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Makanyane DM, Maikoo S, Van Heerden FR, Rhyman L, Ramasami P, Mabuza LP, Ngubane P, Khathi A, Mambanda A, Booysen IN. Bovine serum albumin uptake and polypeptide disaggregation studies of hypoglycemic ruthenium(II) uracil Schiff-base complexes. J Inorg Biochem 2024; 255:112541. [PMID: 38554578 DOI: 10.1016/j.jinorgbio.2024.112541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/01/2024]
Abstract
Our prior studies have illustrated that the uracil ruthenium(II) diimino complex, [Ru(H3ucp)Cl(PPh3)] (1) (H4ucp = 2,6-bis-((6-amino-1,3-dimethyluracilimino)methylene)pyridine) displayed high hypoglycemic effects in diet-induced diabetic rats. To rationalize the anti-diabetic effects of 1, three new derivatives have been prepared, cis-[Ru(bpy)2(urdp)]Cl2 (2) (urdp = 2,6-bis-((uracilimino)methylene)pyridine), trans-[RuCl2(PPh3)(urdp)] (3), and cis-[Ru(bpy)2(H4ucp)](PF6)2 (4). Various physicochemical techniques were utilized to characterize the structures of the novel ruthenium compounds. Prior to biomolecular interactions or in vitro studies, the stabilities of 1-4 were monitored in anhydrous DMSO, aqueous phosphate buffer containing 2% DMSO, and dichloromethane (DCM) via UV-Vis spectrophotometry. Time-dependent stability studies showed ligand exchange between DMSO nucleophiles and chloride co-ligands of 1 and 3, which was suppressed in the presence of an excess amount of chloride ions. In addition, the metal complexes 1 and 3 are stable in both DCM and an aqueous phosphate buffer containing 2% DMSO. In the case of compounds 2 and 4 with no chloride co-ligands within their coordination spheres, high stability in aqueous phosphate buffer containing 2% DMSO was observed. Fluorescence emission titrations of the individual ruthenium compounds with bovine serum albumin (BSA) showed that the metal compounds interact non-discriminately within the protein's hydrophobic cavities as moderate to strong binders. The metal complexes were capable of disintegrating mature amylin amyloid fibrils. In vivo glucose metabolism studies in liver (Chang) cell lines confirmed enhanced glucose metabolism as evidenced by the increased glucose utilization and glycogen synthesis in liver cell lines in the presence of complexes 2-4.
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Affiliation(s)
- Daniel M Makanyane
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Sanam Maikoo
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Fanie R Van Heerden
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius; Centre of Natural Product, Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius; Centre of Natural Product, Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
| | - Lindokuhle P Mabuza
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Phikelelani Ngubane
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Andile Khathi
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Allen Mambanda
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Irvin N Booysen
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
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2
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Shiraishi M, Nabeshima N, Suzuki K, Fujita M, Iwai S. Endonuclease Q as a robust enhancer for nucleic acid amplification. Anal Biochem 2024; 692:115569. [PMID: 38750682 DOI: 10.1016/j.ab.2024.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
Isothermal nucleic acid amplification techniques are attracting increasing attention in molecular diagnosis and biotechnology. However, most existing techniques are complicated by the need for intricate primer design and numerous enzymes and primers. Here, we have developed a simple method, termed NAQ, that employs adding both endonuclease Q (EndoQ) and dUTP/dITP to conventional rolling circle amplification reactions to increase DNA amplification. NAQ does not require intricate primer design or DNA sequence-specific enzymes, and existing isothermal amplification techniques could be readily adapted to include both EndoQ and dUTP/dITP.
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Affiliation(s)
- Miyako Shiraishi
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan; Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, Japan.
| | - Noboru Nabeshima
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, Japan
| | - Keiichiro Suzuki
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, Japan; Institute for Advanced Co-Creation Studies, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, Japan; Graduate School of Frontier Bioscience, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, Japan
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3
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Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. J Biomol Struct Dyn 2024; 42:3958-3968. [PMID: 37261803 DOI: 10.1080/07391102.2023.2217683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Uracil is a common DNA lesion which is recognized and removed by uracil DNA-glycosylase (UDG) as a part of the base excision repair pathway. Excision proceeds by base flipping, and UDG efficiency is thought to depend on the ease of deformability of the bases neighboring the lesion. We used molecular dynamics simulations to assess the flexibility of a large library of dsDNA strands, containing all tetranucleotide motifs with U:A, U:G, T:A or C:G base pairs. Our study demonstrates that uracil damaged DNA largely follows trends in flexibility of undamaged DNA. Measured bending persistence lengths, groove widths, step parameters and base flipping propensities demonstrate that uracil increases the flexibility of DNA, and that U:G base paired strands are more flexible than U:A strands. Certain sequence contexts are more deformable than others, with a key role for the 3' base next to uracil. Flexibilities are large when this base is an A or G, and repressed for a C or T. A 5' T adjacent to the uracil strongly promotes flexibility, but other 5' bases are less influential. DNA bending is correlated to step deformations and base flipping, and bending aids flipping. Our study implies that the link between substrate flexibility and UDG efficiency is widely valid, helps explain why UDG prefers to bind U:G base paired strands, and suggests that the DNA bending angle of the UDG-substrate complex is optimal for base flipping.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
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Böhringer AC, Deters L, Windfelder AG, Merzendorfer H. Dextran sulfate sodium and uracil induce inflammatory effects and disrupt the chitinous peritrophic matrix in the midgut of Tribolium castaneum. Insect Biochem Mol Biol 2023; 163:104029. [PMID: 37907139 DOI: 10.1016/j.ibmb.2023.104029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
Dextran sulfate sodium is used in inflammatory bowel disease (IBD) mice models to trigger chronic intestinal inflammation. In this study, we have analyzed DSS effects in the genetic model and pest beetle, Tribolium castaneum, which can be easily and cost-effectively cultivated and examined in very large quantities compensating for individual variations. We fed the larvae with DSS and uracil, which is known to induce the production of reactive oxygen species by activating DUOX, a member of the NADPH oxidase family. Both chemicals induced IBD-like phenotypes, including impaired growth and development, midgut thickening, epithelial swelling, and a loss of epithelial barrier function. RNAi mediated knockdown of DUOX expression enhanced the effects of DSS and uracil on mortality. Finally, we showed that both treatments result in an altered activity of the intestinal microbiome, similar as observed in IBD patients. Our findings suggest that both chemicals impair the epithelial barrier by increasing the permeability of the peritrophic matrix. The loss of the barrier function may facilitate the entry of midgut bacteria triggering innate immune responses that also affect the intestinal microbiome. As the observed effects resemble those induced by DSS treatment in mice, T. castaneum might be suitable high-throughput invertebrate model for IBD research and preclinical studies.
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Affiliation(s)
| | - Lara Deters
- University of Siegen, Department of Chemistry-Biology, 57068, Siegen, Germany
| | - Anton George Windfelder
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 35392, Gießen, Germany; Experimental Radiology, Department of Medicine, Justus Liebig University, 35392, Gießen, Germany
| | - Hans Merzendorfer
- University of Siegen, Department of Chemistry-Biology, 57068, Siegen, Germany.
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Liu W, Chen L, Miao K, You Y, Li J, Lu J, Zhang Y. Identification and validation of diagnostic biomarkers for intrahepatic cholestasis of pregnancy based on untargeted and targeted metabolomics analyses of urine metabolite profiles. BMC Pregnancy Childbirth 2023; 23:828. [PMID: 38036952 PMCID: PMC10691115 DOI: 10.1186/s12884-023-06102-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Intrahepatic cholestasis of pregnancy (ICP) is a prevalent pregnancy-specific complication that presents with maternal itching and elevated serum bile acid levels. ICP is associated with unfavorable pregnancy outcomes, severely decreasing the pregnant woman's quality of life. Timely identification of ICP is crucial for effective management and improved outcomes. METHODS We collected urine samples from 8 patients with ICP and 8 healthy individuals. We used Liquid Chromatography-Mass Spectrometry (LC-MS) to detect metabolite expression levels, then conducted a series of bioinformatic analyses to explore the potential biological meanings of differentially expressed metabolites, and preliminarily discovered several candidate biomarkers. To validate these candidate biomarkers, we performed Gas Chromatography-Mass Spectrometry (GC-MS) detection and analyzed their diagnostic values using receiver operating characteristic (ROC) curve. RESULTS Untargeted metabolomics data showed that 6129 positive peaks and 6218 negative peaks were extracted from each specimen. OPLS-DA analysis and the heat map for cluster analysis showed satisfactory capability in discriminating ICP specimens from controls. Subsequent analysis extracted 64 significantly differentially expressed metabolites, which could be potential biomarkers for diagnosis of ICP. Based on the KEGG enrichment analyses, six candidate biomarkers were preliminarily identified. Two most promising biomarkers (3-hydroxypropionic acid and uracil) were validated by targeted metabolomics analyses with the area under the curve (AUC) of 0.920 and 0.850 respectively. CONCLUSION Based on preliminary screening from untargeted metabolomics and subsequent validation through targeted metabolomics, 3-hydroxypropionic acid and uracil were identified as promising diagnostic biomarkers for ICP.
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Affiliation(s)
- Weici Liu
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, Wuxi, Jiangsu, 214023, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Lingyan Chen
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Keyan Miao
- Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yilan You
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Jingyang Li
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Jianfeng Lu
- Wuxi Maternal and Child Health Care Hospital, Wuxi, Jiangsu, 214023, China.
| | - Yan Zhang
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, Wuxi, Jiangsu, 214023, China.
- Wuxi Maternal and Child Health Care Hospital, Wuxi, Jiangsu, 214023, China.
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Yu YM, Bu FZ, Meng SS, Yan CW, Wu ZY, Li YT. The first nano-cocrystal formulation of marine drug cytarabine with uracil based on cocrystal nanonization strategy for long-acting injection exhibiting enhanced antitumor activity. Int J Pharm 2023; 644:123300. [PMID: 37567370 DOI: 10.1016/j.ijpharm.2023.123300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
To emphasize the superiority of uracil (UR) in ameliorating biopharmaceutical characteristics of marine antitumor medicine cytarabine (ARA), thus gaining some innovative opinions for the exploitation of nanococrystal formulation, a cocrystal nanonization strategy is proposed by integrating cocrystallization and nanosize preparation techniques. For one thing, based on UR's unique structural features and natures together with advantages of preferential uptake by tumor cells, cocrystallizing ARA with UR is expected to improve the in vitro/vivo performances. For another, the nanonization procedure is oriented towards maintaining the long-term effective drug level. Along this route, a cocrystal of ARA with UR, viz., ARA-UR, is successfully synthesized and then transformed into nano-cocrystal. The cocrystal structure is precisely confirmed by various methods, demonstrating that a 1:1 ARA and UR in the crystal forms cytosine-UR hydrogen-bonding interactions, thus constructing supramolecular frameworks by strong π-π stacking interplays; while the nano-cocrystal is block-shaped particles of 562.70 nm with zeta potential -33.40 mV. The properties of cocrystal ARA-UR and its nano-cocrystal in vitro/vivo are comparatively explored by theoretical calculations and experimental analyses, revealing that permeability of both is significantly increased than ARA per se. Notably, the meliorative natures of both the cocrystal and nano-cocrystal in vitro bring excellent antitumor activity, but the latter has greater strengths over the former. More notably, the nano-cocrystal can sustain effective concentration for a relatively longer time, causing lengthened retention time and better absorption in vivo. The contribution offers a fire-new dosage form of ARA for long-lasting delivery, thus filling the vacancy in nanococrystal studies about marine drugs.
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Affiliation(s)
- Yue-Ming Yu
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China
| | - Fan-Zhi Bu
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China
| | - Su-Su Meng
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China
| | - Cui-Wei Yan
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China.
| | - Zhi-Yong Wu
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China.
| | - Yan-Tuan Li
- School of Medicine and Pharmacy and College of Marine Life Science, Ocean University of China, Qingdao, Shandong 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 266003, PR China.
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Rani P, Chahal S, Kumar R, Mayank, Kumar P, Negi A, Singh R, Kumar S, Kataria R, Joshi G, Sindhu J. Electro-organic synthesis of C-5 sulfenylated amino uracils: Optimization and exploring topoisomerase-I based anti-cancer profile. Bioorg Chem 2023; 138:106660. [PMID: 37320914 DOI: 10.1016/j.bioorg.2023.106660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
Cancer is spreading worldwide and is one of the leading causes of death. The use of existing chemotherapeutic agents is frequently limited due to side effects. As a result, it is critical to investigate new agents for cancer treatment. In this context, we developed an electrochemical method for the synthesis of a series of thiol-linked pyrimidine derivatives (3a-3p) and explored their anti-cancer potential. The biological profile of the synthesized compounds was evaluated against breast (MDAMB-231 and MCF-7) and colorectal (HCT-116) cancer cell lines. 3b and 3d emerged to be the most potent agents, with IC50 values ranging between 0.98 to 2.45 µM. Target delineation studies followed by secondary anticancer parameters were evaluated for most potent compounds, 3b and 3d. The analysis revealed compounds possess DNA intercalation potential and selective inhibition towards human topoisomerase (hTopo1). The analysis was further corroborated by DNA binding studies and in silico-based molecular modeling studies that validated the intercalating binding mode between the compounds and the DNA.
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Affiliation(s)
- Payal Rani
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Sandhya Chahal
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Roshan Kumar
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda 151401, India
| | - Mayank
- Institut interdisciplinaire d'innovation technologique - 3IT USherbrooke, Sherbrooke, Quebec, Canada
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Arvind Negi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
| | - Rajvir Singh
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Sudhir Kumar
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India; Department of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Ramesh Kataria
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Gaurav Joshi
- Department of Pharmaceutical Science, Hemvati Nandan Bahuguna Garhwal (A Central) University, Srinagar-246174, Dist. Garhwal, (Uttarakhand), India; Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement Town Dehradun, Uttarakhand- 248002.
| | - Jayant Sindhu
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India.
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Deng XR, Hu AW, Hu SQ, Yang WL, Sun C, Xiao SJ, Yang GP, Zheng QQ, Liang RP, Zhang L, Qiu JD. An in-situ strategy to construct uracil-conjugated covalent organic frameworks with tunable fluorescence/recognition characteristics for sensitive and selective Mercury(II) detection. Anal Chim Acta 2023; 1252:341056. [PMID: 36935154 DOI: 10.1016/j.aca.2023.341056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/25/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023]
Abstract
Previous researches of covalent organic frameworks (COFs) have shown their potential as fluorescent probes, but the regulation of their optical properties and recognition characteristics still remains a challenge, and most of reports required complicated post-decoration to improve the sensing performance. In this context, we propose a novel in-situ strategy to construct uracil-conjugated COFs and modulate their fluorescence properties for sensitive and selective mercury(II) detection. By using 1,3,6,8-tetrakis(4-formylphenyl)pyrene (TFPPy) and 1,3,6,8-tetrakis(4-aminophenyl)pyrene (TAPPy) as fundamental blocks and 5-aminouraci (5-AU) as the functional monomer, a series of COFs (Py-COFs and Py-U-COFs-1 to Py-U-COFs-5) with tunable fluorescence were solvothermally synthesized through an in-situ Schiff base reaction. The π-conjugated framework serves as a signal reporter, the evenly and densely distributed uracil acts as a mercury(II) receptor, and the regular pores (channels) make the rapid and sensitive detection of the mercury(II) possible. In this research, we manage to regulate the crystalline structure, the fluorescence properties, and the sensing performance of COFs by simply changing the molar ratio of precursors. We expect this research to open up a new strategy for effective and controllable construction of functionalized COFs for environmental analysis.
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Affiliation(s)
- Xi-Rui Deng
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - A-Wei Hu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Sheng-Qian Hu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Wen-Li Yang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Chen Sun
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Sai-Jin Xiao
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology (ECUT), Nanchang, 330013, PR China
| | - Gui-Ping Yang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Qiong-Qing Zheng
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Ru-Ping Liang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China
| | - Li Zhang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China.
| | - Jian-Ding Qiu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, PR China; State Key Laboratory of Nuclear Resources and Environment, East China University of Technology (ECUT), Nanchang, 330013, PR China.
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9
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Knikman JE, Rosing H, Guchelaar HJ, Cats A, Beijnen JH. Assay performance and stability of uracil and dihydrouracil in clinical practice. Cancer Chemother Pharmacol 2023; 91:257-266. [PMID: 36905444 DOI: 10.1007/s00280-023-04518-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
PURPOSE Measurement of endogenous uracil (U) is increasingly being used as a dose-individualization method in the treatment of cancer patients with fluoropyrimidines. However, instability at room temperature (RT) and improper sample handling may cause falsely increased U levels. Therefore we aimed to study the stability of U and dihydrouracil (DHU) to ensure proper handling conditions. METHODS Stability of U and DHU in whole blood, serum, and plasma at RT (up to 24 h) and long-term stability (≥ 7 days) at - 20 °C were studied in samples from 6 healthy individuals. U and DHU levels of patients were compared using standard serum tubes (SSTs) and rapid serum tubes (RSTs). The performance of our validated UPLC-MS/MS assay was assessed over a period of 7 months. RESULTS U and DHU levels significantly increased at RT in whole blood and serum after blood sampling with increases of 12.7 and 47.6% after 2 h, respectively. A significant difference (p = 0.0036) in U and DHU levels in serum was found between SSTs and RSTs. U and DHU were stable at - 20 °C at least 2 months in serum and 3 weeks in plasma. Assay performance assessment fulfilled the acceptance criteria for system suitability, calibration standards, and quality controls. CONCLUSION A maximum of 1 h at RT between sampling and processing is recommended to ensure reliable U and DHU results. Assay performance tests showed that our UPLC-MS/MS method was robust and reliable. Additionally, we provided a guideline for proper sample handling, processing and reliable quantification of U and DHU.
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Affiliation(s)
- Jonathan E Knikman
- Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Hilde Rosing
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Cats
- Department of Gastroenterology and Hepatology, Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos H Beijnen
- Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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10
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Tybirk L, Hoffmann-Lücke E, Greibe E. Instability of uracil in whole blood might affect cancer treatment with fluoropyrimidines. Clin Chim Acta 2023; 538:87-90. [PMID: 36347332 DOI: 10.1016/j.cca.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/23/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND AND AIMS Measurement of plasma uracil is used before cancer treatment with fluoropyrimidines to determine if patients tolerate a full dose. Incorrect preanalytical handling may cause falsely elevated concentration and result in suboptimal cancer treatment. We aimed to examine the stability of uracil in whole blood stored at room temperature (RT) and the effect of centrifugation temperature. MATERIALS AND METHODS EDTA tubes (6x4 mL) were collected from 25 healthy volunteers. Five samples were stored 0, 1.5, 2, 3, and 4 h at RT and centrifuged at 4 °C. The sixth sample was centrifuged at RT after 1.5 h. Uracil was measured using an in-house LC-MS/MS method. RESULTS Storage of whole blood at RT followed by centrifugation at 4 °C caused a rapid increase in uracil concentration. Already after 1.5 h, the mean change (20.5 % (95 % CI: 11.9-29.2 %)) exceeded the maximum permissible difference. Centrifugation at RT instead of 4 °C after 1.5 h resulted in a smaller increase (7.0 % (95 % CI: 0.7-13.4 %)), although not statistically significant (p = 0.0527). CONCLUSION Uracil was unstable in samples processed according to current recommendations. Our data indicates better stability when centrifugation is performed at RT compared with 4 °C but further research into this is necessary.
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Affiliation(s)
- Lea Tybirk
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Blvd. 99, 8200 Aarhus N, Denmark.
| | - Elke Hoffmann-Lücke
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Blvd. 99, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Health, Aarhus University, Palle Juul-Jensens Blvd. 82, 8200 Aarhus N, Denmark
| | - Eva Greibe
- Department of Clinical Biochemistry, Aarhus University Hospital, Palle Juul-Jensens Blvd. 99, 8200 Aarhus N, Denmark; Department of Clinical Medicine, Health, Aarhus University, Palle Juul-Jensens Blvd. 82, 8200 Aarhus N, Denmark
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11
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Chang C, Yang Y, Li J, Park SH, Fang GC, Liang C, Cao W. Screening of glycosylase activity on oxidative derivatives of methylcytosine: Pedobacter heparinus SMUG2 as a formylcytosine- and carboxylcytosine-DNA glycosylase. DNA Repair (Amst) 2022; 119:103408. [PMID: 36179537 DOI: 10.1016/j.dnarep.2022.103408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022]
Abstract
5-Methylcytosine (mC) is an epigenetic mark that impacts transcription, development, diseases including cancer and aging. The demethylation process involves Tet-mediated stepwise oxidation of mC to hmC, fC, or caC, excision of fC or caC by thymine-DNA glycosylase (TDG), and subsequent base excision repair. Thymine-DNA glycosylase (TDG) belongs to uracil-DNA glycosylase (UDG) superfamily, which is a group of enzymes that are initially found to be responsible for excising the deaminated bases from DNA and generating apurinic/apyrimidinic (AP) sites. mC oxidative derivatives may also be generated from Fenton chemistry and γ-irradiation. In screening DNA glycosylase activity in UDG superfamily, we identified new activity on fC- and caC-containing DNA in family 2 MUG/TDG and family 6 HDG enzymes. Surprisingly, we found a glycosylase SMUG2 from bacterium Pedobacter heparinus (Phe), a subfamily of family 3 SMUG1 DNA glycosylase, displayed catalytic activity towards not only DNA containing uracil, but also fC and caC. Given the sequence and structural differences between the family 3 and other family enzymes, we investigated the catalytic mechanism using mutational, enzyme kinetics and molecular modeling approaches. Mutational analysis and kinetics measurements identified I62, N63 and F76 of motif 1, and H205 of motif 2 in Phe SMUG2 as important catalytic residues, of which H205 of motif 2 played a critical role in catalyzing the removal of fC and caC. A catalytic model underlying the roles of these residues was proposed. The structural and catalytic differences between Phe SMUG2 and human TDG were compared by molecular modeling and molecular dynamics simulations. This study expands our understanding of DNA glycosylase capacity in UDG superfamily and provides insights into the molecular mechanism of fC and caC excision in Phe SMUG2.
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12
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Srivastava A, Pandey BK, Gupta S, Mishra S. Interaction of glucosamine with uracil and thymine: a computational study. J Mol Model 2022; 28:277. [PMID: 36018526 DOI: 10.1007/s00894-022-05291-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
The present study delves into the interaction of the monomer of glucosamine with uracil and thymine in vacuum and in different phases by density functional theory (DFT). Both the molecular geometries were optimized at B3LYP with a 6-31G(d,p) basis set. The binding energy, interaction energy, and solubility were calculated from the optimized molecular geometry. The dipole moment and the electronic energies were found of the optimized product in different solvents (water, ethanol, methanol, heptane, cyclohexane, and CCl4) which describes the solubility of the interactive molecule in polar and non-polar solvents. The electronic energies are nearly the same for all the solvents. Observed theoretical results are expected to guide future relevant experimental research on gene delivery by glucosamine. This will also help in enhancing pharmaceutical research as carrier drug delivery, tissue repair, gene delivery, spermicidal activity, anti-tumor, and anti-microbial resistance.
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Affiliation(s)
- Aditi Srivastava
- Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010, India
| | - B K Pandey
- Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010, India.
| | - Shivani Gupta
- Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010, India
| | - Saurav Mishra
- Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010, India
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13
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Jindal G, Kaur N. Uracil-Appended Fluorescent Sensor for Cu 2+ and Hg 2+ Ions: Real-Life Utilities Including Recognition of Vitamin B 2 (Riboflavin) in Milk Products and Invisible Ink Applications. J Fluoresc 2022. [PMID: 35751749 DOI: 10.1007/s10895-022-02994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
Abstract
A simple uracil-appended fluorescent sensor (1) has been developed by one pot reaction and characterized by using common spectroscopic methods such as UV-vis, Fluorescence, HRMS and FT-IR analyses. Upon addition of various metal ions to the CH3CN solution of sensor 1, the fluorescence was quenched in the presence of Cu2+ / Hg2+ ions. The limit of detection for Cu2+ and Hg2+ was calculated to be 3.31 and 0.316 µM, respectively. Further, the sensor was applied for real-life applications in the determination of Vitamin B2 (riboflavin) and its presence in milk products. With the incorporation of different sources of vitamin-B to acetonitrile solution of it, there was discernible fluorescence enhancement only in the presence of vitamin B2. Also, it has been successfully applied for the detection of Vitamin B2 (riboflavin) in milk and curd. Moreover, based on the fluorescent color changes, the sensor was utilized for invisible ink applications.
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14
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Menestrina Dewes M, Cé da Silva L, Fazenda Meireles Y, Viana de Freitas M, Frank Bastiani M, Feltraco Lizot L, Zilles Hahn R, Venzon Antunes M, Linden R. Evaluation of the Tasso-SST® capillary blood microsampling device for the measurement of endogenous uracil levels. Clin Biochem 2022; 107:1-6. [PMID: 35709975 DOI: 10.1016/j.clinbiochem.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 06/12/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Uracil (U) plasma or serum levels can be used as surrogates of dihydropyrimidine dehydrogenase (DPD) activity, which is strongly related to the occurrence of severe or fatal toxicity after administration of fluoropyrimidines (FP) chemotherapy. Obtaining blood plasma or serum for U measurement usually requires a phlebotomy procedure by a qualified professional. An alternative to conventional blood drawn is the use of the Tasso-SST® device, which allows the collection of a small blood volume from skin capillaries. This study aimed to implement a sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for the determination of U in small serum samples and to compare U concentrations measured in venous plasma, obtained after phlebotomy, and serum obtained with the Tasso-SST® device. METHODS Fifty microliter samples were prepared through simple protein precipitation with trichloroacetic acid. Chromatographic separation was performed with a porous graphitic carbon stationary phase and mass spectrometric detection used positive electrospray ionization. The assay was validated according to international guidelines. RESULTS The linear range of the assay was 5-250 ng/mL. Measurement accuracy was in the range of 98.8-108.2%, inter-assay precision was 4.3-7.3%, and intra-assay precision was 3.4-6.1%. The average matrix effect was -6.42%. The extraction yield was 95-103.3%. U concentrations measured in serum obtained with the Tasso-SST® device and venous blood plasma were highly correlated (rs = 0.910, P < 0.0001), and no systematic or proportional bias between U levels measured in both matrices was found. CONCLUSIONS The use of blood microsampling with the Tasso-SST® device is a useful alternative for the measurement of U and the identification of patients with DPD deficiency.
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Affiliation(s)
- Milene Menestrina Dewes
- Analytical Toxicology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil; Graduate Program on Toxicology and Analytical Toxicology, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Laura Cé da Silva
- Analytical Toxicology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil; Graduate Program on Toxicology and Analytical Toxicology, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | | | | | | | - Roberta Zilles Hahn
- Analytical Toxicology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Marina Venzon Antunes
- Analytical Toxicology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil; Graduate Program on Toxicology and Analytical Toxicology, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Rafael Linden
- Analytical Toxicology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil; Graduate Program on Toxicology and Analytical Toxicology, Universidade Feevale, Novo Hamburgo, RS, Brazil.
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15
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Gerakines PA, Qasim D, Frail S, Hudson RL. Radiolytic Destruction of Uracil in Interstellar and Solar System Ices. Astrobiology 2022; 22:233-241. [PMID: 34672795 DOI: 10.1089/ast.2021.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Uracil is one of the four RNA nucleobases and a component of meteoritic organics. If delivered to the early Earth, uracil could have been involved in the origins of the first RNA-based life, and so this molecule could be a biomarker on other worlds. Therefore, it is important to understand uracil's survival to ionizing radiation in extraterrestrial environments. Here we present a study of the radiolytic destruction kinetics of uracil and mixtures of uracil diluted in H2O or CO2 ice. All samples were irradiated by protons with an energy of 0.9 MeV, and experiments were performed at 20 and 150 K to determine destruction rate constants at temperatures relevant to interstellar and Solar System environments. We show that uracil is destroyed much faster when H2O ice or CO2 ice is present than when these two ices are absent. Moreover, destruction is faster for CO2-dominated ices than for H2O-dominated ones and, to a lesser extent, at 150 K compared with 20 K. Extrapolation of our laboratory results to astronomical timescales shows that uracil will be preserved in ices with half-lives of up to ∼107 years on cold planetary bodies such as comets or Pluto. An important implication of our results is that for extraterrestrial environments, the application of laboratory data measured for the radiation-induced destruction of pure (neat) uracil samples can greatly underestimate the molecule's rate of destruction and significantly overestimate its lifetime, which can lead to errors of over 1000%.
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Affiliation(s)
- Perry A Gerakines
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Danna Qasim
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington, District of Columbia, USA
- Center for Research and Exploration in Space Science and Technology, NASA/GSFC, Greenbelt, Maryland, USA
| | - Sarah Frail
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Reggie L Hudson
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
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16
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Sadahiro S, Sakamoto K, Tsuchiya T, Takahashi T, Ohge H, Sato T, Kondo K, Ogata Y, Baba H, Itabashi M, Ikeda M, Hamada M, Maeda K, Masuko H, Takahashi K, Sakamoto J, Kusano M, Hyodo I, Taguri M, Morita S. Prospective observational study of the efficacy of oral uracil and tegafur plus leucovorin for stage II colon cancer with risk factors for recurrence using propensity score matching (JFMC46-1201). BMC Cancer 2022; 22:170. [PMID: 35168560 PMCID: PMC8845390 DOI: 10.1186/s12885-022-09267-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background The efficacy of adjuvant chemotherapy for high-risk stage II colon cancer (CC) has not been well established. We compared the effects of surgery with and without oral uracil and tegafur plus leucovorin (UFT/LV) in patients with high-risk stage II CC, adjusting for potential risk factors. Methods We enrolled patients with histologically confirmed stage II colon adenocarcinoma with at least one of the following conditions: T4 disease, perforation/penetration, poorly differentiated adenocarcinoma/mucinous carcinoma, or < 12 dissected lymph nodes. Patients chose to be non-randomized or randomized to undergo surgery alone (NR-Group S or R-Group S) or surgery followed by 6 months of UFT/LV (NR-Group U or R-Group U). The primary endpoint was disease-free survival (DFS) after adjusting for previously reported risk factors using propensity score matching (1:2) and inverse probability of treatment weighting (IPTW) in the non-randomized arm. Results Overall, 1,902 (98%) and 36 (2%) patients were enrolled in the non-randomized and randomized arms, respectively. There were too few patients in the randomized arm and these were therefore excluded from the analysis. Of the 1,902 patients, 402 in NR-Group S and 804 in NR-Group U were propensity score-matched. The 3-year DFS rate (95% confidence interval) was significantly higher in NR-Group U (80.9% [77.9%–83.4%]) than in NR-Group S (74.0% [69.3%–78.0%]) (hazard ratio, 0.64 [0.50–0.83]; P = 0.0006). The 3-year overall survival rate was not significantly different between NR-Group S and NR-Group U. Significantly higher 3-year DFS (P = 0.0013) and overall survival (P = 0.0315) rates were observed in NR-Group U compared with NR-Group S using IPTW. Conclusions Adjuvant chemotherapy with UFT/LV showed a significant survival benefit over surgery alone in patients with high-risk stage II CC characterized by at least one of the following conditions: T4 disease, perforation/penetration, poorly differentiated adenocarcinoma/mucinous carcinoma, or < 12 dissected lymph nodes. Trial registration Japan Registry of Clinical Trials: jRCTs031180155 (date of registration: 25/02/2019) (UMIN Clinical Trials Registry: UMIN000007783, date of registration: 18/04/2012). Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09267-z.
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Affiliation(s)
- Sotaro Sadahiro
- Department of Surgery, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Tsuchiya
- Department of Surgery, Sendai City Medical Center, 5-22-1 Tsurugaya, Miyagino-ku, Sendai, Miyagi, 983-0824, Japan
| | - Takao Takahashi
- Department of Digestive Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Toshihiko Sato
- Department of Surgery, Yamagata Prefectural Central Hospital, 1800 Aoyagi, Yamagata, 990-2292, Japan
| | - Ken Kondo
- Department of Surgery, Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi, 460-0001, Japan
| | - Yutaka Ogata
- Department of Surgery, Kurume University Hospital Cancer Center, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Michio Itabashi
- Department of Surgery, Division of Inflammatory Bowel Disease Surgery, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Masataka Ikeda
- Department of Gastroenterological Surgery, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Madoka Hamada
- Division of Gastrointestinal Surgery, Kansai Medical University Hospital, 2-3-1 Shinmachi Hirakata, Osaka, 573-1191, Japan
| | - Kiyoshi Maeda
- Department of Gastroenterological Surgery, Osaka City General Hospital, 2-13-22 Miyakojimahondori, Miyakojima-ku, Osaka, 534-0021, Japan
| | - Hiroyuki Masuko
- Department of Surgery, Nikko Memorial Hospital, 1-5-13 Shintomi-cho, Muroran, Hokkaido, 051-8501, Japan
| | - Keiichi Takahashi
- Tokyo Metropolitan Health and Hospitals Corporation Ohkubo Hospital, 2-44-1 Kabuki-cho, Shinjuku-ku, Tokyo, 160-8488, Japan
| | - Junichi Sakamoto
- Tokai Central Hospital, 4-6-2 Sohara Higashijima-cho, Kakamigahara, Gifu, 504-8601, Japan
| | - Mitsuo Kusano
- Department of Physical Medicine, Yoichi Hospital, 19-1-1 Kurokawa-cho Yoichi, Hokkaido, 046-0003, Japan
| | - Ichinosuke Hyodo
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto, Matsuyama, Ehime, 791-0280, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Satoshi Morita
- Department of Biomedical Statistics and Bioinformatics, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
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Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT. Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. Fungal Biol Biotechnol 2021; 8:10. [PMID: 34656184 PMCID: PMC8520639 DOI: 10.1186/s40694-021-00117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD. Results Heterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9. Conclusions Activity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure–function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-021-00117-4.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aurin M Vos
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mats Wassink
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter L Hagedoorn
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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18
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Abstract
The Maillard reaction, a spontaneous 'one pot' reaction between amino acids and reducing sugars that occurs at low reactant concentrations and low temperatures, is a good candidate for having played a role in the origin of life on the Earth. In view of the probability that RNA and DNA were preceded by an evolutionary forerunner with a more straightforward prebiotic synthesis, it is a testament to the prescience of Oró and colleagues that, in 1975, they drew attention to the Maillard reaction, in particular evidence that melanoidin polymers (the end-product of the reaction) contain '…heterocyclic nitrogen compounds similar to the nitrogenous bases' (Nissenbaum in J Mol Evol 6:253-270, 1975). Indeed, reports of the Maillard reaction product, 2-Acetyl-6-(Hydroxymethyl)-5,6-Dihydro-4H-Pyridinone (AHDP), with a structure reminiscent of the pyrimidine nucleobase uracil, suggest the Maillard reaction might have played a key role in the synthesis of components of a proto-RNA polymer, with AHDP and two structurally related products predicted to be similar to uracil in the latter's ability to form non-standard base pair interactions. It is possible that the primary function of these interactions was to allow molecules such as AHDP to separate out of the prebiotic chemical clutter. If this were the case, catalysis, and coding-made possible by the polymerization of proto-nucleoside monomers into linear sequence strings-would have been evolving properties.
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Affiliation(s)
- Harold S Bernhardt
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
| | - Warren P Tate
- Emeritus Professor, Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Burns KE, Chavani O, Jeong SH, Duley JA, Porter D, Findlay M, Strother RM, Helsby NA. Comparison of a thymine challenge test and endogenous uracil-dihydrouracil levels for assessment of fluoropyrimidine toxicity risk. Cancer Chemother Pharmacol 2021; 87:711-716. [PMID: 33687515 DOI: 10.1007/s00280-021-04240-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/01/2021] [Indexed: 01/16/2023]
Abstract
PURPOSE Standard dosages of fluoropyrimidine chemotherapy result in severe toxicity in a substantial proportion of patients, however, routine pre-therapeutic toxicity prediction remains uncommon. A thymine (THY) challenge test can discriminate risk of severe gastrointestinal toxicity in patients receiving fluoropyrimidine monotherapy. We aimed to measure endogenous plasma uracil (U) and its ratio to dihydrouracil (DHU), and assess the performance of these parameters compared with the THY challenge test to evaluate risk of severe toxicity. METHODS Plasma samples, previously collected from 37 patients receiving 5-fluorouracil (5-FU) or capecitabine monotherapy for a THY challenge test (ACTRN12615000586516; retrospectively registered), were assessed for endogenous plasma concentrations of U and DHU using a validated LC-MS/MS method. Renal function was estimated from blood creatinine, and patients with ≥ grade 3 toxicity (CTCAE v4.0) were classified as cases. RESULTS There were no differences in median endogenous U plasma concentrations or U/DHU ratios between severe toxicity cases and non-cases. Significant differences between cases and non-cases were noted when these measures were normalised to the estimated renal function (CrCL), Unorm p = 0.0004; U/DHUnorm p = 0.0083. These two parameters had a sensitivity of 29%, compared with 57% for the THY challenge test in the same patients. Genotyping for clinically relevant DPYD variants was inferior to either of these pyrimidine phenotyping tests (sensitivity of 14%). CONCLUSIONS The endogenous uracil-based parameters, adjusted to CrCL, were more predictive of increased risk of severe fluoropyrimidine toxicity than DPYD genotyping. However, endogenous U measurement detected fewer cases of severe toxicity than the THY challenge test.
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Affiliation(s)
- Kathryn E Burns
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | | | - Soo Hee Jeong
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - John A Duley
- School of Pharmacy, University of Queensland, Brisbane, Australia
| | - David Porter
- Cancer and Blood, Auckland City Hospital, Grafton, Auckland, New Zealand
| | - Michael Findlay
- Cancer and Blood, Auckland City Hospital, Grafton, Auckland, New Zealand.,Cancer Trials New Zealand, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - R Matthew Strother
- Department of Oncology, Canterbury District Health Board and Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Nuala A Helsby
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
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20
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Sambathkumar S, Manivannan C, Baskaran S, Kumar RR, Anbazhagan V. A study on the interaction of nile blue with Uracils: A spectroscopic and computational approach. Spectrochim Acta A Mol Biomol Spectrosc 2021; 246:119011. [PMID: 33038853 DOI: 10.1016/j.saa.2020.119011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The present work focuses the investigation on fluorescence quenching of nile blue (NB) in presence of various substituted uracil molecules. UV-Visible absorption studies signify the possibility of ground state complex formation between NB and uracil molecules. The increase in concentration of quencher molecules greatly influences the emission spectra of NB. The bimolecular quenching rate constant (kq) were calculated and found to depend on the position and electronic properties of substituent in quencher molecules. Fluorescence quenching experiments were performed at different temperature to calculate the thermodynamic parameters. The fluorescence lifetime measurements show that the quenching process proceeds through static quenching. The mechanism of fluorescence quenching includes the possibility of proton transfer. The bond dissociation enthalpy (BDE) reveals the release of H from the quencher molecules. The quencher molecules possess antioxidant activity and identified using deoxyribose degradation assay. The position of substituent and its electronic property are key features to address the antioxidant activity of uracil molecules.
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Affiliation(s)
- S Sambathkumar
- PG and Research Department of Chemistry, Vivekanandha College of Arts and Sciences for Women (Autonomous), Tiruchengode, Namakkal 637 205, Tamil Nadu, India.
| | - C Manivannan
- Photonics Laboratory, Department of Chemistry, Bannari Amman Institute of Technology, Sathyamangalam 638 401, Erode, Tamil Nadu, India
| | - S Baskaran
- Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - R Raj Kumar
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, PR China
| | - V Anbazhagan
- Department of Chemistry, Vinayaka Mission's Kirupananda Variyar Arts and Science College, Vinayaka Missions Research Foundation (Deemed to be University), Salem 636 308, Tamil Nadu, India
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21
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Starczak M, Gawronski M, Olinski R, Gackowski D. Quantification of DNA Modifications Using Two-Dimensional Ultraperformance Liquid Chromatography Tandem Mass Spectrometry (2D-UPLC-MS/MS). Methods Mol Biol 2021; 2198:91-108. [PMID: 32822025 DOI: 10.1007/978-1-0716-0876-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Our hereby presented methodology is suitable for reliable assessment of the most common DNA modifications which arise as a product of fundamental metabolic processes. 8-oxoguanine, one of the oxidatively modified DNA bases is a typical biomarker of oxidative stress. A noncanonical base, uracil, may also be present in small quantities in DNA. Ten-eleven translocation (TET) proteins are involved in oxidation of 5-methylcytosine to 5-hydroxymethylcytosine which can be further oxidized to 5-formylcytosine and 5-carboxycytosine. 5-hydroxymethyluracil may be formed in deamination reaction of 5-hydroxymethylcytosine or can also be generated by TET enzymes. All the above mentioned modifications seem to play some regulatory roles. Here, we provide a protocol for isotope-dilution automated online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS) for direct measurement of 5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, 5-carboxy-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxyuridine, 2'-deoxyuridine, and 8-oxo-2'-deoxyguanosine. We also provide optimized protocols for extraction of DNA, fully compatible with the downstream MS/MS analysis.
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Affiliation(s)
- Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Maciej Gawronski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland.
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22
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Rouquette L, Stalport F, Cottin H, Colas C, Georgelin T, Chaouche-Mechidal N, Lasne J, Mahfouf S, Raulin F, Selliez L, Szopa C, Coll P. Dimerization of Uracil in a Simulated Mars-like UV Radiation Environment. Astrobiology 2020; 20:1363-1376. [PMID: 33179968 DOI: 10.1089/ast.2019.2157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The search for organic molecules at the surface of Mars is a key objective in astrobiology, given that many organic compounds are possible biosignatures and their presence is of interest with regard to the habitability of Mars. Current environmental conditions at the martian surface are harsh and affect the stability of organic molecules. For this reason, and because current and future Mars rovers collect samples from the upper surface layer, it is important to assess the fate of organic molecules under the conditions at the martian surface. Here, we present an experimental study of the evolution of uracil when exposed to UV radiation, pressure, and temperature conditions representative of the surface of Mars. Uracil was selected because it is a nucleobase that composes RNA, and it has been detected in interplanetary bodies that could be the exogenous source of this molecule by meteoritic delivery to the surface of Mars. Our results show that the experimental quantum efficiency of photodecomposition of uracil is 0.16 ± 0.14 molecule/photon. Although these results suggest that uracil is quickly photodegraded when directly exposed to UV light on Mars, such exposure produces dimers that are more stable over time than the monomer. The identified dimers could be targets of interest for current and future Mars space missions.
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Affiliation(s)
- Laura Rouquette
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Fabien Stalport
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Hervé Cottin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Cyril Colas
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans, France
- Centre de Biophysique Moléculaire (CBM), UPR CNRS 4301, Université d'Orléans, Orléans, France
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire (CBM), UPR CNRS 4301, Université d'Orléans, Orléans, France
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Sorbonne Université, Paris, France
| | - Naïla Chaouche-Mechidal
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Jerome Lasne
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Sara Mahfouf
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - François Raulin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Laura Selliez
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR CNRS7328, Université d'Orléans, Orléans Cedex, France
- Laboratoire atmosphères, milieux, observations spatiales, Institut Pierre Simon Laplace, UMR 8190, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
| | - Cyril Szopa
- Laboratoire atmosphères, milieux, observations spatiales, Institut Pierre Simon Laplace, UMR 8190, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
- Institut Universitaire de France, Paris, France
| | - Patrice Coll
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
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Ramesh D, Vijayakumar BG, Kannan T. Therapeutic potential of uracil and its derivatives in countering pathogenic and physiological disorders. Eur J Med Chem 2020; 207:112801. [PMID: 32927231 DOI: 10.1016/j.ejmech.2020.112801] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
Uracil is one of the most notable pharmacophores in medicinal chemistry as the pyrimidine nucleobase forms an integral part of many commercial drugs. Though the name uracil is usually associated with cancer drugs, there are many uracil-based compounds which can treat different diseases when they are employed. So far, there has been no in-depth review concerning uracil drugs in the market, or in the different stages of clinical trials, including those approved or discontinued. The current work focuses on the importance of uracil and its derivatives in treating different diseases. The use of uracil compounds in treating viral infections, cancer, diabetic, thyroid and autosomal recessive disorders are discussed in the review. The mechanism of action of each uracil drug with emphasis on their structure and properties are discussed in detail. The targeted action of these drugs on sites or on the different stages of a disorder/pathogenic life cycle are also discussed. This review encompasses uracil drugs approved as well as those in development from the 1950's onwards. The utility of uracil in drug discovery and its association with a wide range of diseases is brought forth within this review to demonstrate its potential to a wider audience.
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, 605014, India
| | | | - Tharanikkarasu Kannan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, 605014, India.
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24
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Özkan E, Nemutlu E, Beksac MS, Kır S. GC-MS analysis of seven metabolites for the screening of pregnant women with Down Syndrome fetuses. J Pharm Biomed Anal 2020; 188:113427. [PMID: 32683283 DOI: 10.1016/j.jpba.2020.113427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/18/2020] [Accepted: 06/11/2020] [Indexed: 01/14/2023]
Abstract
Down Syndrome is a genetic disorder caused by the presence of all or part of a third copy of chromosome 21. Metabolomics is identification and quantification of small-molecule metabolites (molecular weight <1000 Da) in tissues, cells and physiological fluids within a certain period time. Metabolites are intermediate products of various types of biochemical reactions that participate in bonding metabolic pathways. In this study, metabolites such as 2-Hydroxybutyric acid, 3-Hydroxybutyric acid, β-Hydroxyisovaleric acid, Uracil, Glutamic acid, Maltose and Melezitose were chosen as the possible determinants/markers for the prenatal screening of Down Syndrome. Quantitative analysis of the metabolites conducted by GCMS method using 5 % phenyl / 95 % dimethylpolysiloxane (30 m ×0.25 mm, 0.25 μm film thickness) capillary column. The oven temperature was held constant at 60 °C for 1 min and ramped at 10 °C /min to 200 °C then ramped at 30 °C/min to 320 °C and hold for 6 min before cool-down, as helium mobile phase and flow rate of 2.8 mL/min and adding Myristic acid-d27 as an internal standard. Our method was validated by parameters of system suitability, stability, linearity, sensitivity, accuracy, precision, selectivity, robustness and ruggedness. The developed and validated method was applied to plasma samples taken from pregnant women with Down Syndrome (study group) and euploid fetuses (healthy group). The levels of these seven metabolites are statistically different (p < 0.05 for all) between the groups. It can be concluded that these relevant metabolites might be used for the prenatal screening of Down Syndrome.
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Affiliation(s)
- Ece Özkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhıye, Ankara, Turkey.
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhıye, Ankara, Turkey
| | - Mehmet Sinan Beksac
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Hacettepe University, 06100 Sıhhıye, Ankara, Turkey
| | - Sedef Kır
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhıye, Ankara, Turkey
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25
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Bittner AJ, Huntley RB, Mourad GS, Schultes NP. An Erwinia amylovora uracil transporter mutant retains virulence on immature apple and pear fruit. Microb Pathog 2020; 147:104363. [PMID: 32615243 DOI: 10.1016/j.micpath.2020.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. A previous study revealed that an E. amylovora uracil auxotroph was still virulent and can cause disease, suggesting that uracil can be obtained from the host environment. The E. amylovora genome contains a locus encoding for a uracil transporter belonging to the nucleobase cation symporter 2 family, displaying a high level of amino acid sequence similarity to the Escherichia coli UraA. Expression of E. amylovora UraA in nucleobase transporter-deficient E. coli strains, coupled with radiolabeled uptake studies reveal that E. amylovora UraA is a high affinity uracil transporter with a Km of 0.57 μM. Both E. coli and E. amylovora carrying extra copies of E. amylovora UraA are sensitive to growth on the toxic analog 5-fluorouracil. An E. amylovora ΔuraA::Camr mutant is still able to grow and cause disease symptoms on immature pears and apples.
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26
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Nassar IF, Farargy AFE, Abdelrazek FM, Hamza Z. Synthesis of new uracil derivatives and their sugar hydrazones with potent antimicrobial, antioxidant and anticancer activities. Nucleosides Nucleotides Nucleic Acids 2020; 39:991-1010. [PMID: 32126887 DOI: 10.1080/15257770.2020.1736300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
6-(4-Chloro-3-nitrophenyl)-4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile (4) was prepared and was reacted with ethyl chloroacetate, hydrazine hydrate, 4-chloroaniline, formaldehyde, acetic anhydride, formic acid, carbon disulfide, 4-cyanobenzaldehyde, triethyl orthoformate, D-sugars, 4-aminoacetophenone, benzoyl choride and cyclohexanone to afford a series of new uracil derivatives (5-18). Examination of some of the prepared compounds for their antimicrobial, antioxidant and anticancer activities was conducted. Among the tested samples, compound 17 was the most active substance against the gram-positive bacteria and was more potent than the reference drug Cefoperazone. Moreover, the antibacterial activity of 17 was higher against gram-negative bacteria. Compounds 6 and 13 reached a higher scavenging ability toward DPPH radicals and are better candidates for antioxidant activity. Also, compounds 6 and 13 had no significant anticancer activity toward liver cancer (Hep G2) and breast cancer (MCF-7) cell lines.
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Affiliation(s)
- Ibrahim F Nassar
- Faculty of Specific Education, Ain Shams University, Abassia, Cairo, Egypt
| | - Ahmed F El Farargy
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Fathy M Abdelrazek
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Zeinab Hamza
- Food Toxicology and Contaminants Department, National Research Centre, Dokki, Giza, Egypt
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Blechert O, Mei H, Zang X, Zheng H, Liang G, Liu W. Auxotrophic mutations of Trichophyton rubrum created by in vitro synthesized Cas9 ribonucleoprotein. BMC Biotechnol 2020; 20:6. [PMID: 31959181 PMCID: PMC6971929 DOI: 10.1186/s12896-020-0601-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Trichophyton rubrum is an obligate human parasitic fungus and responsible for approximately 80-90% of dermatomycosis in human. Molecular genetic manipulations of this pathogen are challenging and available tools and protocols are only rudimentary. We adapt molecular genetics methods of well established fungal model organism, to knock out genes in T. rubrum. For the adaptation, crucial modifications are necessary. With the implementation of in vitro synthesized Cas9-sgRNA ribonucleoprotein complex, it is possible to adapt molecular genetic methods, to knock out genes in T. rubrum. RESULTS The gene knock-out method is based on integration of a selection marker into the target site, to interrupt the gene translation. The target gene gets preassigned by the homologous sequence of the in vitro synthesized Cas9-sgRNA ribonucleoprotein complex. To develop the method, we first isolated and characterized a T. rubrum strain with a high amount of microconidia. Next, we developed a transformation protocol, whereby the Cas9-sgRNA ribonucleoprotein gets delivered into the fungal protoplast by the PEG method. We knocked out the URA3 gene and resulted, as predicted, uracil auxotrophic strains. These strains can be used for specific gene knock-outs by reintegrating the URA3 fragment and selection on uracil lacking cultivation media. Exemplary, we knocked out the TRP3 gene and got the predicted phenotype, tryptophan auxotrophic strains. The mutation had been verified by sequencing. CONCLUSIONS We developed a method, based on in vitro synthesized Cas9-sgRNA ribonucleoprotein complex, for target specific gene knock-outs in T. rubrum. We knocked out the Ura3 gene and resulted uracil auxotrophic strains. These strains were used for target specific gene knock-outs by reintegrating the Ura3 fragment into the target gene site to interrupt the gene transcription. The developed method allows to adapt sophisticate gene manipulation methods of model fungal species to non-model species.
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Affiliation(s)
- Oliver Blechert
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China
| | - Huan Mei
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China
| | - Xiaohui Zang
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China
| | - Hailin Zheng
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, Jiangsu, 210042, People's Republic of China
| | - Guanzhao Liang
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China
| | - Weida Liu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu, 210042, People's Republic of China.
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, Jiangsu, 210042, People's Republic of China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China.
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Weiser BP. Analysis of uracil DNA glycosylase (UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions. Biochim Biophys Acta Proteins Proteom 2019; 1868:140347. [PMID: 31866506 DOI: 10.1016/j.bbapap.2019.140347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
Replication Protein A (RPA) is a single-stranded DNA binding protein that interacts with DNA repair proteins including Uracil DNA Glycosylase (UNG2). Here, I report DNA binding and activity assays using purified recombinant RPA and UNG2. Using synthetic DNA substrates, RPA was found to promote UNG2's interaction with ssDNA-dsDNA junctions regardless of the DNA strand polarity surrounding the junction. RPA stimulated UNG2's removal of uracil bases paired with adenine or guanine in DNA as much as 17-fold when the uracil was positioned 21 bps from ssDNA-dsDNA junctions, and the largest degree of UNG2 stimulation occurred when RPA was in molar excess compared to DNA. I found that RPA becomes sequestered on ssDNA regions surrounding junctions which promotes its spatial targeting of UNG2 near the junction. However, when RPA concentration exceeds free ssDNA, RPA promotes UNG2's activity without spatial constraints in dsDNA regions. These effects of RPA on UNG2 were found to be mediated primarily by interactions between RPA's winged-helix domain and UNG2's N-terminal domain, but when the winged-helix domain is unavailable, a secondary interaction between UNG2's N-terminal domain and RPA can occur. This work supports a widespread role for RPA in stimulating uracil base excision repair.
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Affiliation(s)
- Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
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29
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Kaur N, Jindal G. "Switch on" fluorescent sensor for the detection of fluoride ions in solution and commercial tooth paste. Spectrochim Acta A Mol Biomol Spectrosc 2019; 223:117361. [PMID: 31306959 DOI: 10.1016/j.saa.2019.117361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
A simple and novel uracil based chemosensor (1) has been developed by one step reaction, which selectively detected F- ions via "switch on" fluorescence mode. Upon the addition of F- ion to CH3CN solution of 1, the non-fluorescent probe became highly fluorescent, showing a color change from colorless to fluorescent blue, when irradiated with 280nm light. 1H NMR studies revealed the binding sites of chemosensor 1, where C-5 hydrogen and amine hydrogens formed hydrogen bonding with F- ion. This binding mode was further confirmed using DFT calculations. Significantly, the detection limit of chemosensor 1 towards F- has been evaluated to be 47.6nM, which is lower than the maximum values of F- (1.5mg/L) ions permitted by WHO. The in-situ generated 1-F- complex has been used for secondary sensing of Ca(NO3)2, one of the component of the fertilizer. Moreover, the sensor has been successfully applied for detection of fluoride ion in commercial tooth paste.
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Affiliation(s)
- Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh 160014, India.
| | - Gitanjali Jindal
- Department of Chemistry, Panjab University, Chandigarh 160014, India.
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Pei L, Li DZ, Zhang LJ. Theoretical insights into the hydrogen bonding interaction in the complexation of epinephrine with uracil. J Mol Model 2019; 25:252. [PMID: 31353431 DOI: 10.1007/s00894-019-4123-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 11/28/2022]
Abstract
The present study is aimed at probing the hydrogen bonding interaction between epinephrine and uracil by means of density functional theory calculations concerning their complexation's geometries, interaction energies, and vibrational frequencies. Geometry optimization was carried out giving 19 stable geometries of epinephrine-uracil complex with interaction energies in a range of - 21.51 to - 62.37 kJ mol-1 using the basis set superposition error (BSSE) correction. The analysis of structure and vibration shows that the hydrogen bonding elongates the length of corresponding bond O(N)-H and decreases the symmetric stretching vibrational frequency, which indicates red-shifted H-bonding interactions in all the geometries. Additionally, the analysis with theories of natural bond orbital (NBO), atoms in molecules (AIM), and the reduced density gradient (RDG) of hydrogen bonding properties and characteristics of the 19 geometries suggests that the hydrogen bonding in all the optimized structures of epinephrine-uracil complex is kind of a closed-shell interaction and mainly electrostatic dominant.
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Affiliation(s)
- Ling Pei
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China.
| | - Da-Zhi Li
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
| | - Li-Juan Zhang
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
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Bua S, Osman SM, AlOthman Z, Supuran CT, Nocentini A. Benzenesulfonamides incorporating nitrogenous bases show effective inhibition of β-carbonic anhydrases from the pathogenic fungi Cryptococcus neoformans, Candida glabrata and Malassezia globosa. Bioorg Chem 2019; 86:39-43. [PMID: 30684862 DOI: 10.1016/j.bioorg.2019.01.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 01/17/2019] [Indexed: 12/12/2022]
Abstract
There is an urgent need for new chemotherapic agents to treat human fungal infections due to emerging and spreading globally resistance mechanisms. Among the new targets that have been recently investigated for the development of antifungal drugs there are the metallo-enzymes Carbonic Anhydrases (CAs, EC 4.2.1.1). The inhibition of the β-CAs identified in many pathogenic fungi leads to an impairment of parasite growth and virulence, which in turn leads to a significant anti-infective effect. Based on antifungal nucleoside antibiotics, the inhibition of the β-CAs from the resistance-showing fungi Candida glabrata (CgNce103), Cryptococcus neoformans (Can2) and Malasszia globosa (MgCA) with a series of benzenesulfonamides bearing nitrogenous bases, such as uracil and adenine, is here reported. Many such compounds display low nanomolar (<100 nM) inhibitory potency against Can2 and CgNce103, whereas the activity of MgCA is considerably less affected (inhibition constants in the range 138.8-5601.5 nM). The β-CAs inhibitory data were compared with those against α-class human ubiquitous isoforms. Interesting selective inhibitory activities for the target fungal CAs over hCA I and II were reported, which make nitrogenous base benzenesulfonamides interesting tools and leads for further investigations in search of new antifungal with innovative mechanisms of action.
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Affiliation(s)
- Silvia Bua
- University of Florence, NEUROFARBA Department, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Sameh M Osman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Department, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
| | - Alessio Nocentini
- University of Florence, NEUROFARBA Department, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy.
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Yang Y, Park SH, Alford-Zappala M, Lee HW, Li J, Cunningham RP, Cao W. Role of endonuclease III enzymes in uracil repair. Mutat Res 2019; 813:20-30. [PMID: 30590231 PMCID: PMC6378108 DOI: 10.1016/j.mrfmmm.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Endonuclease III is a DNA glycosylase previously known for its repair activity on oxidative pyrimidine damage. Uracil is a deamination product derived from cytosine. Uracil DNA N-glycosylase (UNG) and mismatch-specific uracil DNA glycosylase (MUG) are two known repair enzymes with enzymatic activity on uracil in E. coli. Here we report a G/U specific uracil DNA glycosylase activity in E. coli endonuclease III (endo III, Nth), which is comparable to MUG but significantly lower than its thymine glycol DNA glycosylase activity. The possibility that the novel activity is due to contamination is ruled out by expressing the wild type nth gene and an active site mutant in a uracil-repair-deficient genetic background. Consistent with the biochemical analysis, analyses of lac+ reversion and mutation frequencies in the presence of human AID induced cytosine deamination indicate the endo III can play a role in repair of cytosine deamination. In addition to E. coli, UDG activity is found in endo III homologs from other organisms. E. coli nucleoside diphosphate kinase (Ndk) was also tested for UDG activity because it was previously reported as an uracil repair enzyme. Under the assay conditions, very limited UDG activity was detected in single-stranded uracil-containing DNA from E. coli Ndk and no UDG activity was detected in human Ndk homologs. This study provides definitive clarification on uracil repair by endo III and reveals that endonuclease III is a G/U-specific UDG that can be viewed as a prototype for the human MBD4 uracil DNA glycosylase.
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Affiliation(s)
- Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Sung-Hyun Park
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Maria Alford-Zappala
- Department of Biological Sciences, The University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Hyun-Wook Lee
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Jing Li
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
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Silva R, Aguiar TQ, Oliveira C, Domingues L. Physiological characterization of a pyrimidine auxotroph exposes link between uracil phosphoribosyltransferase regulation and riboflavin production in Ashbya gossypii. N Biotechnol 2018; 50:1-8. [PMID: 30590201 DOI: 10.1016/j.nbt.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 01/13/2023]
Abstract
The blockage of the de novo pyrimidine biosynthetic pathway at the orotidine-5'-phosphate decarboxylase level was previously demonstrated to affect riboflavin production in the industrial producer fungus Ashbya gossypii. However, the molecular basis for the unusual sensitivity to uracil displayed by the pyrimidine auxotroph A. gossypii Agura3 was unknown. Here, uridine was shown to be the only intermediate of the pyrimidine salvage pathway able to fully restore this mutant's growth. Conversely, uracil, which is routinely used to rescue pyrimidine auxotrophs, had a dose-dependent growth-inhibitory effect. Uracil phosphoribosyltransferase (UPRT) is the pyrimidine salvage pathway enzyme responsible for converting uracil to uridine monophosphate in the presence of phosphoribosyl pyrophosphate (PRPP). Characterization of the A. gossypii UPRT, as produced and purified from Escherichia coli, revealed that uracil concentrations above 1 mM negatively affected its activity, thus explaining the hypersensitivity of the Agura3 mutant to uracil. Accordingly, overexpression of the AgUPRT encoding-gene in A. gossypii Agura3 led to similar growth on rich medium containing 5 mM uracil or uridine. Decreased UPRT activity ultimately favors the preservation of PRPP, which otherwise may be directed to other pathways. In A. gossypii, increased PRPP availability promotes overproduction of riboflavin. Thus, this UPRT modulation mechanism reveals a putative means of saving precursors essential for riboflavin overproduction by this fungus. A similar uracil-mediated regulation mechanism of the UPRT activity is reported only in two protozoan parasites, whose survival depends on the availability of PRPP. Physiological evidence here discussed indicate that it may be extended to other distantly related flavinogenic fungi.
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Affiliation(s)
- Rui Silva
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Carla Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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DuVal MG, Hinge VK, Snyder N, Kanyo R, Bratvold J, Pokrishevsky E, Cashman NR, Blinov N, Kovalenko A, Allison WT. Tryptophan 32 mediates SOD1 toxicity in a in vivo motor neuron model of ALS and is a promising target for small molecule therapeutics. Neurobiol Dis 2019; 124:297-310. [PMID: 30528257 DOI: 10.1016/j.nbd.2018.11.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 11/11/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
SOD1 misfolding, toxic gain of function, and spread are proposed as a pathological basis of amyotrophic lateral sclerosis (ALS), but the nature of SOD1 toxicity has been difficult to elucidate. Uniquely in SOD1 proteins from humans and other primates, and rarely in other species, a tryptophan residue at position 32 (W32) is predicted to be solvent exposed and to participate in SOD1 misfolding. We hypothesized that W32 is influential in SOD1 acquiring toxicity, as it is known to be important in template-directed misfolding. We tested if W32 contributes to SOD1 cytotoxicity and if it is an appropriate drug target to ameliorate ALS-like neuromuscular deficits in a zebrafish model of motor neuron axon morphology and function (swimming). Embryos injected with human SOD1 variant with W32 substituted for a serine (SOD1W32S) had reduced motor neuron axonopathy and motor deficits compared to those injected with wildtype or disease-associated SOD1. A library of FDA-approved small molecules was ranked with virtual screening based on predicted binding to W32, and subsequently filtered for analogues using a pharmacophore model based on molecular features of the uracil moiety of a small molecule previously predicted to interact with W32 (5'-fluorouridine or 5'-FUrd). Along with testing 5'-FUrd and uridine, a lead candidate from this list was selected based on its lower toxicity and improved blood brain barrier penetrance; telbivudine significantly rescued SOD1 toxicity in a dose-dependent manner. The mechanisms whereby the small molecules ameliorated motor neuron phenotypes were specifically mediated through human SOD1 and its residue W32, because these therapeutics had no measurable impact on the effects of UBQLN4D90A, EtOH, or tryptophan-deficient human SOD1W32S. By substituting W32 for a more evolutionarily conserved residue (serine), we confirmed the significant influence of W32 on human SOD1 toxicity to motor neuron morphology and function; further, we performed pharmaceutical targeting of the W32 residue for rescuing SOD1 toxicity. This unique residue offers future novel insights into SOD1 stability and toxic gain of function, and therefore poses an potential target for drug therapy.
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Owiti N, Stokdyk K, Kim N. The etiology of uracil residues in the Saccharomyces cerevisiae genomic DNA. Curr Genet 2019; 65:393-9. [PMID: 30328489 DOI: 10.1007/s00294-018-0895-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/11/2018] [Accepted: 10/13/2018] [Indexed: 11/29/2022]
Abstract
Non-canonical residue in DNA is a major and conserved source of genome instability. The appearance of uracil residues in DNA accompanies a significant mutagenic consequence and is regulated at multiple levels, from the concentration of available dUTP in the nucleotide pool to the excision repair for removal from DNA. Recently, an interesting phenomenon of transcription-associated elevation in uracil-derived mutations was described in Saccharomyces cerevisiae genome. While trying to understand the variability in mutagenesis, we uncovered that the frequency of uracil incorporation into DNA can vary depending on the transcription rate and that the non-replicative, repair-associated DNA synthesis underlies the higher uracil density of the actively transcribed genomic loci. This novel mechanism brings together the chemical vulnerability of DNA under transcription and the uracil-associated mutagenesis, and has the potential to apply to other non-canonical residues of mutagenic importance.
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Catala GN, Bestwick CS, Russell WR, Tortora K, Giovannelli L, Moyer MP, Lendoiro E, Duthie SJ. Folate, genomic stability and colon cancer: The use of single cell gel electrophoresis in assessing the impact of folate in vitro, in vivo and in human biomonitoring. Mutat Res 2018; 843:73-80. [PMID: 31421742 DOI: 10.1016/j.mrgentox.2018.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/29/2018] [Accepted: 08/29/2018] [Indexed: 01/10/2023]
Abstract
Intake of folate (vitamin B9) is strongly inversely linked with human cancer risk, particularly colon cancer. In general, people with the highest dietary intake of folate or with high blood folate levels are at a reduced risk (approx. 25%) of developing colon cancer. Folate acts in normal cellular metabolism to maintain genomic stability through the provision of nucleotides for DNA replication and DNA repair and by regulating DNA methylation and gene expression. Folate deficiency can accelerate carcinogenesis by inducing misincorporation of uracil into DNA, by increasing DNA strand breakage, by inhibiting DNA base excision repair capacity and by inducing DNA hypomethylation and consequently aberrant gene and protein expression. Conversely, increasing folate intake may improve genomic stability. This review describes key applications of single cell gel electrophoresis (the comet assay) in assessing genomic instability (misincorporated uracil, DNA single strand breakage and DNA repair capacity) in response to folate status (deficient or supplemented) in human cells in vitro, in rodent models and in human case-control and intervention studies. It highlights an adaptation of the SCGE comet assay for measuring genome-wide and gene-specific DNA methylation in human cells and colon tissue.
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Affiliation(s)
- Gema Nadal Catala
- Natural Products Group, Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Charles S Bestwick
- Natural Products Group, Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Wendy R Russell
- Natural Products Group, Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Katia Tortora
- Department NEUROFARBA, Section of Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Lisa Giovannelli
- Department NEUROFARBA, Section of Pharmacology and Toxicology, University of Florence, Florence, Italy
| | | | - Elena Lendoiro
- Department of Toxicology, Institute of Forensic Sciences, University of Santiago of Compostela, Santiago de Compostela, Spain; School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Susan J Duthie
- Natural Products Group, Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK; School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK.
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Kawai K, Sunami E, Hata K, Tanaka T, Nishikawa T, Otani K, Sasaki K, Nozawa H. Phase I/II Study of Preoperative Chemoradiotherapy With TEGAFIRI for Locally Advanced Rectal Cancer. Clin Colorectal Cancer 2018; 17:240-246. [PMID: 29934092 DOI: 10.1016/j.clcc.2018.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Chemoradiotherapy (CRT) is the standard treatment for locally advanced rectal cancer; however, the optimal chemotherapy sequence to administer simultaneously with radiotherapy remains unclear. We conducted a phase I/II study to test a new regimen, TEGAFIRI (combination tegafur, uracil [UFT], leucovorin [LV], irinotecan), for patients with locally advanced rectal cancer. PATIENTS AND METHODS A total of 22 patients with locally advanced lower rectal adenocarcinoma were enrolled in the present study. The radiation dose was 50.4 Gy in 28 fractions. UFT (300 mg/m2/d) and LV (75 mg/body weight/d) were administered orally 3 times daily. Irinotecan was administered as an intravenous infusion at 3 escalating dose levels. The initial dose was 50 mg/m2 (level 1; n = 7), the intermediate was 70 mg/m2 (level 2; n = 8), and the maximum was 80 mg/m2 (level 3; n = 7). The drug was administered on days 1, 15, 29, and 43. RESULTS Dose-limiting toxicity was not observed at any dosing level. The most frequent adverse event was leukopenia (50%), followed by diarrhea (45.5%), anal pain (31.8%), and neutropenia (27.3%). All were well-managed with the appropriate drugs. The total pathologic complete response rate was 22.7%, and the proportion of good responders was 28.6%, 50%, and 71.4% at levels 1, 2, and 3, respectively. None of the patients experienced local recurrence. The 5-year relapse-free and overall survival rates were 80.4% and 80.8%, respectively. CONCLUSION TEGAFIRI is a promising CRT regimen that results in marked tumor regression and good local control. Moreover, its adverse events are well-tolerated.
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Affiliation(s)
- Kazushige Kawai
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan.
| | - Eiji Sunami
- Department of Coloproctological Surgery, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Keisuke Hata
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan
| | - Toshiaki Tanaka
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan
| | | | - Kensuke Otani
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan
| | - Kazuhito Sasaki
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan
| | - Hiroaki Nozawa
- Department of Surgical Oncology, University of Tokyo, Tokyo, Japan
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Brela MZ, Boczar M, Malec LM, Wójcik MJ, Nakajima T. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics. Spectrochim Acta A Mol Biomol Spectrosc 2018; 197:194-201. [PMID: 29395929 DOI: 10.1016/j.saa.2018.01.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Colasurdo DD, Pila MN, Iglesias DA, Laurella SL, Ruiz DL. Tautomerism of uracil and related compounds: A mass spectrometry study. Eur J Mass Spectrom (Chichester) 2018; 24:214-224. [PMID: 29232994 DOI: 10.1177/1469066717712461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
It has been demonstrated that uracil has a preponderant tautomeric form, but it is also known that different tautomers co-exist in this equilibrium. In this work, mass spectrometry is used as a helpful tool to analyse the equilibria, using derivative compounds to forbid the presence of some tautomers and ion trap mass spectrometry to follow relevant fragmentation pathways. Theoretical calculations were performed to confirm tautomers abundance by energy minimization in gas phase. Analysis of mass spectra of uracil, three methyl-substituted uracils, 2-thiouracil and three benzouracils suggest that uracil exists mainly as three tautomers in gas phase: one major structure that corresponds to the classical structure of uracil (pyrimidine-2,4(1H,3H)-dione) bearing two carbonyls and two NH moieties, and two minor enolic forms (4-hydroxypyrimidin-2(1H)-one and 2-hydroxypyrimidin-4(1H)-one). Such tautomeric distribution is supported by theoretical calculations, which show that they are the three most stable tautomers.
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Affiliation(s)
- Diego D Colasurdo
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Matías N Pila
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Dacio A Iglesias
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sergio L Laurella
- 2 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CIC, Universidad Nacional de La Plata, La Plata, Argentina
| | - Danila L Ruiz
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
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Saragani Y, Hizi A, Rahav G, Zaouch S, Bakhanashvili M. Cytoplasmic p53 contributes to the removal of uracils misincorporated by HIV-1 reverse transcriptase. Biochem Biophys Res Commun 2018; 497:804-810. [PMID: 29470985 DOI: 10.1016/j.bbrc.2018.02.159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/18/2018] [Indexed: 01/15/2023]
Abstract
HIV-1 reverse transcriptase (RT) in the cytoplasm of HIV-infected cells efficiently inserts the non-canonical dUTP into the proviral DNA, and extends the dU-terminated DNA. The misincorporation of dUTP leads to mutagenesis, and uracils can down-regulate viral gene expression. However, uracilation might also protect HIV DNA from auto-integration in the cytoplasm. Tumor suppressor p53 protein, exhibiting inherent 3'→5' exonuclease activity, provides a potential host-derived repair mechanism during HIV reverse transcription for the misincorporation of various wrong nucleotides, leading to both base-base mismatches and incorporated non-canonical ribonucleotides. Since the presence of proofreading activity is essential for DNA synthesis accuracy, we elucidated the potential involvement of cytoplasmic p53 in the U-editing activities during insertion of dUTP into DNA by recombinant HIV-1 RT (using isogenic p53-proficient and -deficient HCT116 cells). The biochemical data show that p53 in cytoplasm can participate through the intermolecular pathway in a dU-damage-associated repair mechanism by its ability to remove preformed 3'-terminal dUs, thus preventing further extension of 3' dU-terminated primer during DNA synthesis by HIV-1 RT. The specific depletion of p53 from cytoplasmic lysates of repair-proficient p53-harboring cells reduced this negative effect. Accordingly, the increased abundance of p53 in nutlin-treated cells correlates with enhanced error-correction functions, namely, removal of incorporated uracil. The data substantiate the significance of p53 as a potential proofreader for removal of non-canonical dUTP from HIV DNA, thus preventing the consequences of dUTP misincorporation in cell-type specific infectivity of HIV.
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Affiliation(s)
- Yossi Saragani
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Amnon Hizi
- Dep. Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Sara Zaouch
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Mary Bakhanashvili
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel.
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Jacobs BAW, Snoeren N, Samim M, Rosing H, de Vries N, Deenen MJ, Beijnen JH, Schellens JHM, Koopman M, van Hillegersberg R. The impact of liver resection on the dihydro uracil:uracil plasma ratio in patients with colorectal liver metastases. Eur J Clin Pharmacol 2018; 74:737-44. [PMID: 29430582 DOI: 10.1007/s00228-018-2426-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/01/2018] [Indexed: 12/30/2022]
Abstract
PURPOSE The dihydrouracil (DHU):uracil (U) plasma ratio is a promising marker for identification of dihydropyrimidine dehydrogenase (DPD)-deficient patients. The objective of this study was to determine the effect of liver resection on the DHU:U plasma ratio in patients with colorectal liver metastases (CRLM). METHODS An observational study was performed in which DHU:U plasma ratios in patients with CRLM were analyzed prior to and 1 day after liver resection. In addition, the DHU:U plasma ratio was quantified in six additional patients 4-8 weeks after liver resection to explore long-term effects on the DHU:U plasma ratio. Quantification of U and DHU plasma levels was performed using a validated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) assay. RESULTS The median (range) DHU:U plasma ratio in 15 patients prior to liver resection was 10.7 (2.6-14.4) and was significantly reduced to 5.5 (< quantification limit (LLOQ-10.5) 1 day after resection (p = 0.0026). This reduction was caused by a decrease in DHU plasma levels from 112.0 (79.8-153) ng/mL to 41.2 (< LLOQ-160) ng/mL 1 day after resection (p = 0.0004). Recovery of the DHU:U plasma ratio occurred 4-8 weeks after liver resection, which was shown by a median (range) DHU:U plasma ratio in six patients of 9.1 (6.9-14.5). CONCLUSION Liver resection leads to very low DHU:U plasma ratios 1 day after liver resection, which is possibly caused by a reduction in DPD activity. Quantification of the DHU:U plasma ratios directly after liver resection could lead to false-positive identification of DPD deficiency and is therefore not advised.
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Lee W, Kim S, Song I, Kwon Y, Park S, Oh BK, Oh HB, Lee J. Microbial production of uracil by an isolated Methylobacterium sp. WJ4 using methanol. Enzyme Microb Technol 2018; 111:63-66. [PMID: 29421038 DOI: 10.1016/j.enzmictec.2017.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/27/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
In this study, we report the production of uracil from methanol by an isolated methylotrophic bacterium, Methylobacterium sp. WJ4. The use of methanol as alternative carbon feedstock is attractive option in biotechnology. As a feedstock of biotechnological processes, methanol has distinct advantages over methane. This is not only due to physical and chemical considerations, but also to the properties of the pertinent organisms. Besides, with a wide array of biological activities and synthetic accessibility, uracil is considered as privileged structures in drug discovery. Uracil analogues have been applied to treatments of patients with cancer or viral infections. In this respect, it is meaningful to produce uracil using methanol. The effect of process parameters and methanol concentration for uracil production were investigated and optimized. Uracil production was remarkably increased to 5.76mgg cell dry weight-1 in optimized condition. The results were significant for further understanding of methylotrophic bacteria on uracil production.
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Affiliation(s)
- Wangjun Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Sangwoo Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Insu Song
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Yuhyun Kwon
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Soohyun Park
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Byung-Keun Oh
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea.
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Ilyina MG, Khamitov EM, Mustafin AG, Khursan SL. Controlled stabilization of anionic forms of the uracil derivatives: A DFT study. J Mol Graph Model 2017; 79:65-71. [PMID: 29145035 DOI: 10.1016/j.jmgm.2017.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 11/29/2022]
Abstract
Relative stabilities of the N1/N3/О5/О6 anions of 42 substituted uracils in gas phase and aqueous solutions have been theoretically studied using approximation IEFPCM (SMD) - TPSS/aug-cc-pVTZ. The specific solvation of uracil and its anions has been simulated with the first hydrate shell made up with 5 water molecules. The nonspecific solvation has been accounted in terms of the SMD model. We have found a series of relative stability under conditions of both specific and nonspecific hydration. The series is ranked according to the increase of the relative stability of the N3 anion. In gas phase, the N1 anion is significantly more stable than its N3 counterpart: the ΔGgas values vary in the range from 19.54 (5OH6СН3U) to 83.14 (5NO26NH2U) kJ/mol that is caused by a more effective delocalization of the excess charge through the uracil framework in the N1 anion. The hydration pronouncedly diminishes ΔG to the range from -0.02 (5OH6СН3U) to 38.16 (5Br6NO2U) kJ/mol due to the fact that the polar solvent is prone to stabilize more polar anionic states of uracils. Therefore, less polar uracil anions are more stable. We have defined the main factor influencing the N1/N3/О5/О6 distribution of anions, viz. the presence of the substituents in 5 and 6 positions of the pyrimidine ring. Herewith, the most favorable mechanism of the influence of 5-substituents has been previously defined as resonant whereas, as we found in this work, the inductive mechanism is more pronounced in the case of 6-substituents.
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Affiliation(s)
- Margarita G Ilyina
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Institute of Petroleum Refining and Petrochemistry, Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, 12 Initsiativnaya Str., Ufa 450065, Republic of Bashkortostan, Russia.
| | - Edward M Khamitov
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia; Institute of Petroleum Refining and Petrochemistry, Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, 12 Initsiativnaya Str., Ufa 450065, Republic of Bashkortostan, Russia
| | - Akhat G Mustafin
- Bashkir State University, Department of Chemistry, Chair of Physical Chemistry and Chemical Ecology, 32 Zaki Validi Str., Ufa 450074, Russia; Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia
| | - S L Khursan
- Ufa Institute of Chemistry, Russian Academy of Sciences, Laboratory of Chemical Physics, 69 Prospekt Oktyabrya, Ufa 450054, Russia
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Akinyemi TE, Wu RR, Nei YW, Cunningham NA, Roy HA, Steill JD, Berden G, Oomens J, Rodgers MT. Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu] + and [Ura+Ag]<sup/>. J Am Soc Mass Spectrom 2017; 28:2438-2453. [PMID: 28895083 DOI: 10.1007/s13361-017-1771-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/22/2017] [Accepted: 07/22/2017] [Indexed: 05/17/2023]
Abstract
The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]+ and [Ura+Ag]+, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]+ and [Ura+Ag]+ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]+ and [Ura+Ag]+. B3LYP suggests that Cu+ exhibits a slight preference for O4 binding, whereas Ag+ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu+ and Ag+ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]+ than [Ura+Cu]+. The dissociation behavior and relative stabilities of the [Ura+M]+ complexes, M+ = Cu+, Ag+, H+, and Na+) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu+ and Ag+ are compared with previous and present results for those of H+ and Na+. Graphical Abstract ᅟ.
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Affiliation(s)
- T E Akinyemi
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - R R Wu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - J D Steill
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Facility, Radboud University Nijmegen, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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Li J, Yang Y, Guevara J, Wang L, Cao W. Identification of a prototypical single-stranded uracil DNA glycosylase from Listeria innocua. DNA Repair (Amst) 2017; 57:107-115. [PMID: 28719838 PMCID: PMC5568478 DOI: 10.1016/j.dnarep.2017.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/23/2022]
Abstract
A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase. The UDG activity on DNA bubble structures provides clue to its physiological significance in vivo. Mutagenesis and molecular modeling analyses reveal that Lin SMUG1-like glycosylase has similar functional motifs with SMUG1 enzymes; however, it contains a distinct catalytic doublet S67-S68 in motif 1 that is not found in any families in the UDG superfamily. Experimental investigation shows that the S67M-S68N double mutant is catalytically more active than either S67M or S68N single mutant. Coupled with mutual information analysis, the results indicate a high degree of correlation in the evolution of SMUG1-like enzymes. This study underscores the functional and catalytic diversity in the evolution of enzymes in UDG superfamily.
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Affiliation(s)
- Jing Li
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Jose Guevara
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 060 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
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Wenderoth M, Pinecker C, Voß B, Fischer R. Establishment of CRISPR/Cas9 in Alternaria alternata. Fungal Genet Biol 2017; 101:55-60. [PMID: 28286319 DOI: 10.1016/j.fgb.2017.03.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 10/20/2022]
Abstract
The filamentous fungus Alternaria alternata is a potent producer of many secondary metabolites, some of which like alternariol or alternariol-methyl ether are toxic and/or cancerogenic. Many Alternaria species do not only cause post-harvest losses of food and feed, but are aggressive plant pathogens. Despite the great economic importance and the large number of research groups working with the fungus, the molecular toolbox is rather underdeveloped. Gene deletions often result in heterokaryotic strains and therefore, gene-function analyses are rather tedious. In addition, A. alternata lacks a sexual cycle and classical genetic approaches cannot be combined with molecular biological methods. Here, we show that CRISPR/Cas9 can be efficiently used for gene inactivation. Two genes of the melanin biosynthesis pathway, pksA and brm2, were chosen as targets. Several white mutants were obtained after several rounds of strain purification through protoplast regeneration or spore inoculation. Mutation of the genes was due to deletions from 1bp to 1.5kbp. The CRISPR/Cas9 system was also used to inactivate the orotidine-5-phosphate decarboxylase gene pyrG to create a uracil-auxotrophic strain. The strain was counter-selected with fluor-orotic acid and could be re-transformed with pyrG from Aspergillus fumigatus and pyr-4 from Neurospora crassa. In order to test the functioning of GFP, the fluorescent protein was fused to a nuclear localization signal derived from the StuA transcription factor of Aspergillus nidulans. After transformation bright nuclei were visible.
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Affiliation(s)
- Maximilian Wenderoth
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany
| | - Christoph Pinecker
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany
| | - Benjamin Voß
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany. http://www.iab.kit.de
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Abstract
Intestinal dual oxidase (DUOX) activation is the first line of host defense against enteric infection in Drosophila. DUOX enzymatic activity is mainly controlled by phospholipase C-β (PLCβ)-dependent calcium mobilization, whereas DUOX gene expression is mainly controlled by the MEKK1-p38 mitogen-activated protein kinase pathway. Furthermore, bacterial-derived uracil molecules act as ligands for DUOX activation. However, our current understanding of uracil-induced signal transduction pathways remain incomplete. We have recently found that uracil stimulates Hedgehog signaling, which in turn upregulates cadherin99C (Cad99C) expression in enterocytes. Cad99C molecules, along with PLCβ and protein kinase C, induce the formation of signaling endosomes that facilitate intracellular calcium mobilization for DUOX activity. These observations illustrate the complexity of signaling cascades in uracil-induced signaling pathways. Here, we further demonstrated the role of lipid raft formation and calmodulin-dependent protein kinase-II on endosome formation and calcium mobilization, respectively. Moreover, we will provide a brief discussion on two different models for uracil recognition and uracil-induced DUOX activation in Drosophila enterocytes.
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Affiliation(s)
- Kyung-Ah Lee
- a School of Biological Science, Seoul National University and National Creative Research Initiative Center for Hologenomics, Seoul National University , Seoul , South Korea.,b Institute of Molecular Biology and Genetics, Seoul National University , Seoul , South Korea
| | - Boram Kim
- a School of Biological Science, Seoul National University and National Creative Research Initiative Center for Hologenomics, Seoul National University , Seoul , South Korea
| | - Hyejin You
- a School of Biological Science, Seoul National University and National Creative Research Initiative Center for Hologenomics, Seoul National University , Seoul , South Korea
| | - Won-Jae Lee
- a School of Biological Science, Seoul National University and National Creative Research Initiative Center for Hologenomics, Seoul National University , Seoul , South Korea.,b Institute of Molecular Biology and Genetics, Seoul National University , Seoul , South Korea
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Mo WB, Su CH, Huang JY, Liu J, Chen ZF, Cheng KG. Synthesis of acyl oleanolic acid- uracil conjugates and their anti-tumor activity. Chem Cent J 2016; 10:69. [PMID: 27928425 PMCID: PMC5117584 DOI: 10.1186/s13065-016-0217-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 11/10/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Oleanolic acid, which can be isolated from many foods and medicinal plants, has been reported to possess diverse biological activities. It has been found that the acylation of the hydroxyl groups of the A-ring in the triterpene skeleton of oleanolic acid could be favorable for biological activities. The pyrimidinyl group has been constructed in many new compounds in various anti-tumor studies. RESULTS Five acyl oleanolic acid-uracil conjugates were synthesized. Most of the IC50 values of these conjugates were lower than 10.0 μM, and some of them were even under 0.1 μM. Cytotoxicity selectivity detection revealed that conjugate 4c exhibited low cytotoxicity towards the normal human liver cell line HL-7702. Further studies revealed that 4c clearly possessed apoptosis inducing effects, could arrest the Hep-G2 cell line in the G1 phase, induce late-stage apoptosis, and activate effector caspase-3/9 to trigger apoptosis. CONCLUSIONS Conjugates of five different acyl OA derivatives with uracil were synthesized and identified as possessing high selectivity toward tumor cell lines. These conjugates could induce apoptosis in Hep-G2 cells by triggering caspase-3/9 activity.Graphical abstractFive acyl oleanolic aicd-uracil conjugates were synthesized. These conjugates exhibited selective cytotoxicity toward tumor cells achieved via inducing apoptosis by activation of caspase-3/9.
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Affiliation(s)
- Wei-Bin Mo
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004 People's Republic of China ; Biochemistry and Pharmacology of Sport School, Guangxi Normal University, Guilin, 541004 People's Republic of China
| | - Chun-Hua Su
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004 People's Republic of China ; School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, 541004 People's Republic of China
| | - Jia-Yan Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004 People's Republic of China ; School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, 541004 People's Republic of China
| | - Jun Liu
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing, 210009 People's Republic of China
| | - Zhen-Feng Chen
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004 People's Republic of China ; School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, 541004 People's Republic of China
| | - Ke-Guang Cheng
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004 People's Republic of China ; School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, 541004 People's Republic of China
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Galarza AFA, Linden R, Antunes MV, Hahn RZ, Raymundo S, da Silva ACC, Staggemeier R, Spilki FR, Schwartsmann G. Endogenous plasma and salivary uracil to dihydrouracil ratios and DPYD genotyping as predictors of severe fluoropyrimidine toxicity in patients with gastrointestinal malignancies. Clin Biochem 2016; 49:1221-1226. [PMID: 27399164 DOI: 10.1016/j.clinbiochem.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/20/2016] [Accepted: 07/06/2016] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to evaluate the use of plasma and saliva uracil (U) to dihydrouracil (UH2) metabolic ratio and DPYD genotyping, as a means to identify patients with dihydropyrimidine dehydrogenase (DPD) deficiency and fluoropyrimidine toxicity. METHODS Paired plasma and saliva samples were obtained from 60 patients with gastrointestinal cancer, before fluoropyrimidine treatment. U and UH2 concentrations were measured by LC-MS/MS. DPYD was genotyped for alleles *7, *2A, *13 and Y186C. Data on toxicity included grade 1 to 4 neutropenia, mucositis, diarrhea, nausea/vomiting and cutaneous rash. RESULTS 35% of the patients had severe toxicity. There was no variant allele carrier for DPYD. The [UH2]/[U] metabolic ratios were 0.09-26.73 in plasma and 0.08-24.0 in saliva, with higher correlation with toxicity grade in saliva compared to plasma (rs=-0.515 vs rs=-0.282). Median metabolic ratios were lower in patients with severe toxicity as compared to those with absence of toxicity (0.59 vs 2.83 saliva; 1.62 vs 6.75 plasma, P<0.01). A cut-off of 1.16 for salivary ratio was set (AUC 0.842), with 86% sensitivity and 77% specificity for the identification of patients with severe toxicity. Similarly, a plasma cut-off of 4.0 (AUC 0.746), revealed a 71% sensitivity and 76% specificity. CONCLUSIONS DPYD genotyping for alleles 7, *2A, *13 and Y186C was not helpful in the identification of patients with severe DPD deficiency in this series of patients. The [UH2]/[U] metabolic ratios, however, proved to be a promising functional test to identify the majority of cases of severe DPD activity, with saliva performing better than plasma.
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Affiliation(s)
- Andrés Fernando Andrade Galarza
- Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Serviço de Oncologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Rafael Linden
- Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | - Roberta Zilles Hahn
- Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Suziane Raymundo
- Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | - Rodrigo Staggemeier
- Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | - Gilberto Schwartsmann
- Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Serviço de Oncologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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Khalili G. A new synthesis of S-aryl uracils from aryl thiols and 6-amino uracils in the presence of NCS. Mol Divers 2016; 20:963-968. [PMID: 27379848 DOI: 10.1007/s11030-016-9685-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/19/2016] [Indexed: 11/28/2022]
Abstract
Sulfenylchloride intermediates generated from the reaction of aryl thiols with N-chlorosuccinimide were trapped by 6-amino uracil derivatives to yield 6-amino-5-(arylthio)-pyrimidine-2,4(1H,3H)-dione compounds at room temperature.
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Affiliation(s)
- Gholamhossein Khalili
- Chemistry Department, Islamic Azad University, Bushehr Branch, PO Box 7519619555, Bushehr, Iran.
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