-3, Bax, Bcl2 and PARP cleavage. Like other DNMT inhibitors, zebularine decreased expression of DNMTs post-transcriptionally as well as expression of other epigenetic regulators like methyl CpG binding proteins and global acetyl H3 and H4 protein levels. Its capacity to reexpress epigenetically silenced genes in human breast cancer cells at low doses was confirmed by its ability to induce expression of estrogen and progesterone receptor mRNA in association with changes suggestive of active chromatin at the ER promoter as evidenced by ChIP. Finally, its effect in combination with other DNMT or HDAC inhibitors like decitabine or vorinostat was explored. The combination of 50 muM zebularine with decitabine or vorinostat significantly inhibited cell proliferation and colony formation in MDA-MB-231 cells compared with either drug alone. These findings suggest that zebularine is an effective DNMT inhibitor and demethylating agent in human breast cancer cell lines and potentiates the effects of other epigenetic therapeutics like decitabine and vorinostat.
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8
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Ludek OR, Schroeder GK, Wolfenden R, Marquez VE. Synthesis of conformationally locked carbocyclic 1,3-diazepinone nucleosides as inhibitors of cytidine deaminase. NUCLEIC ACIDS SYMPOSIUM SERIES (2004) 2008:659-60. [PMID: 18776552 DOI: 10.1093/nass/nrn333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We synthesized a series of carbocyclic nucleoside inhibitors of cytidine deaminase (CDA) based on a seven-membered 1,3-diazepin-2-one moiety. In the key step, the seven-membered ring was formed by a ring-closing-metathesis reaction. Therefore, the bis-allyl-urea moiety had to be protected by benzoylation in order to obtain an orientation suitable for ring closure. To our surprise, the analogue built on a flexible sugar template (4) showed a 100-fold stronger inhibition of CDA than the derivative with the preferred south-conformation.
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Affiliation(s)
- Olaf R Ludek
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
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9
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Senior MM, Chan TM, Li G, Huang Y, Stamford A. Unambiguous structural characterization of hydantoin reaction products using 2D HMBC NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:240-4. [PMID: 17278178 DOI: 10.1002/mrc.1956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Data from two-dimensional (2D) NMR experiments were used to identify the reaction products resulting from the opening of pyroglutamates with isocyanates or thioisocyanates. The reaction has the potential to produce compounds that would have very similar one-dimensional proton ((1)H) or carbon-13 ((13)C) NMR spectra. Careful analysis of (1)H--(1)H COSY, (1)H--(1)H NOESY, and HMBC data, including chemical shifts and coupling constants, were used to distinguish correctly between carbamoyl-2-pyrrolidinone, hydantoin, and perhydro-1,3-diazepine-2,4-dione type structures that could result from this reaction. This work describes their preparation and subsequent identification using 2D NMR spectroscopy, and includes complete (13)C assignments of the reaction products. The 2D NMR techniques and analysis described here can be applied successfully to other synthetic reactions with the potential to produce isomeric products.
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Affiliation(s)
- Mary M Senior
- Schering Plough Research Institute, Department of Analytical Spectroscopy, 2015 Galloping Hill Road, Bldg. K15 LL-0450, Kenilworth, NJ 07033, USA.
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10
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Peyrane F, Cesario M, Clivio P. Photochemical Ring Expansion of 4-Azidouracil: a Route to 5H-1,3,5-Triazepin-2,4-dione in the Nucleoside Series. J Org Chem 2006; 71:1742-5. [PMID: 16468839 DOI: 10.1021/jo0524066] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Under aqueous conditions, 4-azidouracil/tetrazolo[1,5-c]pyrimidin-5(6H)-one nucleosides undergo a very efficient photochemical nitrogen elimination and ring expansion to 1,3,5-triazepin-2,4-dione nucleosides whose structure has been confirmed by X-ray crystallography. In contrast, when the photolysis was attempted under anhydrous conditions in the presence of a nucleophile, a ring contraction reaction occurred, affording 2-oxoimidazolone nucleosides. A mechanism to account for the formation of ring expansion and contraction reactions and involving a carbodiimide intermediate is proposed which is reminiscent of the known photochemical behavior of 2-azidopyridines/tetrazolo[1,5-a]pyridines.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, UPR 2301 CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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11
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Chung SJ, Fromme JC, Verdine GL. Structure of Human Cytidine Deaminase Bound to a Potent Inhibitor. J Med Chem 2005; 48:658-60. [PMID: 15689149 DOI: 10.1021/jm0496279] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human cytidine deaminase (CDA) is an enzyme prominent for its role in catalyzing metabolic processing of nucleoside-type anticancer and antiviral agents. It is thus a promising target for the development of small molecule therapeutic adjuvants. We report the first crystal structure of human CDA as a complex with a tight-binding inhibitor, diazepinone riboside 1. The structure reveals that inhibitor 1 is able to establish a canonical pi/pi-interaction with a key active site residue, Phe 137.
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Affiliation(s)
- Sang J Chung
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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12
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Taillefumier C, Thielges S, Chapleur Y. Anomeric spiroannelated 1,4-diazepine 2,5-diones from furano exo-glycals: towards a new class of spironucleosides. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.01.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Zhou HB, Alper H. Synthesis of seven-membered ring diazepin-2-ones via palladium-catalyzed highly regioselective cyclization of 2-vinylpyrrolidines with aryl isocyanates. J Org Chem 2003; 68:3439-45. [PMID: 12713344 DOI: 10.1021/jo020526x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first palladium-catalyzed ring-expansion reaction of 2-vinylpyrrolidines with aryl isocyanates to form seven-membered ring heterocycles is described. This regioselective reaction requires 5 mol % of Pd(2)(dba)(3).CHCl(3) and 10 mol % of dppp at 40-60 degrees C in THF and results in the formation of 1,3-diazepin-2-ones in good isolated yields. When Pd(OAc)(2) and PPh(3) were utilized in the reaction, an intramolecular hydrogen migration occurs resulting in the formation of conjugated diene derivatives of urea.
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Affiliation(s)
- Hai-Bing Zhou
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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14
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Shutalev AD, Zavodnik VE, Gurskaya GV. New pyrimidine cyclonucleosides with hydrogenated aglycones: synthesis and X-ray structures. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1831-46. [PMID: 11200277 DOI: 10.1080/15257770008045464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Acid catalysed transformations of (6S)-6,5'-anhydro-6-hydroxy-1-(2',3'-O-isopropylidene-beta-D-ribofuranosyl)hexahydropyrimidine-2-thione are studied. (6R)-6,2'-anhydro-6-hydroxy-1-(alpha-D-ribofuranosyl)hexahydropyrimidine-2-thione was formed as a thermodynamically stable product. Two intermediates, (6S)-6,5'-anhydro-6-hydroxy-1-(beta-D-ribofuranosyl)hexahydropyrimidine-2-thione and 6-hydroxy-1-(D-ribosyl)hexahydropyrimidine-2-thione and products of cleavage of glycosidic bond were identified in the reaction mixtures. Results of X-ray structural determination of the synthesised nucleosides are presented.
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Affiliation(s)
- A D Shutalev
- Department of Organic Chemistry, State Academy of Fine Chemical Technology, Moscow, Russia
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15
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Minakawa N, Sasaki T, Matsuda A. Nucleosides and nucleotides 179. Ring-expanded purine nucleosides. The synthesis and cytotoxicity of imidazo[4,5-c]azepine nucleosides. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00832-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Lewis JP, Carter, CW, Hermans J, Pan W, Lee TS, Yang W. Active Species for the Ground-State Complex of Cytidine Deaminase: A Linear-Scaling Quantum Mechanical Investigation. J Am Chem Soc 1998. [DOI: 10.1021/ja973522w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James P. Lewis
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
| | - Charles W. Carter,
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
| | - Jan Hermans
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
| | - Wei Pan
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
| | - Tai-Sung Lee
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
| | - Weitao Yang
- Contribution from the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260, and Department of Chemistry, Duke University, Durham, North Carolina 27708-0354
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17
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Xiang S, Short SA, Wolfenden R, Carter CW. The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization. Biochemistry 1997; 36:4768-74. [PMID: 9125497 DOI: 10.1021/bi963091e] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of the cytidine deaminase-uridine product complex prepared either by cocrystallizing enzyme with uridine or by diffusing cytidine into ligand-free crystals show that the product binds as a 4-ketopyrimidine. They reveal four additional features of the catalytic process. (1) A water molecule bound to a site previously observed to bind the incoming 4-NH2 group represents the site for the leaving ammonia molecule. The conserved Pro 128 accommodates both moieties by orienting the carbonyl group of the previous residue. (2) The Glu 104 carboxylate group rotates from its hydrogen bond to the O4 hydroxyl group in transition-state analog complexes, forming a new hydrogen bond to the leaving group moiety. Thus, after stabilizing the hydroxyl group in the transition state, Glu 104 transfers a proton from that group to the leaving amino group, promoting enol-to-keto isomerization of the product. (3) Difference Fourier comparisons with transition-state complexes indicate that the pyrimidine ring rotates toward the zinc by approximately 10 degrees. The active site thus "pulls" the ring and 4-NH2 group in opposite directions during catalysis. To preserve coplanarity of the 4-keto group with the pyrimidine ring, the N1-C1' glycosidic bond bends by approximately 19 degrees out of the ring plane. This distortion may "spring-load" the product complex and promote dissociation. Failure to recognize a similar distortion could explain an earlier crystallographic interpretation of the adenosine deaminase-inosine complex [Wilson, D. K., & Quiocho, F. A. (1994) Nat. Struct. Biol. 1, 691-694]. (4) The Zn-Sgamma132 bond, which lengthens in transition-state complexes, shortens as the O4 atom returns to a state of lower negative charge in the planar product, consistent with our previous proposal that this bond buffers the zinc bond valence, compensating buildup of negative charge on the oxygen nucleophile during catalysis.
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Affiliation(s)
- S Xiang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 27599-7260, USA
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Cristalli G, Volpini R, Vittori S, Camaioni E, Rafaiani G, Potenza S, Vita A. Diazepinone Nucleosides as Inhibitors of Cytidine Deaminase. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Shutalev AD, Ignatova LA. N-glycosides. 9. Reaction of 3,5-O-isopropylidenexylofuranosylamine with ?-isothiocyanatoaldehydes. Synthesis of new cyclonucleosides with a hexahydropyrimidine aglycone. Chem Heterocycl Compd (N Y) 1993. [DOI: 10.1007/bf00534395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bouffard DY, Laliberté J, Momparler RL. Kinetic studies on 2',2'-difluorodeoxycytidine (Gemcitabine) with purified human deoxycytidine kinase and cytidine deaminase. Biochem Pharmacol 1993; 45:1857-61. [PMID: 8494545 DOI: 10.1016/0006-2952(93)90444-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Phosphorylation of cytosine analogs by deoxycytidine kinase (dCK) and deamination by cytidine deaminase (CDA) are two important processes in the activation and elimination of these drugs. We have investigated the kinetic parameters of 2',2'-difluorodeoxycytidine (dFdC) using purified enzymes from human cells. Deoxycytidine (CdR) and dFdC had Km values of 1.5 and 4.6 microM for dCK, respectively. Feedback inhibition of dCK by deoxycytidine 5'-triphosphate (dCTP) was also studied. Our results show that dCTP produced a greater inhibition of the phosphorylation of dFdC than CdR with concentrations of dCTP ranging from 1 to 25 microM. dFdC was a good substrate for CDA. Kinetic studies with this enzyme gave Km values for CdR and dFdC of 46.3 and 95.7 microM, respectively. The effect of competitive inhibitors of CDA on the deamination of dFdC was also investigated. Diazepinone riboside was a more potent inhibitor than tetrahydrouridine using either CdR or dFdC as the substrate. Inhibitors of CDA could be useful in clinical trials in patients with cancer to increase the chemotherapeutic effectiveness of dFdC.
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Affiliation(s)
- D Y Bouffard
- Département de Pharmacologie, Université de Montréal, Québec, Canada
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Laliberté J, Marquez VE, Momparler RL. Potent inhibitors for the deamination of cytosine arabinoside and 5-aza-2'-deoxycytidine by human cytidine deaminase. Cancer Chemother Pharmacol 1992; 30:7-11. [PMID: 1375134 DOI: 10.1007/bf00686478] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deamination of the nucleoside analogues ARA-C and 5-AZA-CdR by CR deaminase results in a loss of antileukemic activity. To prevent the inactivation of these analogues, inhibitors of CR deaminase may prove to be useful agents. In the present study we investigated the effects of the deaminase inhibitors Zebularine, 5-F-Zebularine, and diazepinone riboside on the deamination of CR, ARA-C, and 5-AZA-CdR using highly purified human CR deaminase (EC 3.5.4.5). These inhibitors produced a competitive type of inhibition with each substrate, the potency of which followed the patterns diazepinone riboside greater than 5-F-Zebularine and THU greater than Zebularine. 5-AZA-CdR was more sensitive than ARA-C to the inhibition produced by these deaminase inhibitors. The inhibition constants for diazepinone riboside lay in the range of 5-15 nM, suggesting that this inhibitor could be an excellent candidate for use in combination chemotherapy with either ARA-C or 5-AZA-CdR in patients with leukemia.
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Affiliation(s)
- J Laliberté
- Département de Pharmacologie, Université de Montréal, Québec, Canada
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Incomplete Factorial Search for Conditions Leading to High Quality Crystals of Escherichia coli Cytidine Deaminase Complexed to a Transition State Analog Inhibitor. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83491-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine. Bioorg Chem 1987. [DOI: 10.1016/0045-2068(87)90011-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ashley GW, Bartlett PA. A phosphorus-containing pyrimidine analog as a potent inhibitor of cytidine deaminase. Biochem Biophys Res Commun 1982; 108:1467-74. [PMID: 6758781 DOI: 10.1016/s0006-291x(82)80072-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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