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Roston D, Islam Z, Kohen A. Kinetic isotope effects as a probe of hydrogen transfers to and from common enzymatic cofactors. Arch Biochem Biophys 2014; 544:96-104. [PMID: 24161942 PMCID: PMC3946509 DOI: 10.1016/j.abb.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Enzymes use a number of common cofactors as sources of hydrogen to drive biological processes, but the physics of the hydrogen transfers to and from these cofactors is not fully understood. Researchers study the mechanistically important contributions from quantum tunneling and enzyme dynamics and connect those processes to the catalytic power of enzymes that use these cofactors. Here we describe some progress that has been made in studying these reactions, particularly through the use of kinetic isotope effects (KIEs). We first discuss the general theoretical framework necessary to interpret experimental KIEs, and then describe practical uses for KIEs in the context of two case studies. The first example is alcohol dehydrogenase, which uses a nicotinamide cofactor to catalyze a hydride transfer, and the second example is thymidylate synthase, which uses a folate cofactor to catalyze both a hydride and a proton transfer.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Zahidul Islam
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA.
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Lee HS, Chen M, Kim JH, Kim WH, Ahn S, Maeng K, Allegra CJ, Kaye FJ, Hochwald SN, Zajac-Kaye M. Analysis of 320 gastroenteropancreatic neuroendocrine tumors identifies TS expression as independent biomarker for survival. Int J Cancer 2014; 135:128-37. [PMID: 24347111 DOI: 10.1002/ijc.28675] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/05/2013] [Indexed: 11/06/2022]
Abstract
Thymidylate synthase (TS), a critical enzyme for DNA synthesis and repair, is both a potential tumor prognostic biomarker as well as a tumorigenic oncogene in animal models. We have now studied the clinical implications of TS expression in gastroenteropancreatic (GEP) neuroendocrine tumors (NETs) and compared these results to other cell cycle biomarker genes. Protein tissue arrays were used to study TS, Ki-67, Rb, pRb, E2F1, p18, p21, p27 and menin expression in 320 human GEP-NETs samples. Immunohistochemical expression was correlated with univariate and multivariate predictors of survival utilizing Kaplan Meier and Cox proportional hazards models. Real time RT-PCR was used to validate these findings. We found that 78 of 320 GEP-NETs (24.4%) expressed TS. NETs arising in the colon, stomach and pancreas showed the highest expression of TS (47.4%, 42.6% and 37.3%, respectively), whereas NETs of the appendix, rectum and duodenum displayed low TS expression (3.3%, 12.9% and 15.4%, respectively). TS expression in GEP-NETs was associated with poorly differentiated endocrine carcinoma, angiolymphatic invasion, lymph node metastasis and distant metastasis (p < 0.05). Patients with TS-positive NETs had markedly worse outcomes than TS-negative NETs as shown by univariate (p < 0.001) and multivariate (p = 0.01) survival analyses. Expression of p18 predicted survival in TS-positive patients that received chemotherapy (p = 0.015). In conclusion, TS protein expression was an independent prognostic biomarker for GEP-NETs. The strong association of increased TS expression with aggressive disease and early death supports the role of TS as a cancer promoting agent in these tumors.
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Affiliation(s)
- Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Korea
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Renard BL, Maurin B, Chambert S, Décout JL. Key steps from the “RNA World” to the “DNA World”. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140205002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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204
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Nenajdenko V. Fluorine-Containing Diazines in Medicinal Chemistry and Agrochemistry. FLUORINE IN HETEROCYCLIC CHEMISTRY VOLUME 2 2014. [PMCID: PMC7121506 DOI: 10.1007/978-3-319-04435-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The combination of a fluorine atom and a diazine ring, which both possess unique structural and chemical features, can generate new relevant building blocks for the discovery of efficient fluorinated biologically active agents. Herein we give a comprehensive review on the biological activity and synthesis of fluorine containing, pyrimidine, pyrazine and pyridazine derivatives with relevance to medicinal and agrochemistry.
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205
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Lv YT, Du PJ, Wang QY, Tan Y, Sun ZB, Su ZL, Kang CM. A Novel Approach to Cloning and Expression of Human Thymidylate Synthase. Asian Pac J Cancer Prev 2013; 14:7523-7. [DOI: 10.7314/apjcp.2013.14.12.7523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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206
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Inhibition of DNA glycosylases via small molecule purine analogs. PLoS One 2013; 8:e81667. [PMID: 24349107 PMCID: PMC3857224 DOI: 10.1371/journal.pone.0081667] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022] Open
Abstract
Following the formation of oxidatively-induced DNA damage, several DNA glycosylases are required to initiate repair of the base lesions that are formed. Recently, NEIL1 and other DNA glycosylases, including OGG1 and NTH1 were identified as potential targets in combination chemotherapeutic strategies. The potential therapeutic benefit for the inhibition of DNA glycosylases was validated by demonstrating synthetic lethality with drugs that are commonly used to limit DNA replication through dNTP pool depletion via inhibition of thymidylate synthetase and dihydrofolate reductase. Additionally, NEIL1-associated synthetic lethality has been achieved in combination with Fanconi anemia, group G. As a prelude to the development of strategies to exploit the potential benefits of DNA glycosylase inhibition, it was necessary to develop a reliable high-throughput screening protocol for this class of enzymes. Using NEIL1 as the proof-of-principle glycosylase, a fluorescence-based assay was developed that utilizes incision of site-specifically modified oligodeoxynucleotides to detect enzymatic activity. This assay was miniaturized to a 1536-well format and used to screen small molecule libraries for inhibitors of the combined glycosylase/AP lyase activities. Among the top hits of these screens were several purine analogs, whose postulated presence in the active site of NEIL1 was consistent with the paradigm of NEIL1 recognition and excision of damaged purines. Although a subset of these small molecules could inhibit other DNA glycosylases that excise oxidatively-induced DNA adducts, they could not inhibit a pyrimidine dimer-specific glycosylase.
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207
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Sulzyc-Bielicka V, Domagala P, Bielicki D, Safranow K, Domagala W. Thymidylate synthase expression and p21(WAF1)/p53 phenotype of colon cancers identify patients who may benefit from 5-fluorouracil based therapy. Cell Oncol (Dordr) 2013; 37:17-28. [PMID: 24277474 PMCID: PMC3921584 DOI: 10.1007/s13402-013-0159-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2013] [Indexed: 01/09/2023] Open
Abstract
Background Studies on the expression of thymidylate synthase (TS) in colorectal cancers (CRCs) have failed to provide unequivocal prognostic or predictive information. Here, we assessed the prognostic significance of TS expression in Astler-Coller stage B2 and C CRCs defined by a p21WAF1/p53 immunophenotype in patients subjected to 5-fluorouracil (5FU)-based adjuvant therapy. Methods A cohort of 189 CRCs was asssessed for TS, p21WAF1 and p53 expression on tissue microarrays using immunohistochemistry, and associations with disease-free survival (DFS) and overall survival (OS) of the patients were assessed using univariate and multivariate analyses. Results TS expression led to the stratification of patients with colon cancer, but not rectal cancer, with immunophenotypes other than p21WAF1+/p53- (referred to as P&P) into subgroups characterized by a worse (P&P TS+) and a better (P&P TS-) DFS and OS, in univariate (P = 0.006 and P = 0.005, respectively) and multivariate (P = 0.0004 and P = 0.002, respectively) analyses. The p21WAF1+/p53- immunophenotype was associated with a favorable prognosis, irrespective of TS expression. Conclusions The strong association observed between the P&P TS+ immunophenotype and a worse DFS and OS suggests a predictive significance of TS expression for 5FU-based adjuvant therapy in patients with colon cancers exhibiting the P&P immunophenotype. In addition, our findings suggest that the appropriate target for assessment of TS expression as a prognostic/predictive marker is a subgroup of colon cancers with an immunophenotype other than p21WAF1+/p53-, and that only in this subgroup high TS expression is associated with an unfavorable DFS and OS. Therefore, we suggest that assessing TS expression in conjunction with p21WAF1/p53 immunophenotyping of colon cancers may improve the selection of patients suitable for 5FU-based adjuvant chemotherapy.
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208
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Wilk P, Jarmuła A, Ruman T, Banaszak K, Rypniewski W, Cieśla J, Dowierciał A, Rode W. Crystal structure of phosphoramide-phosphorylated thymidylate synthase reveals pSer127, reflecting probably pHis to pSer phosphotransfer. Bioorg Chem 2013; 52:44-9. [PMID: 24321279 DOI: 10.1016/j.bioorg.2013.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
Abstract
Crystal structure is presented of the binary complex between potassium phosphoramidate-phosphorylated recombinant C. elegans thymidylate synthase and dUMP. On each monomer a single phosphoserine residue (Ser127) was identified, instead of expected phosphohistidine. As (31)P NMR studies of both the phosphorylated protein and of potassium phosphoramidate potential to phosphorylate different amino acids point to histidine as the only possible site of the modification, thermodynamically favored intermolecular phosphotransfer from histidine to serine is suggested.
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Affiliation(s)
- Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
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209
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Hamdane D, Bruch E, Un S, Field M, Fontecave M. Activation of a unique flavin-dependent tRNA-methylating agent. Biochemistry 2013; 52:8949-56. [PMID: 24228791 DOI: 10.1021/bi4013879] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
TrmFO is a tRNA methyltransferase that uses methylenetetrahydrofolate (CH2THF) and flavin adenine dinucleotide hydroquinone as cofactors. We have recently shown that TrmFO from Bacillus subtilis stabilizes a TrmFO-CH2-FADH adduct and an ill-defined neutral flavin radical. The adduct contains a unique N-CH2-S moiety, with a methylene group bridging N5 of the isoalloxazine ring and the sulfur of an active-site cysteine (Cys53). In the absence of tRNA substrate, this species is remarkably stable but becomes catalytically competent for tRNA methylation following tRNA addition using the methylene group as the source of methyl. Here, we demonstrate that this dormant methylating agent can be activated at low pH, and we propose that this process is triggered upon tRNA addition. The reaction proceeds via protonation of Cys53, cleavage of the C-S bond, and generation of a highly reactive [FADH(N5)═CH2]+ iminium intermediate, which is proposed to be the actual tRNA-methylating agent. This mechanism is fully supported by DFT calculations. The radical present in TrmFO is characterized here by optical and EPR/ENDOR spectroscopy approaches together with DFT calculations and is shown to be the one-electron oxidized product of the TrmFO-CH2-FADH adduct. It is also relatively stable, and its decomposition is facilitated by high pH. These results provide new insights into the structure and reactivity of the unique flavin-dependent methylating agent used by this class of enzymes.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-FRE 3488, Collège De France , 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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210
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Shmalenyuk ER, Kochetkov SN, Alexandrova LA. Novel inhibitors ofMycobacterium tuberculosisgrowth based on modified pyrimidine nucleosides and their analogues. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n09abeh004404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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211
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Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC Bioinformatics 2013; 14:302. [PMID: 24098943 PMCID: PMC3840585 DOI: 10.1186/1471-2105-14-302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022] Open
Abstract
Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
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Affiliation(s)
- Chris Schmidt
- Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
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212
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Sulzyc-Bielicka V, Bielicki D, Binczak-Kuleta A, Kaczmarczyk M, Pioch W, Machoy-Mokrzynska A, Ciechanowicz A, Gołębiewska M, Drozdzik M. Thymidylate synthase gene polymorphism and survival of colorectal cancer patients receiving adjuvant 5-fluorouracil. Genet Test Mol Biomarkers 2013; 17:799-806. [PMID: 23968134 DOI: 10.1089/gtmb.2013.0171] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Limited studies indicate a possible association of 5'-UTR thymidylate synthase enhancer region polymorphism and treatment outcome in patients medicated with 5-fluorouracil (5-FU). The study was designed to verify the relationship in patients with colorectal cancer (CRC), a Polish population that received 5-FU-based adjuvant chemotherapy. The study analyzed 145 Astler-Coller B2 and C CRC patients. Genotyping for a variable number of tandem repeats and G to C single-nucleotide polymorphism in the 5'-UTR of the thymidylate synthase (TS) gene was carried out. TS genotypes were classified into high expression (high TS) and low expression types (low TS). High TS was found in 22.8% of patients. The right-side tumors were more frequently associated with high TS than the left-side tumors (p=0.024). High TS was only found in 9.3% of rectal tumors, but in 29.7% of colon cancers (p=0.0042). Disease-free survival after 20 months (DFS 20) was longer in subjects with low TS than in high TS (p=0.043). Patients who underwent chemotherapy had longer DFS 20 in the low TS than in the high TS subgroup (p=0.051). The low TS was found to be an independent good prognostic factor for DFS 20 in the whole group as well as in the subgroup treated with chemotherapy (p=0.024 and p=0.034, respectively). Patients with low TS did not show any differences in DFS 20 whether they were treated with adjuvant chemotherapy or not. Proximal CRC tumors are characterized by higher TS expression genotypes than distal tumors, and are at significantly greater risk of early recurrence during the first 20 months after surgery.
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213
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Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Cell Res 2013; 23:1296-309. [PMID: 23917530 DOI: 10.1038/cr.2013.107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 12/18/2022] Open
Abstract
DNA methylation and demethylation regulate many crucial biological processes in mammals and are linked to many diseases. Active DNA demethylation is believed to be catalyzed by TET proteins and a putative DNA decarboxylase that may share some similarities in sequence, structure and catalytic mechanism with isoorotate decarboxylase (IDCase) that catalyzes decarboxylation of 5caU to U in fungi. We report here the structures of wild-type and mutant IDCases from Cordyceps militaris and Metarhizium anisopliae in apo form or in complexes with 5caU, U, and an inhibitor 5-nitro-uracil. IDCases adopt a typical (β/α)8 barrel fold of the amidohydrolase superfamily and function as dimers. A Zn(2+) is bound at the active site and coordinated by four strictly conserved residues, one Asp and three His. The substrate is recognized by several strictly conserved residues. The functional roles of the key residues at the active site are validated by mutagenesis and biochemical studies. Based on the structural and biochemical data, we present for the first time a novel catalytic mechanism of decarboxylation for IDCases, which might also apply to other members of the amidohydrolase superfamily. In addition, our biochemical data show that IDCases can catalyze decarboxylation of 5caC to C albeit with weak activity, which is the first in vitro evidence for direct decarboxylation of 5caC to C by an enzyme. These findings are valuable in the identification of potential DNA decarboxylase in mammals.
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214
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MARVERTI GAETANO, LIGABUE ALESSIO, LOMBARDI PAOLO, FERRARI STEFANIA, MONTI MARIAGIUSEPPINA, FRASSINETI CHIARA, COSTI MARIAPAOLA. Modulation of the expression of folate cycle enzymes and polyamine metabolism by berberine in cisplatin-sensitive and -resistant human ovarian cancer cells. Int J Oncol 2013; 43:1269-80. [DOI: 10.3892/ijo.2013.2045] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/30/2013] [Indexed: 11/06/2022] Open
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215
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Basta T, Boum Y, Briffotaux J, Becker HF, Lamarre-Jouenne I, Lambry JC, Skouloubris S, Liebl U, Graille M, van Tilbeurgh H, Myllykallio H. Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biol 2013; 2:120120. [PMID: 23155486 PMCID: PMC3498832 DOI: 10.1098/rsob.120120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/11/2012] [Indexed: 11/12/2022] Open
Abstract
Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.
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Affiliation(s)
- Tamara Basta
- Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France
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Parchina A, Froeyen M, Margamuljana L, Rozenski J, De Jonghe S, Briers Y, Lavigne R, Herdewijn P, Lescrinier E. Discovery of an acyclic nucleoside phosphonate that inhibits Mycobacterium tuberculosis ThyX based on the binding mode of a 5-alkynyl substrate analogue. ChemMedChem 2013; 8:1373-83. [PMID: 23836539 DOI: 10.1002/cmdc.201300146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 11/10/2022]
Abstract
The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5-triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the "classic" TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5-(3-octanamidoprop-1yn-1yl)-2'-deoxyuridine-5'-monophosphate (1) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the "5-alkynyl tail") extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH3 group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5-alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6-(5-(3-octanamidoprop-1-yn-1-yl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)hexyl)phosphonate (3 e) exhibited 43 % of inhibitory effect on ThyX at 50 μM. While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.
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Affiliation(s)
- Anastasia Parchina
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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217
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Kaiyawet N, Rungrotmongkol T, Hannongbua S. Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. J Chem Inf Model 2013; 53:1315-23. [PMID: 23705822 DOI: 10.1021/ci400131y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stability of the thymidylate synthase (TS)/2-deoxyuridine-5-monophosphate (dUMP)/5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) ternary complex formation and Michael addition are considered as important steps that are involved in the inhibition mechanism of the anticancer prodrug 5-fluorouracil (5-FU). Here, the effect of three different halogen substitutions on the C-5 position of the dUMP (XdUMPs = FdUMP, CldUMP, and BrdUMP), the normal substrate, on the stability of the TS/dUMP and TS/dUMP/mTHF binary and ternary complexes, respectively, was investigated via molecular dynamics simulation. The simulated results revealed that the stability of all the systems was substantially increased by mTHF binding to the catalytic pocket. In the ternary complex, a much greater stabilization of the dUMP and XdUMPs through electrostatic interactions, including charge-charge and hydrogen bond interactions, was found compared to mTHF. An additional unique hydrogen bond between the substituted fluorine of FdUMP and the hydroxyl group of the TS Y94 residue was observed in both the binary and ternary complexes. The distance between the S(-) atom of the TS C146 residue and the C6 atom of dUMP, at <4 Å in all systems, suggested that a Michael addition with the formation of a S-C6 covalent bond potentially occurred, although the hydrogen atom on C6 of dUMP is substituted by a halogen atom. The MM/PBSA binding free energy revealed the significant role of the bridging waters around the ligands in the increased binding affinity (∼10 kcal/mol) of dUMP/XdUMP, either alone or together with mTHF, toward TS. The order of the averaged binding affinity in the ternary systems was found to be CldUMP ≈ FdUMP > dUMP > BrdUMP, suggesting that CldUMP could be a potent candidate TS inhibitor, the same as FdUMP (the metabolite form of 5-FU).
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Affiliation(s)
- Nopporn Kaiyawet
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
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Galashevskaya A, Sarno A, Vågbø CB, Aas PA, Hagen L, Slupphaug G, Krokan HE. A robust, sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported. DNA Repair (Amst) 2013; 12:699-706. [PMID: 23742752 DOI: 10.1016/j.dnarep.2013.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/06/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
Considerable progress has been made in understanding the origins of genomic uracil and its role in genome stability and host defense; however, the main question concerning the basal level of uracil in DNA remains disputed. Results from assays designed to quantify genomic uracil vary by almost three orders of magnitude. To address the issues leading to this inconsistency, we explored possible shortcomings with existing methods and developed a sensitive LC/MS/MS-based method for the absolute quantification of genomic 2'-deoxyuridine (dUrd). To this end, DNA was enzymatically hydrolyzed to 2'-deoxyribonucleosides and dUrd was purified in a preparative HPLC step and analyzed by LC/MS/MS. The standard curve was linear over four orders of magnitude with a quantification limit of 5 fmol dUrd. Control samples demonstrated high inter-experimental accuracy (94.3%) and precision (CV 9.7%). An alternative method that employed UNG2 to excise uracil from DNA for LC/MS/MS analysis gave similar results, but the intra-assay variability was significantly greater. We quantified genomic dUrd in Ung(+/+) and Ung(-/-) mouse embryonic fibroblasts and human lymphoblastoid cell lines carrying UNG mutations. DNA-dUrd is 5-fold higher in Ung(-/-) than in Ung(+/+) fibroblasts and 11-fold higher in UNG2 dysfunctional than in UNG2 functional lymphoblastoid cells. We report approximately 400-600 dUrd per human or murine genome in repair-proficient cells, which is lower than results using other methods and suggests that genomic uracil levels may have previously been overestimated.
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Affiliation(s)
- Anastasia Galashevskaya
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
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219
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Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J Am Chem Soc 2013; 135:7583-92. [PMID: 23611499 PMCID: PMC3674108 DOI: 10.1021/ja400761x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Calvin Luzum
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Janet S. Finer-Moore
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M. Stroud
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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220
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Roston D, Islam Z, Kohen A. Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions. Molecules 2013; 18:5543-67. [PMID: 23673528 PMCID: PMC4342783 DOI: 10.3390/molecules18055543] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/16/2022] Open
Abstract
Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers.
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Affiliation(s)
| | | | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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221
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Li WW, Gong L, Bayley H. Single-Molecule Detection of 5-Hydroxymethylcytosine in DNA through Chemical Modification and Nanopore Analysis. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300413] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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222
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Li WW, Gong L, Bayley H. Single-Molecule Detection of 5-Hydroxymethylcytosine in DNA through Chemical Modification and Nanopore Analysis. Angew Chem Int Ed Engl 2013; 52:4350-5. [DOI: 10.1002/anie.201300413] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Indexed: 12/16/2022]
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223
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Wang Z, Ferrer S, Moliner V, Kohen A. QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase. Biochemistry 2013; 52:2348-58. [PMID: 23464672 DOI: 10.1021/bi400267q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cleavage of covalent C-H bonds is one of the most energetically demanding, yet biologically essential, chemical transformations. Two C-H bond cleavages are involved in the reaction catalyzed by thymidylate synthase (TSase), which provides the sole de novo source of thymidylate (i.e., the DNA base T) for most organisms. Our QM/MM free energy calculations show that the C-H → O proton transfer has three transition states that are energetically similar but structurally diverse. These characteristics are different from our previous calculation results on the C-H → C hydride transfer, providing an explanation for differences in temperature dependences of KIEs on these two C-H bond activation steps. The calculations also suggest that the traditionally proposed covalent bond between the protein and substrate (the C6-S bond) is very labile during the multistep catalytic reaction. Collective protein motions not only assist cleavage of the C6-S bond to stabilize the transition state of the proton transfer step but also rearrange the H-bond network at the end of this step to prepare the active site for subsequent chemical steps. These computational results illustrate functionalities of specific protein residues that reconcile many previous experimental observations and provide guidance for future experiments to examine the proposed mechanisms. The synchronized conformational changes in the protein and ligands observed in our simulations demonstrate participation of protein motions in the reaction coordinate of enzymatic reactions. Our computational findings suggest the existence of new reaction intermediates not covalently bound to TSase, which may lead to a new class of drugs targeting DNA biosynthesis.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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224
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Patel K, Yerram SR, Azad NA, Kern SE. A thymidylate synthase ternary complex-specific antibody, FTS, permits functional monitoring of fluoropyrimidines dosing. Oncotarget 2013; 3:678-85. [PMID: 22824673 PMCID: PMC3443251 DOI: 10.18632/oncotarget.554] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
5-Fluorouracil (5FU) and similar fluoropyrimidines induce covalent modification of thymidylate synthase (TS) and inhibit its activity. They are often used to treat solid cancers, but drug resistance and toxicity are drawbacks. Therefore, there is an unmet need for a functional assay to quantify fluorouracil activity in tissues, so as to individually tailor dosing. It is cumbersome to separately quantify unmodified and 5FU-modified TS using currently available commercial anti-TS antibodies because they recognize both forms. We report here the first monoclonal antibody (FTS) specific to 5FU-modified TS. By immunoblot assay, the FTS antibody specifically recognizes modified TS in a dose-dependent manner in 5FU-treated cells, in cancer xenograft tissues of 5FU-treated mice, and in the murine tissues. In the same assay, the antibody is nonreactive with unmodified TS in untreated or treated cells and tissues. Speculatively, a high-throughput assay could be enabled by pairing anti-TS antibodies of two specificities, one recognizing only modified TS and another recognizing both forms, to structurally quantify the TS-inhibiting effect of fluorouracil at a cellular or tissue level without requiring prior protein separation. Such a development might aid preclinical analytic studies or make practical the individual tailoring of dosing.
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Affiliation(s)
- Kalpesh Patel
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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225
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Wu SY, Chen TM, Gmeiner WH, Chu E, Schmitz JC. Development of modified siRNA molecules incorporating 5-fluoro-2'-deoxyuridine residues to enhance cytotoxicity. Nucleic Acids Res 2013; 41:4650-9. [PMID: 23449220 PMCID: PMC3632118 DOI: 10.1093/nar/gkt120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are composed of chemically modified nucleotides, which enhance RNA stability and increase affinity in Watson–Crick base pairing. However, the precise fate of such modified nucleotides once the siRNA is degraded within the cell is unknown. Previously, we demonstrated that deoxythymidine release from degraded siRNAs reversed the cytotoxicity of thymidylate synthase (TS)-targeted siRNAs and other TS inhibitor compounds. We hypothesized that siRNAs could be designed with specific nucleoside analogues that, once released, would enhance siRNA cytotoxicity. TS-targeted siRNAs were designed that contained 5-fluoro-2′-deoxyuridine (FdU) moieties at various locations within the siRNA. After transfection, these siRNAs suppressed TS protein and messenger RNA expression with different efficiencies depending on the location of the FdU modification. FdU was rapidly released from the siRNA as evidenced by formation of the covalent inhibitory ternary complex formed between TS protein and the FdU metabolite, FdUMP. These modified siRNAs exhibited 10–100-fold greater cytotoxicity and induced multiple DNA damage repair and apoptotic pathways when compared with control siRNAs. The strategy of designing siRNA molecules that incorporate cytotoxic nucleosides represents a potentially novel drug development approach for the treatment of cancer and other human diseases.
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Affiliation(s)
- Shao-yu Wu
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
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226
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Ferrari S, Ingrami M, Soragni F, Wade RC, Costi MP. Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors. Bioorg Med Chem Lett 2013; 23:663-8. [DOI: 10.1016/j.bmcl.2012.11.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
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227
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Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013; 8:e53851. [PMID: 23382856 PMCID: PMC3561365 DOI: 10.1371/journal.pone.0053851] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rapatbhorn Patrapuvich
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Anna S. Gardberg
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Brianna Armour
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | | | - David M. Dranow
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - James W. Fairman
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - David Fox
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Angela Gillespie
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Mary Trang Nguyen
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Lynn Barrett
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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228
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Characterization of the bipartite degron that regulates ubiquitin-independent degradation of thymidylate synthase. Biosci Rep 2013. [PMID: 23181752 PMCID: PMC3549573 DOI: 10.1042/bsr20120112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
TS (thymidylate synthase) is a key enzyme in the de novo biosynthesis of dTMP, and is indispensable for DNA replication. Previous studies have shown that intracellular degradation of the human enzyme [hTS (human thymidylate synthase)] is mediated by the 26S proteasome, and occurs in a ubiquitin-independent manner. Degradation of hTS is governed by a degron that is located at the polypeptide's N-terminus that is capable of promoting the destabilization of heterologous proteins to which it is attached. The hTS degron is bipartite, consisting of two subdomains: an IDR (intrinsically disordered region) that is highly divergent among mammalian species, followed by a conserved amphipathic α-helix (designated hA). In the present report, we have characterized the structure and function of the hTS degron in more detail. We have conducted a bioinformatic analysis of interspecies sequence variation exhibited by the IDR, and find that its hypervariability is not due to diversifying (or positive) selection; rather, it has been subjected to purifying (or negative) selection, although the intensity of such selection is relaxed or weakened compared with that exerted on the rest of the molecule. In addition, we have verified that both subdomains of the hTS degron are required for full activity. Furthermore, their co-operation does not necessitate that they are juxtaposed, but is maintained when they are physically separated. Finally, we have identified a 'cryptic' degron at the C-terminus of hTS, which is activated by the N-terminal degron and appears to function only under certain circumstances; its role in TS metabolism is not known.
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229
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Cheatum CM, Kohen A. Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer. Top Curr Chem (Cham) 2013; 337:1-39. [PMID: 23539379 PMCID: PMC4699684 DOI: 10.1007/128_2012_407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H → C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes.
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230
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Mathews II. Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design. ACTA ACUST UNITED AC 2013; Suppl 12:004. [PMID: 24563811 DOI: 10.4172/2157-2526.s12-004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The identification of flavin-dependent thymidylate synthase (FDTS) as an essential enzyme and its occurrence in several pathogenic microbes opens opportunities for using FDTS enzyme as an excellent target for new antimicrobial drug discovery. In contrast to the human thymidylate synthase enzyme that utilizes methylene-tetrahydrofolate (CH2H4 folate) for the conversion of dUMP to dTMP, the microbial enzymes utilize an additional non-covalently bound FAD molecule for the hydride transfer from NAD(P)H. The structural and mechanistic differences between the human and microbial enzymes present an attractive opportunity for the design of antimicrobial compounds specific for the pathogens. We have determined the crystal structure of FDTS enzyme in complex with the methyl donor, CH2H4 folate. We describe here the structure of a FDTS mutant and compare it with other FDTS complex structures, including a FDTS-CH2H4 folate complex. We identified a conformational change essential for substrate binding and propose a strategy for the design of FDTS specific inhibitors.
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Affiliation(s)
- Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
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231
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Brunn ND, Sega EG, Kao MB, Hermann T. Targeting a regulatory element in human thymidylate synthase mRNA. Chembiochem 2012; 13:2738-44. [PMID: 23143777 PMCID: PMC3758747 DOI: 10.1002/cbic.201200603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 12/21/2022]
Abstract
Thymidylate synthase (TS) is a key enzyme in the biosynthesis of thymidine. The use of TS inhibitors in cancer chemotherapy suffers from resistance development in tumors through upregulation of TS expression. Autoregulatory translation control has been implicated with TS overexpression. TS binding at its own mRNA, which leads to sequestration of the start codon, is abolished when the enzyme forms an inhibitor complex, thereby relieving translation suppression. We have used the protein-binding site from the TS mRNA in the context of a bicistronic expression system to validate targeting the regulatory motif with stabilizing ligands that prevent ribosomal initiation. Stabilization of the RNA by mutations, which were studied as surrogates of ligand binding, suppresses translation of the TS protein. Compounds that stabilize the TS-binding RNA motif and thereby inhibit ribosomal initiation might be used in combination with existing TS enzyme-targeting drugs to overcome resistance development during chemotherapy.
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Affiliation(s)
- Nicholas D. Brunn
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Phone: (+1) 858 534 4467, Fax: (+1) 858 534 0202
| | | | - Melody B. Kao
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Phone: (+1) 858 534 4467, Fax: (+1) 858 534 0202
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Phone: (+1) 858 534 4467, Fax: (+1) 858 534 0202
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232
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Jarmuła A, Rode W. Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase. J Comput Aided Mol Des 2012; 27:45-66. [PMID: 23239172 DOI: 10.1007/s10822-012-9624-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 12/06/2012] [Indexed: 11/25/2022]
Abstract
Tyrosine nitration is a widespread post-translational modification capable of affecting both the function and structure of the host protein molecule. Enzyme thymidylate synthase (TS), a homodimer, is a molecular target for anticancer therapy. Recently purified TS preparations, isolated from mammalian tissues, were found to be nitrated, suggesting this modification to appear endogenously in normal and tumor tissues. Moreover, human TS (hTS) nitration in vitro led to a by twofold lowered catalytic activity following nitration in average of 1 tyrosine residue per monomer (Dąbrowska-Maś et al. in Org Biomol Chem 10:323-331, 2012), with the modification identified by mass spectrometry at seven different sites (Y33, Y65, Y135, Y213, Y230, Y258 and Y301). In the present paper, combined computational approach, including molecular and essential dynamics and free energy computations, was used to predict the influence on the activity of hTS of nitration of each of the seven tyrosine residues. The simulations were based on the crystal structure of hTS ternary complex with dUMP and Tomudex (PDB code: 1I00), with the Tomudex molecule replaced by the molecule of TS cofactor analogue, tetrahydrofolate. The present results indicate that while with nitration of five out of seven residues (Y33, Y135, Y230, Y258 and Y301), single residue modification appears to have a strong reducing effect on the activity, with the remaining two, Y65 and Y213, no or a weaker influence is apparent. Taken together, these results demonstrate that tyrosine nitrations in the hTS enzyme show clear tendency to influence the structure and dynamics and, in turn, catalytic properties of the host enzyme. These effects are overall distance-dependent.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland.
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233
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Experimental and theoretical studies of enzyme-catalyzed hydrogen-transfer reactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [PMID: 22607755 DOI: 10.1016/b978-0-12-398312-1.00006-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The mechanisms of enzyme-catalyzed reactions are medicinally important and present a fascinating intellectual challenge. Many experimental and theoretical techniques can shed light on these mechanisms, and here, we shall focus on the utility of kinetic isotope effects (KIEs) to study enzymatic reactions that involve hydrogen transfers. We will provide a short background on the prevailing models to interpret KIEs and then present more detailed reviews of two model enzymes: alcohol dehydrogenase and thymidylate synthase. These two examples provide a context to describe the types of experiments and theoretical calculations that drive this field forward and the kind of information each can furnish. We emphasize the importance of cooperation between experimentalists and theoreticians to continue the progress toward a comprehensive theory of enzyme catalysis.
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234
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Carosati E, Tochowicz A, Marverti G, Guaitoli G, Benedetti P, Ferrari S, Stroud RM, Finer-Moore J, Luciani R, Farina D, Cruciani G, Costi MP. Inhibitor of Ovarian Cancer Cells Growth by Virtual Screening: A New Thiazole Derivative Targeting Human Thymidylate Synthase. J Med Chem 2012; 55:10272-6. [DOI: 10.1021/jm300850v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Emanuele Carosati
- Dipartimento
di Chimica, Università degli Studi di Perugia, Via Elce
di Sotto 10, 06123, Perugia, Italy
| | - Anna Tochowicz
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Gaetano Marverti
- Dipartimento di Scienze Biomediche,
Metaboliche e Neuroscienze, Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena,
Italy
| | - Giambattista Guaitoli
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Paolo Benedetti
- Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5
5NE, U.K
| | - Stefania Ferrari
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Robert M. Stroud
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Janet Finer-Moore
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Rosaria Luciani
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Davide Farina
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Gabriele Cruciani
- Dipartimento
di Chimica, Università degli Studi di Perugia, Via Elce
di Sotto 10, 06123, Perugia, Italy
| | - M. Paola Costi
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
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235
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Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A. A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase. J Am Chem Soc 2012; 134:17722-30. [PMID: 23034004 DOI: 10.1021/ja307859m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727, USA
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236
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Nonoo RH, Armstrong A, Mann DJ. Kinetic Template-Guided Tethering of Fragments. ChemMedChem 2012; 7:2082-6. [DOI: 10.1002/cmdc.201200404] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Indexed: 11/11/2022]
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237
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Alam A, Goyal M, Iqbal MS, Pal C, Dey S, Bindu S, Maity P, Bandyopadhyay U. Novel antimalarial drug targets: hope for new antimalarial drugs. Expert Rev Clin Pharmacol 2012; 2:469-89. [PMID: 22112223 DOI: 10.1586/ecp.09.28] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Malaria is a major global threat, that results in more than 2 million deaths each year. The treatment of malaria is becoming extremely difficult due to the emergence of drug-resistant parasites, the absence of an effective vaccine, and the spread of insecticide-resistant vectors. Thus, malarial therapy needs new chemotherapeutic approaches leading to the search for new drug targets. Here, we discuss different approaches to identifying novel antimalarial drug targets. We have also given due attention to the existing validated targets with a view to develop novel, rationally designed lead molecules. Some of the important parasite proteins are claimed to be the targets; however, further in vitro or in vivo structure-function studies of such proteins are crucial to validate these proteins as suitable targets. The interactome analysis among apicoplast, mitochondrion and genomic DNA will also be useful in identifying vital pathways or proteins regulating critical pathways for parasite growth and survival, and could be attractive targets. Molecules responsible for parasite invasion to host erythrocytes and ion channels of infected erythrocytes, essential for intra-erythrocyte survival and stage progression of parasites are also becoming attractive targets. This review will discuss and highlight the current understanding regarding the potential antimalarial drug targets, which could be utilized to develop novel antimalarials.
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Affiliation(s)
- Athar Alam
- Division of Infectious Diseases and Immunology, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India.
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238
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Abstract
The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH(2)H(4)folate). Most organisms, including humans, rely on the thyA- or TYMS-encoded classic thymidylate synthase, whereas, certain microorganisms, including all Rickettsia and other pathogens, use an alternative thyX-encoded flavin-dependent thymidylate synthase (FDTS). Although several crystal structures of FDTSs have been reported, the absence of a structure with folates limits understanding of the molecular mechanism and the scope of drug design for these enzymes. Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate further elucidation of FDTSs' mechanism and the design of structure-based inhibitors as potential leads to new antimicrobial drugs.
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239
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Pozzi C, Ferrari S, Cortesi D, Luciani R, Stroud RM, Catalano A, Costi MP, Mangani S. The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1232-41. [PMID: 22948925 PMCID: PMC10316677 DOI: 10.1107/s0907444912026236] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/10/2012] [Indexed: 11/11/2022]
Abstract
Drug resistance to therapeutic antibiotics poses a challenge to the identification of novel targets and drugs for the treatment of infectious diseases. Infections caused by Enterococcus faecalis are a major health problem. Thymidylate synthase (TS) from E. faecalis is a potential target for antibacterial therapy. The X-ray crystallographic structure of E. faecalis thymidylate synthase (EfTS), which was obtained as a native binary complex composed of EfTS and 5-formyltetrahydrofolate (5-FTHF), has been determined. The structure provides evidence that EfTS is a half-of-the-sites reactive enzyme, as 5-FTHF is bound to two of the four independent subunits present in the crystal asymmetric unit. 5-FTHF is a metabolite of the one-carbon transfer reaction catalysed by 5-formyltetrahydrofolate cyclo-ligase. Kinetic studies show that 5-FTHF is a weak inhibitor of EfTS, suggesting that the EfTS-5-FTHF complex may function as a source of folates and/or may regulate one-carbon metabolism. The structure represents the first example of endogenous 5-FTHF bound to a protein involved in folate metabolism.
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Affiliation(s)
- Cecilia Pozzi
- Dipartimento di Chimica, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Ferrari
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Debora Cortesi
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Rosaria Luciani
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Robert M. Stroud
- Department of Biochemistry and Biophysiscs, University of California, San Francisco, S-412C Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Alessia Catalano
- Dipartimento Farmaco-Chimico, University of Bari ‘Aldo Moro’, Via E. Orabona 4, 70125 Bari, Italy
| | - Maria Paola Costi
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Stefano Mangani
- Dipartimento di Chimica, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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240
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Mishanina TV, Koehn EM, Kohen A. Mechanisms and inhibition of uracil methylating enzymes. Bioorg Chem 2012; 43:37-43. [PMID: 22172597 PMCID: PMC3315608 DOI: 10.1016/j.bioorg.2011.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
Abstract
Uracil methylation is essential for survival of organisms and passage of information from generation to generation with high fidelity. Two alternative uridyl methylation enzymes, flavin-dependent thymidylate synthase and folate/FAD-dependent RNA methyltransferase, have joined the long-known classical enzymes, thymidylate synthase and SAM-dependent RNA methyltransferase. These alternative enzymes differ significantly from their classical counterparts in structure, cofactor requirements and chemical mechanism. This review covers the available structural and mechanistic knowledge of the classical and alternative enzymes in biological uracil methylation, and offers a possibility of using inhibitors specifically aiming at microbial thymidylate production as antimicrobial drugs.
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Affiliation(s)
- Tatiana V. Mishanina
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
| | - Eric M. Koehn
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
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241
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Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc Natl Acad Sci U S A 2012; 109:12638-43. [PMID: 22802648 DOI: 10.1073/pnas.1205020109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Microsporidia of the genus Encephalitozoon are widespread pathogens of animals that harbor the smallest known nuclear genomes. Complete sequences from Encephalitozoon intestinalis (2.3 Mbp) and Encephalitozoon cuniculi (2.9 Mbp) revealed massive gene losses and reduction of intergenic regions as factors leading to their drastically reduced genome size. However, microsporidian genomes also have gained genes through horizontal gene transfers (HGT), a process that could allow the parasites to exploit their hosts more fully. Here, we describe the complete sequences of two intermediate-sized genomes (2.5 Mbp), from Encephalitozoon hellem and Encephalitozoon romaleae. Overall, the E. hellem and E. romaleae genomes are strikingly similar to those of Encephalitozoon cuniculi and Encephalitozoon intestinalis in both form and content. However, in addition to the expected expansions and contractions of known gene families in subtelomeric regions, both species also were found to harbor a number of protein-coding genes that are not found in any other microsporidian. All these genes are functionally related to the metabolism of folate and purines but appear to have originated by several independent HGT events from different eukaryotic and prokaryotic donors. Surprisingly, the genes are all intact in E. hellem, but in E. romaleae those involved in de novo synthesis of folate are all pseudogenes. Overall, these data suggest that a recent common ancestor of E. hellem and E. romaleae assembled a complete metabolic pathway from multiple independent HGT events and that one descendent already is dispensing with much of this new functionality, highlighting the transient nature of transferred genes.
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242
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Kögler M, Busson R, De Jonghe S, Rozenski J, Van Belle K, Louat T, Munier-Lehmann H, Herdewijn P. Synthesis and evaluation of 6-aza-2'-deoxyuridine monophosphate analogs as inhibitors of thymidylate synthases, and as substrates or inhibitors of thymidine monophosphate kinase in Mycobacterium tuberculosis. Chem Biodivers 2012; 9:536-56. [PMID: 22422522 DOI: 10.1002/cbdv.201100285] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A series of 5-substituted analogs of 6-aza-2'-deoxyuridine 5'-monophosphate, 6-aza-dUMP, has been synthesized and evaluated as potential inhibitors of the two mycobacterial thymidylate synthases (i.e., a flavin-dependent thymidylate synthase, ThyX, and a classical thymidylate synthase, ThyA). Replacement of C(6) of the natural substrate dUMP by a N-atom in 6-aza-dUMP 1a led to a derivative with weak ThyX inhibitory activity (33% inhibition at 50 μM). Introduction of alkyl and aryl groups at C(5) of 1a resulted in complete loss of inhibitory activity, whereas the attachment of a 3-(octanamido)prop-1-ynyl side chain in derivative 3 retained the weak level of mycobacterial ThyX inhibition (40% inhibition at 50 μM). None of the synthesized derivatives displayed any significant inhibitory activity against mycobacterial ThyA. The compounds have also been evaluated as potential inhibitors of mycobacterial thymidine monophosphate kinase (TMPKmt). None of the derivatives showed any significant TMPKmt inhibition. However, replacement of C(6) of the natural substrate (dTMP) by a N-atom furnished 6-aza-dTMP (1b), which still was recognized as a substrate by TMPKmt.
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Affiliation(s)
- Martin Kögler
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Minderbroedersstraat 10, B-3000 Leuven
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243
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Abstract
Trypanosomatid parasitic protozoans of the genus Leishmania are autotrophic for both folate and unconjugated pteridines. Leishmania salvage these metabolites from their mammalian hosts and insect vectors through multiple transporters. Within the parasite, folates are reduced by a bifunctional DHFR (dihydrofolate reductase)-TS (thymidylate synthase) and by a novel PTR1 (pteridine reductase 1), which reduces both folates and unconjugated pteridines. PTR1 can act as a metabolic bypass of DHFR inhibition, reducing the effectiveness of existing antifolate drugs. Leishmania possess a reduced set of folate-dependent metabolic reactions and can salvage many of the key products of folate metabolism from their hosts. For example, they lack purine synthesis, which normally requires 10-formyltetrahydrofolate, and instead rely on a network of purine salvage enzymes. Leishmania elaborate at least three pathways for the synthesis of the key metabolite 5,10-methylene-tetrahydrofolate, required for the synthesis of thymidylate, and for 10-formyltetrahydrofolate, whose presumptive function is for methionyl-tRNAMet formylation required for mitochondrial protein synthesis. Genetic studies have shown that the synthesis of methionine using 5-methyltetrahydrofolate is dispensable, as is the activity of the glycine cleavage complex, probably due to redundancy with serine hydroxymethyltransferase. Although not always essential, the loss of several folate metabolic enzymes results in attenuation or loss of virulence in animal models, and a null DHFR-TS mutant has been used to induce protective immunity. The folate metabolic pathway provides numerous opportunities for targeted chemotherapy, with strong potential for 'repurposing' of compounds developed originally for treatment of human cancers or other infectious agents.
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244
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Yang Z, Liu HX, Zhang XF. 2R of Thymidylate Synthase 5'-untranslated Enhanced Region Contributes to Gastric Cancer Risk: a Meta-analysis. Asian Pac J Cancer Prev 2012; 13:1923-7. [DOI: 10.7314/apjcp.2012.13.5.1923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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245
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Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, Taylor H, Ebdon J, Jones BV. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. PLoS One 2012; 7:e35053. [PMID: 22558115 PMCID: PMC3338817 DOI: 10.1371/journal.pone.0035053] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/08/2012] [Indexed: 12/30/2022] Open
Abstract
Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome.
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Affiliation(s)
- Lesley A. Ogilvie
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Jonathan Caplin
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Cinzia Dedi
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - David Diston
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Elizabeth Cheek
- School of Computing, Engineering and Mathematics, University of Brighton, Brighton, United Kingdom
| | - Lucas Bowler
- Sussex Proteomics Centre, University of Sussex, Brighton, United Kingdom
| | - Huw Taylor
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Brian V. Jones
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- * E-mail:
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246
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Vijayaraj R, Devi MLV, Subramanian V, Chattaraj PK. 3D-QSAR studies on the inhibitory activity of trimethoprim analogues against Escherichia coli dihydrofolate reductase. Chem Biol Drug Des 2012; 79:935-42. [PMID: 22304783 DOI: 10.1111/j.1747-0285.2012.01351.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. To construct highly predictive 3D-QSAR models, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were used. The predicted models show statistically significant cross-validated and non-cross-validated correlation coefficient of r2 CV and r2 nCV, respectively. The final 3D-QSAR models were validated using structurally diverse test set compounds. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives. The results obtained from the CoMFA and CoMSIA study delineate the substituents on the trimethoprim analogues responsible for the enhanced potency and also provide valuable directions for the design of new trimethoprim analogues with improved affinity.
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Affiliation(s)
- Ramadoss Vijayaraj
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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247
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Mishanina TV, Koehn EM, Conrad JA, Palfey BA, Lesley SA, Kohen A. Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase. J Am Chem Soc 2012; 134:4442-8. [PMID: 22295882 DOI: 10.1021/ja2120822] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. It has recently been shown that FDTS catalysis does not rely on an enzymatic nucleophile and that the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and it has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist efforts directed toward the rational design of inhibitors as leads for future antibiotics.
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248
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Saeed M, Tewson TJ, Erdahl CE, Kohen A. A fast chemoenzymatic synthesis of [11C]-N5,N10-methylenetetrahydrofolate as a potential PET tracer for proliferating cells. Nucl Med Biol 2012; 39:697-701. [PMID: 22300960 DOI: 10.1016/j.nucmedbio.2011.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Thymidylate synthase and folate receptors are well-developed targets of cancer therapy. Discovery of a simple and fast method for the conversion of 11CH3Ito[11C]-formaldehyde (11CH2O) encouraged us to label the co-factor of this enzyme. Preliminary studies conducted on cell lines have demonstrated a preferential uptake of [11-14C]-(R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (14CH2H4folate) by cancerous cell vs. normal cells from the same organ (Saeed M., Sheff D. and Kohen A. Novel positron emission tomography tracer distinguishes normal from cancerous cells. J Biol Chem 2011;286:33872-33878), pointing out 11CH2H4folate as a positron emission tomography (PET) tracer for cancer imaging. Herein we report the synthesis of 11CH2H4folate, which may serve as a potential PET tracer. METHODS In a remotely controlled module, methyl iodide (11CH3I) was bubbled into a reaction vial containing trimethylamine N-oxide in N,N-Dimethylformamide (DMF) and heated to 70°C for 2 min. Formaldehyde (11CH2O) formed after the completion of reaction was then mixed with a solution of freshly prepared tetrahydrofolate (H4folate) by using a fast chemoenzymatic approach to accomplish synthesis of 11CH2H4folate. Purification of the product was carried out by loading the crude reaction mixture on a SAX cartridge, washing with water to remove unbound impurities and finally eluting with a saline solution. RESULTS The synthesis and purification of 11CH2H4folate were completed within 5 min. High-performance liquid chromatography analysis of the product after SAX purification indicates that more than 90% of the radioactivity that was retained on the SAX cartridge was in 11CH2H4folate, with minor (<10%) radioactivity due to unreacted 11CH2O. CONCLUSION We present a fast (∼5 min) synthesis and purification of 11CH2H4folate as a potential PET tracer. The final product is received in physiologically compatible buffer (100 mM sodium phosphate, pH 7.0 containing 500 mM NaCl) and ready for use in vivo.
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Affiliation(s)
- Muhammad Saeed
- Department of Chemistry, University of Iowa, IA 52242, USA
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Burand JP, Kim W, Afonso CL, Tulman ER, Kutish GF, Lu Z, Rock DL. Analysis of the genome of the sexually transmitted insect virus Helicoverpa zea nudivirus 2. Viruses 2012; 4:28-61. [PMID: 22355451 PMCID: PMC3280521 DOI: 10.3390/v4010028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/30/2011] [Accepted: 12/31/2011] [Indexed: 01/10/2023] Open
Abstract
The sexually transmitted insect virus Helicoverpa zea nudivirus 2 (HzNV-2) was determined to have a circular double-stranded DNA genome of 231,621 bp coding for an estimated 113 open reading frames (ORFs). HzNV-2 is most closely related to the nudiviruses, a sister group of the insect baculoviruses. Several putative ORFs that share homology with the baculovirus core genes were identified in the viral genome. However, HzNV-2 lacks several key genetic features of baculoviruses including the late transcriptional regulation factor, LEF-1 and the palindromic hrs, which serve as origins of replication. The HzNV-2 genome was found to code for three ORFs that had significant sequence homology to cellular genes which are not generally found in viral genomes. These included a presumed juvenile hormone esterase gene, a gene coding for a putative zinc-dependent matrix metalloprotease, and a major facilitator superfamily protein gene; all of which are believed to play a role in the cellular proliferation and the tissue hypertrophy observed in the malformation of reproductive organs observed in HzNV-2 infected corn earworm moths, Helicoverpa zea.
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Affiliation(s)
- John P. Burand
- Department of Plant, Soil and Insect Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA;
| | - Woojin Kim
- Department of Plant, Soil and Insect Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA;
| | - Claudio L. Afonso
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY 11944, USA; (C.L.A.); (E.R.T.); (G.F.K.); (Z.L.); (D.L.R.)
| | - Edan R. Tulman
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY 11944, USA; (C.L.A.); (E.R.T.); (G.F.K.); (Z.L.); (D.L.R.)
| | - Gerald F. Kutish
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY 11944, USA; (C.L.A.); (E.R.T.); (G.F.K.); (Z.L.); (D.L.R.)
| | - Zhiqiang Lu
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY 11944, USA; (C.L.A.); (E.R.T.); (G.F.K.); (Z.L.); (D.L.R.)
| | - Daniel L. Rock
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Greenport, NY 11944, USA; (C.L.A.); (E.R.T.); (G.F.K.); (Z.L.); (D.L.R.)
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Dąbrowska-Maś E, Frączyk T, Ruman T, Radziszewska K, Wilk P, Cieśla J, Zieliński Z, Jurkiewicz A, Gołos B, Wińska P, Wałajtys-Rode E, Leś A, Nizioł J, Jarmuła A, Stefanowicz P, Szewczuk Z, Rode W. Tyrosinenitration affects thymidylate synthase properties. Org Biomol Chem 2012; 10:323-31. [DOI: 10.1039/c1ob06360j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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