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Markowicz J, Uram Ł, Wołowiec S, Rode W. Biotin Transport-Targeting Polysaccharide-Modified PAMAM G3 Dendrimer as System Delivering α-Mangostin into Cancer Cells and C. elegans Worms. Int J Mol Sci 2021; 22:ijms222312925. [PMID: 34884739 PMCID: PMC8657743 DOI: 10.3390/ijms222312925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/21/2023] Open
Abstract
The natural xanthone α-mangostin (αM) exhibits a wide range of pharmacological activities, including antineoplastic and anti-nematode properties, but low water solubility and poor selectivity of the drug prevent its potential clinical use. Therefore, the targeted third-generation poly(amidoamine) dendrimer (PAMAM G3) delivery system was proposed, based on hyperbranched polymer showing good solubility, high biocompatibility and low immunogenicity. A multifunctional nanocarrier was prepared by attaching αM to the surface amine groups of dendrimer via amide bond in the ratio 5 (G32B12gh5M) or 17 (G32B10gh17M) residues per one dendrimer molecule. Twelve or ten remaining amine groups were modified by conjugation with D-glucoheptono-1,4-lactone (gh) to block the amine groups, and two biotin (B) residues as targeting moieties. The biological activity of the obtained conjugates was studied in vitro on glioma U-118 MG and squamous cell carcinoma SCC-15 cancer cells compared to normal fibroblasts (BJ), and in vivo on a model organism Caenorhabditis elegans. Dendrimer vehicle G32B12gh at concentrations up to 20 µM showed no anti-proliferative effect against tested cell lines, with a feeble cytotoxicity of the highest concentration seen only with SCC-15 cells. The attachment of αM to the vehicle significantly increased cytotoxic effect of the drug, even by 4- and 25-fold for G32B12gh5M and G32B10gh17M, respectively. A stronger inhibition of cells viability and influence on other metabolic parameters (proliferation, adhesion, ATP level and Caspase-3/7 activity) was observed for G32B10gh17M than for G32B12gh5M. Both bioconjugates were internalized efficiently into the cells. Similarly, the attachment of αM to the dendrimer vehicle increased its toxicity for C. elegans. Thus, the proposed α-mangostin delivery system allowed the drug to be more effective in the dendrimer-bound as compared to free state against both cultured the cancer cells and model organism, suggesting that this treatment is promising for anticancer as well as anti-nematode chemotherapy.
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Affiliation(s)
- Joanna Markowicz
- Faculty of Chemistry, Rzeszow University of Technology, 6 Powstancow Warszawy Ave., 35-959 Rzeszow, Poland;
- Correspondence: (J.M.); (W.R.)
| | - Łukasz Uram
- Faculty of Chemistry, Rzeszow University of Technology, 6 Powstancow Warszawy Ave., 35-959 Rzeszow, Poland;
| | - Stanisław Wołowiec
- Medical College, Rzeszow University, 1a Warzywna Str., 35-310 Rzeszow, Poland;
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
- Correspondence: (J.M.); (W.R.)
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Prokopowicz M, Jarmuła A, Casamayou-Boucau Y, Gordon F, Ryder A, Sobich J, Maj P, Cieśla J, Zieliński Z, Fita P, Rode W. Advanced Spectroscopy and APBS Modeling for Determination of the Role of His190 and Trp103 in Mouse Thymidylate Synthase Interaction with Selected dUMP Analogues. Int J Mol Sci 2021; 22:2661. [PMID: 33800923 PMCID: PMC7962005 DOI: 10.3390/ijms22052661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
A homo-dimeric enzyme, thymidylate synthase (TS), has been a long-standing molecular target in chemotherapy. To further elucidate properties and interactions with ligands of wild-type mouse thymidylate synthase (mTS) and its two single mutants, H190A and W103G, spectroscopic and theoretical investigations have been employed. In these mutants, histidine at position 190 and tryptophan at position 103 are substituted with alanine and glycine, respectively. Several emission-based spectroscopy methods used in the paper demonstrate an especially important role for Trp 103 in TS ligands binding. In addition, the Advanced Poisson-Boltzmann Solver (APBS) results show considerable differences in the distribution of electrostatic potential around Trp 103, as compared to distributions observed for all remaining Trp residues in the mTS family of structures. Together, spectroscopic and APBS results reveal a possible interplay between Trp 103 and His190, which contributes to a reduction in enzymatic activity in the case of H190A mutation. Comparison of electrostatic potential for mTS complexes, and their mutants, with the substrate, dUMP, and inhibitors, FdUMP and N4-OH-dCMP, suggests its weaker influence on the enzyme-ligand interactions in N4OH-dCMP-mTS compared to dUMP-mTS and FdUMP-mTS complexes. This difference may be crucial for the explanation of the "abortive reaction" inhibitory mechanism of N4OH-dCMP towards TS. In addition, based on structural analyses and the H190A mutant capacity to form a denaturation-resistant complex with N4-OH-dCMP in the mTHF-dependent reaction, His190 is apparently responsible for a strong preference of the enzyme active center for the anti rotamer of the imino inhibitor form.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, MISMaP College, University of Warsaw, ul. Banacha 2C, 02-097 Warsaw, Poland
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Yannick Casamayou-Boucau
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Fiona Gordon
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Alan Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Justyna Sobich
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Maj
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Joanna Cieśla
- Faculty of Chemistry, Warsaw University of Technology, ul Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Fita
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
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Maj P, Mori M, Sobich J, Markowicz J, Uram Ł, Zieliński Z, Quaglio D, Calcaterra A, Cau Y, Botta B, Rode W. Alvaxanthone, a Thymidylate Synthase Inhibitor with Nematocidal and Tumoricidal Activities. Molecules 2020; 25:molecules25122894. [PMID: 32586022 PMCID: PMC7356228 DOI: 10.3390/molecules25122894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 11/16/2022] Open
Abstract
With the aim to identify novel inhibitors of parasitic nematode thymidylate synthase (TS), we screened in silico an in-house library of natural compounds, taking advantage of a model of nematode TS three-dimensional (3D) structure and choosing candidate compounds potentially capable of enzyme binding/inhibition. Selected compounds were tested as (i) inhibitors of the reaction catalyzed by TSs of different species, (ii) agents toxic to a nematode parasite model (C. elegans grown in vitro), (iii) inhibitors of normal human cell growth, and (iv) antitumor agents affecting human tumor cells grown in vitro. The results pointed to alvaxanthone as a relatively strong TS inhibitor that causes C. elegans population growth reduction with nematocidal potency similar to the anthelmintic drug mebendazole. Alvaxanthone also demonstrated an antiproliferative effect in tumor cells, associated with a selective toxicity against mitochondria observed in cancer cells compared to normal cells.
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Affiliation(s)
- Piotr Maj
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland; (P.M.); (J.S.); (Z.Z.)
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy; (M.M.); (Y.C.)
| | - Justyna Sobich
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland; (P.M.); (J.S.); (Z.Z.)
| | - Joanna Markowicz
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland; (J.M.); (Ł.U.)
| | - Łukasz Uram
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland; (J.M.); (Ł.U.)
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland; (P.M.); (J.S.); (Z.Z.)
| | - Deborah Quaglio
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018–2022, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.Q.); (A.C.); (B.B.)
| | - Andrea Calcaterra
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018–2022, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.Q.); (A.C.); (B.B.)
| | - Ylenia Cau
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, via Aldo Moro 2, 53100 Siena, Italy; (M.M.); (Y.C.)
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018–2022, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.Q.); (A.C.); (B.B.)
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland; (P.M.); (J.S.); (Z.Z.)
- Correspondence: ; Tel.: +48-608-351-155; Fax: +48-22-822-5342
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Markowicz J, Uram Ł, Sobich J, Mangiardi L, Maj P, Rode W. Antitumor and anti-nematode activities of α-mangostin. Eur J Pharmacol 2019; 863:172678. [PMID: 31542481 DOI: 10.1016/j.ejphar.2019.172678] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
α-Mangostin, one of the major xanthones isolated from pericarp of mangosteen (Garcinia mangostana Linn), exhibits a wide range of pharmacological activities, including antioxidant, anti-inflammatory, antimicrobial as well as anticancer, both in in vitro and in vivo studies. In the present study, α-mangostin' anti-cancer and anti-parasitic properties were tested in vitro against three human cell lines, including squamous carcinoma (SCC-15) and glioblastoma multiforme (U-118 MG), compared to normal skin fibroblasts (BJ), and in vivo against Caenorhabditis elegans. The drug showed cytotoxic activity, manifested by decrease of cell viability, inhibition of proliferation, induction of apoptosis and reduction of adhesion at concentrations lower than 10 μM (the IC50 values were 6.43, 9.59 and 8.97 μM for SCC-15, U-118 MG and BJ, respectively). The toxicity, causing cell membrane disruption and mitochondria impairment, was selective against squamous carcinoma with regard to normal cells. Moreover, for the first time anti-nematode activity of α-mangostin toward C. elegans was described (the LC50 = 3.8 ± 0.5 μM), with similar effect exerted by mebendazole, a well-known anthelmintic drug.
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Affiliation(s)
- Joanna Markowicz
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959, Rzeszów, Poland.
| | - Łukasz Uram
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959, Rzeszów, Poland
| | - Justyna Sobich
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Laura Mangiardi
- Center for Life NanoScience, CLNS@Sapienza, Italian Institute of Technology (IIT), Viale Regina Elena 291, 00161 Rome, Italy and Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Piotr Maj
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Wojciech Rode
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959, Rzeszów, Poland; Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
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Sobich J, Prokopowicz M, Maj P, Wilk P, Zieliński Z, Frączyk T, Rode W. Thymidylate synthase-catalyzed, tetrahydrofolate-dependent self-inactivation by 5-FdUMP. Arch Biochem Biophys 2019; 674:108106. [PMID: 31520592 DOI: 10.1016/j.abb.2019.108106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022]
Abstract
In view of previous crystallographic studies, N4-hydroxy-dCMP, a slow-binding thymidylate synthase inhibitor apparently caused "uncoupling" of the two thymidylate synthase-catalyzed reactions, including the N5,10-methylenetetrahydrofolate one-carbon group transfer and reduction, suggesting the enzyme's capacity to use tetrahydrofolate as a cofactor reducing the pyrimidine ring C(5) in the absence of the 5-methylene group. Testing the latter interpretation, a possibility was examined of a TS-catalyzed covalent self-modification/self-inactivation with certain pyrimidine deoxynucleotides, including 5-fluoro-dUMP and N4-hydroxy-dCMP, that would be promoted by tetrahydrofolate and accompanied with its parallel oxidation to dihydrofolate. Electrophoretic analysis showed mouse recombinant TS protein to form, in the presence of tetrahydrofolate, a covalently bound, electrophoretically separable 5-fluoro-dUMP-thymidylate synthase complex, similar to that produced in the presence of N5,10-methylenetetrahydrofolate. Further studies of the mouse enzyme binding with 5-fluoro-dUMP/N4-hydroxy-dCMP by TCA precipitation of the complex on filter paper showed it to be tetrahydrofolate-promoted, as well as to depend on both time in the range of minutes and the enzyme molecular activity, indicating thymidylate synthase-catalyzed reaction to be responsible for it. Furthermore, the tetrahydrofolate- and time-dependent, covalent binding by thymidylate synthase of each 5-fluoro-dUMP and N4-hydroxy-dCMP was shown to be accompanied by the enzyme inactivation, as well as spectrophotometrically confirmed dihydrofolate production, the latter demonstrated to depend on the reaction time, thymidylate synthase activity and temperature of the incubation mixture, further documenting its catalytic character.
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Affiliation(s)
- Justyna Sobich
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Prokopowicz
- Warsaw University, College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, and Faculty of Physics, Warszawa, Poland
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tomasz Frączyk
- Medical University of Warsaw, Department of Immunology, Transplantology and Internal Medicine, Warszawa, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
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Dabrowska M, Uram L, Zielinski Z, Rode W, Sikora E. Oxidative stress and inhibition of nitric oxide generation underlie methotrexate-induced senescence in human colon cancer cells. Mech Ageing Dev 2018; 170:22-29. [DOI: 10.1016/j.mad.2017.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/10/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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Uram Ł, Nizioł J, Maj P, Sobich J, Rode W, Ruman T. N(4)-[B-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan)methyl]-2'-deoxycytidine as a potential boron delivery agent with respect to glioblastoma. Biomed Pharmacother 2017; 95:749-755. [PMID: 28888921 DOI: 10.1016/j.biopha.2017.08.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/21/2017] [Accepted: 08/29/2017] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a central nervous system tumor of grade IV, according to the WHO classification, extremely resistant to all currently used forms of therapy, including resection, radiotherapy, chemotherapy or combined therapy. Therefore, more effective treatment strategies of this tumor are needed, with boron neutron capture therapy (BNCT) being a potential solution, provided a proper cancer cells-targeted 10B delivery agent is found. In search of such an agent, toxicity and capacity to target DNA of a boronated derivative of 2'-deoxycytidine, N(4)-[B-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan)methyl]-2'-deoxycytidine (1), was tested against human tumor vs. normal cells. The present in vitro results revealed 1 to show low toxicity for human U-118 MG glioma cells (in the mM range) and even by 3-4 - fold lower against normal human fibroblasts. In accord, induction of apoptosis dependent on caspase-3 and caspase-7 was detected at high (>20mM) concentration of 1. Although demonstrated to be susceptible to phosphorylation by human deoxycytidine kinase and to undergo incorporation in cellular DNA, the boron analogue did not disturb cell proliferation when applied at non-toxic concentrations and showed low toxicity to a model metazoan organism, Caenorhabditis elegans. Thus, N(4)-[B-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan)methyl]-2'-deoxycytidine appears a promising candidate for a 10B delivery agent to be used in BNCT, with C. elegans indicated as a good model for in vivo studies.
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Affiliation(s)
- Łukasz Uram
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland.
| | - Joanna Nizioł
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
| | - Piotr Maj
- Nencki Institute of Experimental Biology,3 Pasteur Street, 02-093 Warsaw, Poland
| | - Justyna Sobich
- Nencki Institute of Experimental Biology,3 Pasteur Street, 02-093 Warsaw, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology,3 Pasteur Street, 02-093 Warsaw, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
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Jarmuła A, Wilk P, Maj P, Ludwiczak J, Dowierciał A, Banaszak K, Rypniewski W, Cieśla J, Dąbrowska M, Frączyk T, Bronowska AK, Jakowiecki J, Filipek S, Rode W. Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS. J Mol Graph Model 2017; 77:33-50. [PMID: 28826032 DOI: 10.1016/j.jmgm.2017.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 01/01/2023]
Abstract
Three crystal structures are presented of nematode thymidylate synthases (TS), including Caenorhabditis elegans (Ce) enzyme without ligands and its ternary complex with dUMP and Raltitrexed, and binary complex of Trichinella spiralis (Ts) enzyme with dUMP. In search of differences potentially relevant for the development of species-specific inhibitors of the nematode enzyme, a comparison was made of the present Ce and Ts enzyme structures, as well as binary complex of Ce enzyme with dUMP, with the corresponding mammalian (human, mouse and rat) enzyme crystal structures. To complement the comparison, tCONCOORD computations were performed to evaluate dynamic behaviors of mammalian and nematode TS structures. Finally, comparative molecular docking combined with molecular dynamics and free energy of binding calculations were carried out to search for ligands showing selective affinity to T. spiralis TS. Despite an overall strong similarity in structure and dynamics of nematode vs mammalian TSs, a pool of ligands demonstrating predictively a strong and selective binding to TsTS has been delimited. These compounds, the E63 family, locate in the dimerization interface of TsTS where they exert species-specific interactions with certain non-conserved residues, including hydrogen bonds with Thr174 and hydrophobic contacts with Phe192, Cys191 and Tyr152. The E63 family of ligands opens the possibility of future development of selective inhibitors of TsTS and effective agents against trichinellosis.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Macromolecular Crystallography (BESSY-MX), Berlin, Germany
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Jan Ludwiczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, 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
| | - Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tomasz Frączyk
- 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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Dowierciał A, Jarmuła A, Wilk P, Rypniewski W, Kowalska M, Frączyk T, Cieśla J, Rode W. Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme. Struct Chem 2016. [DOI: 10.1007/s11224-016-0840-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Dabrowska M, Skoneczny M, Zielinski Z, Rode W. Wnt signaling in regulation of biological functions of the nurse cell harboring Trichinella spp. Parasit Vectors 2016; 9:483. [PMID: 27589866 PMCID: PMC5010673 DOI: 10.1186/s13071-016-1770-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/22/2016] [Indexed: 01/11/2023] Open
Abstract
Background The nurse cell (NC) constitutes in mammalian skeletal muscles a confined intracellular niche to support the metabolic needs of muscle larvae of Trichinella spp. encapsulating species. The main biological functions of NC were identified as hypermitogenic growth arrest and pro-inflammatory phenotype, both inferred to depend on AP-1 (activator protein 1) transcription factor. Since those functions, as well as AP-1 activity, are known to be regulated among other pathways, also by Wnt (Wingless-Type of Mouse Mammary Tumor Virus Integration Site) signaling, transcription profiling of molecules participating in Wnt signaling cascades in NC, was performed. Methods Wnt signaling-involved gene expression level was measured by quantitative RT-PCR approach with the use of Qiagen RT2 Profiler PCR Arrays and complemented by that obtained by searching microarray data sets characterizing NC transcriptome. Results The genes involved in inhibition of canonical Wnt/β-catenin signaling cascade as well as leading to β-catenin degradation were found expressed in NC at high level, indicating inhibition of this cascade activity. High expression in NC of genes transmitting the signal of Wnt non-canonical signaling cascades leading to activation of AP-1 transcription factor, points to predominant role of non-canonical Wnt signaling in a long term maintenance of NC biological functions. Conclusions Canonical Wnt/β-catenin signaling cascade is postulated to play a role at the early stages of NC formation when muscle regeneration process is triggered. Following mis-differentiation of infected myofiber and setting of NC functional specificity, are inferred to be controlled among other pathways, by Wnt non-canonical signaling cascades. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1770-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magdalena Dabrowska
- Laboratory of Comparative Enzymology, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., Warsaw, 02-093, Poland.
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego St., Warsaw, 02-106, Poland
| | - Zbigniew Zielinski
- Laboratory of Comparative Enzymology, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., Warsaw, 02-093, Poland
| | - Wojciech Rode
- Laboratory of Comparative Enzymology, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., Warsaw, 02-093, Poland
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Antosiewicz A, Jarmuła A, Przybylska D, Mosieniak G, Szczepanowska J, Kowalkowska A, Rode W, Cieśla J. Human dihydrofolate reductase and thymidylate synthase form a complex in vitro and co-localize in normal and cancer cells. J Biomol Struct Dyn 2016; 35:1474-1490. [PMID: 27187663 DOI: 10.1080/07391102.2016.1186560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Enzymes involved in thymidylate biosynthesis, thymidylate synthase (TS), and dihydrofolate reductase (DHFR) are well-known targets in cancer chemotherapy. In this study, we demonstrated for the first time, that human TS and DHFR form a strong complex in vitro and co-localize in human normal and colon cancer cell cytoplasm and nucleus. Treatment of cancer cells with methotrexate or 5-fluorouracil did not affect the distribution of either enzyme within the cells. However, 5-FU, but not MTX, lowered the presence of DHFR-TS complex in the nucleus by 2.5-fold. The results may suggest the sequestering of TS by FdUMP in the cytoplasm and thereby affecting the translocation of DHFR-TS complex to the nucleus. Providing a strong likelihood of DHFR-TS complex formation in vivo, the latter complex is a potential new drug target in cancer therapy. In this paper, known 3D structures of human TS and human DHFR, and some protozoan bifunctional DHFR-TS structures as templates, are used to build an in silico model of human DHFR-TS complex structure, consisting of one TS dimer and two DHFR monomers. This complex structure may serve as an initial 3D drug target model for prospective inhibitors targeting interfaces between the DHFR and TS enzymes.
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Affiliation(s)
- Anna Antosiewicz
- a Faculty of Chemistry , Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw , Poland
| | - Adam Jarmuła
- b Nencki Institute of Experimental Biology , Polish Academy of Sciences , Pasteura 3, 02-093 , Warsaw , Poland
| | - Dorota Przybylska
- b Nencki Institute of Experimental Biology , Polish Academy of Sciences , Pasteura 3, 02-093 , Warsaw , Poland
| | - Grażyna Mosieniak
- b Nencki Institute of Experimental Biology , Polish Academy of Sciences , Pasteura 3, 02-093 , Warsaw , Poland
| | - Joanna Szczepanowska
- b Nencki Institute of Experimental Biology , Polish Academy of Sciences , Pasteura 3, 02-093 , Warsaw , Poland
| | - Anna Kowalkowska
- a Faculty of Chemistry , Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw , Poland
| | - Wojciech Rode
- b Nencki Institute of Experimental Biology , Polish Academy of Sciences , Pasteura 3, 02-093 , Warsaw , Poland
| | - Joanna Cieśla
- a Faculty of Chemistry , Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw , Poland
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12
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Cieśla J, Mitkowski P, Gojdź A, Jarmuła A, Rode W. Overproduction in bacteria of mouse thymidylate synthase forms with point mutations in N4-hydroxy-dCMP binding site. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Serça D, Deshmukh C, Pighini S, Oudone P, Vongkhamsao A, Guédant P, Rode W, Godon A, Chanudet V, Descloux S, Guérin F. Nam Theun 2 Reservoir four years after commissioning: significance of drawdown methane emissions and other pathways. ACTA ACUST UNITED AC 2016. [DOI: 10.1051/hydro/2016001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Ludwiczak J, Maj P, Wilk P, Frączyk T, Ruman T, Kierdaszuk B, Jarmuła A, Rode W. Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N(4)-hydroxy-dCMP. Mol Biosyst 2016; 12:1333-41. [PMID: 26916840 DOI: 10.1039/c6mb00026f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Considering its importance for chemotherapeutic drug resistance, the possible effect of thymidylate synthase inhibition by post-translational modification was tested, e.g. phosphorylation, by comparing sensitivities to inhibition by two slow-binding inhibitors, 5-fluoro-dUMP and N(4)-hydroxy-dCMP, of two fractions of purified recombinant mouse enzyme preparations, phosphorylated and non-phosphorylated, separated by metal oxide/hydroxide affinity chromatography on Al(OH)3 beads. The modification, found to concern histidine residues and influence kinetic properties by lowering Vmax, altered both the pattern of dependence of the inactivation rate on time from linear to biphasic, as well as slow-binding inhibition parameters, with each inhibitor studied. Being present on only one subunit of at least a great majority of phosphorylated enzyme molecules, it probably introduced dimer asymmetry, causing the altered time dependence of the inactivation rate pattern (biphasic with the phosphorylated enzyme) and resulting in asymmetric binding of each inhibitor studied. The latter is reflected by the ternary complexes, stable under denaturing conditions, formed by only the non-phosphorylated subunit of the phosphorylated enzyme with each of the two inhibitors and N(5,10)-methylenetetrahydrofolate. Inhibition of the phosphorylated enzyme by N(4)-hydroxy-dCMP was found to be strongly dependent on [Mg(2+)], cations demonstrated previously to also influence the activity of endogenous mouse TS isolated from tumour cells.
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Affiliation(s)
- Jan Ludwiczak
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warszawa, Poland.
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15
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Frączyk T, Ruman T, Wilk P, Palmowski P, Rogowska-Wrzesinska A, Cieśla J, Zieliński Z, Nizioł J, Jarmuła A, Maj P, Gołos B, Wińska P, Ostafil S, Wałajtys-Rode E, Shugar D, Rode W. Properties of phosphorylated thymidylate synthase. Biochim Biophys Acta 2015; 1854:1922-1934. [PMID: 26315778 DOI: 10.1016/j.bbapap.2015.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/24/2015] [Accepted: 08/18/2015] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichinella spiralis and Caenorhabditis elegans TSs, expressed in Escherichia coli, the phosphorylated, compared to non-phosphorylated recombinant enzyme forms, showed a decrease in Vmax(app), bound their cognate mRNA (only rat enzyme studied), and repressed translation of their own and several heterologous mRNAs (human, rat and mouse enzymes studied). However, attempts to determine the modification site(s), whether endogenously expressed in mammalian cells, or recombinant proteins, did not lead to unequivocal results. Comparative ESI-MS/analysis of IEF fractions of TS preparations from parental and FdUrd-resistant mouse leukemia L1210 cells, differing in sensitivity to inactivation by FdUMP, demonstrated phosphorylation of Ser(10) and Ser(16) in the resistant enzyme only, although PGS staining pointed to the modification of both L1210 TS proteins. The TS proteins phosphorylated in bacterial cells were shown by (31)P NMR to be modified only on histidine residues, like potassium phosphoramidate (KPA)-phosphorylated TS proteins. NanoLC-MS/MS, enabling the use of CID and ETD peptide fragmentation methods, identified several phosphohistidine residues, but certain phosphoserine and phosphothreonine residues were also implicated. Molecular dynamics studies, based on the mouse TS crystal structure, allowed one to assess potential of several phosphorylated histidine residues to affect catalytic activity, the effect being phosphorylation site dependent.
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Affiliation(s)
- Tomasz Frączyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Rzeszów, Poland
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Palmowski
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Nizioł
- Rzeszów University of Technology, Faculty of Chemistry, Rzeszów, Poland
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Gołos
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Patrycja Wińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sylwia Ostafil
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Wałajtys-Rode
- Warsaw University of Technology, Faculty of Chemistry, Institute of Biotechnology, Warsaw, Poland
| | - David Shugar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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Chanudet V, Guédant P, Rode W, Godon A, Guérin F, Serça D, Deshmukh C, Descloux S. Evolution of the physico-chemical water quality in the Nam Theun 2 Reservoir and downstream rivers for the first 5 years after impoundment. ACTA ACUST UNITED AC 2015. [DOI: 10.1051/hydro/2015001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Sekuła J, Nizioł J, Rode W, Ruman T. Gold nanoparticle-enhanced target (AuNPET) as universal solution for laser desorption/ionization mass spectrometry analysis and imaging of low molecular weight compounds. Anal Chim Acta 2015; 875:61-72. [PMID: 25937107 DOI: 10.1016/j.aca.2015.01.046] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 11/16/2022]
Abstract
Preparation is described of a durable surface of cationic gold nanoparticles (AuNPs), covering commercial and custom-made MALDI targets, along with characterization of the nanoparticle surface properties and examples of the use in MS analyses and MS imaging (IMS) of low molecular weight (LMW) organic compounds. Tested compounds include nucleosides, saccharides, amino acids, glycosides, and nucleic bases for MS measurements, as well as over one hundred endogenous compounds in imaging experiment. The nanoparticles covering target plate were enriched in sodium in order to promote sodium-adduct formation. The new surface allows fast analysis, high sensitivity of detection and high mass determination accuracy. Example of application of new Au nanoparticle-enhanced target for fast and simple MS imaging of a fingerprint is also presented.
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Affiliation(s)
- Justyna Sekuła
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland
| | - Joanna Nizioł
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland.
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18
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Sekuła J, Nizioł J, Rode W, Ruman T. Silver nanostructures in laser desorption/ionization mass spectrometry and mass spectrometry imaging. Analyst 2015; 140:6195-209. [DOI: 10.1039/c5an00943j] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Silver nanoparticles have been successfully applied as a matrix replacement for the laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF-MS).
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Affiliation(s)
- Justyna Sekuła
- Rzeszów University of Technology
- Faculty of Chemistry
- Bioorganic Chemistry Laboratory
- 35-959 Rzeszów
- Poland
| | - Joanna Nizioł
- Rzeszów University of Technology
- Faculty of Chemistry
- Bioorganic Chemistry Laboratory
- 35-959 Rzeszów
- Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology
- 02-093 Warsaw
- Poland
| | - Tomasz Ruman
- Rzeszów University of Technology
- Faculty of Chemistry
- Bioorganic Chemistry Laboratory
- 35-959 Rzeszów
- Poland
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19
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Rode W, Jarmuńa A. [Thymidylate synthase-catalyzed reaction mechanism]. Postepy Biochem 2015; 61:274-283. [PMID: 26677574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Thymidylate synthase ThyA (EC 2.1.1.45;-encoded by the Tyms gene), having been for 60 years a molecular target in chemotherapy, catalyses the dUMP pyrimidine ring C(5) methylation reaction, encompassing a transfer of one-carbon group (the methylene one, thus at the formaldehyde oxidation level) from 6R-N5,10-methylenetetrahydrofolate, coupled with a reduction of this group to the methyl one, with concomitant generation of 7,8-dihydrofolate and thymidylate. New facts are presented, concerning (i) molecular mechanism of the catalyzed reaction, including the substrate selectivity mechanism, (ii) mechanism of inhibition by a particular inhibitor, N4-hydroxy-dCMP, (iii) structural properties of the enzyme, (iv) cellular localization, (v) potential posttranslational modifications of the enzyme protein and their influence on the catalytic properties and (vi) non-catalytic activities of the enzyme.
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Nizioł J, Zieliński Z, Leś A, Dąbrowska M, Rode W, Ruman T. Synthesis, reactivity and biological activity of N(4)-boronated derivatives of 2'-deoxycytidine. Bioorg Med Chem 2014; 22:3906-12. [PMID: 24999002 DOI: 10.1016/j.bmc.2014.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/02/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022]
Abstract
By seeking new stable boron-containing nucleoside derivatives, potential BNCT boron delivery agents, a novel synthetic approach was tested, aimed at a boron attachment via a single bond to an aliphatic carbon of sp(3) hybridization. The latter allowed successful modification of deoxycytidine in the reaction with 2-(iodomethyl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane of the deoxynucleoside amino group. For new compounds, detailed NMR, LDI HRMS (Laser Desorption/Ionization High-Resolution Mass Spectrometry) analyses along with in vivo phosphorylation studies, toxicity assays and DFT modelling are presented.
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Affiliation(s)
- Joanna Nizioł
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Andrzej Leś
- University of Warsaw, Faculty of Chemistry, Quantum Chemistry Laboratory, 1 Pasteur Street, Warsaw 02-093, Poland; Pharmaceutical Research Institute, Rydygier Street 8, Warsaw 01-793, Poland
| | - Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Bioorganic Chemistry Laboratory, 6 Powstańców Warszawy Ave., 35-959 Rzeszów, Poland.
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21
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Jagielska E, Płucienniczak A, Dąbrowska M, Dowierciał A, Rode W. Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence. Parasit Vectors 2014; 7:175. [PMID: 24716800 PMCID: PMC4022200 DOI: 10.1186/1756-3305-7-175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/27/2014] [Indexed: 12/31/2022] Open
Abstract
Background Thymidylate synthase is a housekeeping gene, designated ancient due to its role in DNA synthesis and ubiquitous phyletic distribution. The genomic sequences were characterized coding for thymidylate synthase in two species of the genus Trichinella, an encapsulating T. spiralis and a non-encapsulating T. pseudospiralis. Methods Based on the sequence of parasitic nematode Trichinella spiralis thymidylate synthase cDNA, PCR techniques were employed. Results Each of the respective gene structures encompassed 6 exons and 5 introns located in conserved sites. Comparison with the corresponding gene structures of other eukaryotic species revealed lack of common introns that would be shared among selected fungi, nematodes, mammals and plants. The two deduced amino acid sequences were 96% identical. In addition to the thymidylate synthase gene, the intron-less retrocopy, i.e. a processed pseudogene, with sequence identical to the T. spiralis gene coding region, was found to be present within the T. pseudospiralis genome. This pseudogene, instead of the gene, was confirmed by RT-PCR to be expressed in the parasite muscle larvae. Conclusions Intron load, as well as distribution of exon and intron phases in thymidylate synthase genes from various sources, point against the theory of gene assembly by the primordial exon shuffling and support the theory of evolutionary late intron insertion into spliceosomal genes. Thymidylate synthase pseudogene expressed in T. pseudospiralis muscle larvae is designated a retrogene.
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Affiliation(s)
| | | | | | | | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dąbrowska M, Gołos B, Wałajtys-Rode E, Zieliński Z, Wińska P, Cieśla J, Moczoń T, Rode W. Uncommon and parallel developmental patterns of thymidylate synthase expression and localization in Trichinella spiralis and Caenorhabditis elegans. Pteridines 2013. [DOI: 10.1515/pterid-2013-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Trichinella spiralis is a parasitic nematode causing trichinellosis, a serious disease, and Caenorhabditis elegans is a free-living nematode, which is used as a model in parasitological studies. High levels of thymidylate synthase (EC 2.1.1.45; ThyA) and certain other enzymes involved in thymidylate biosynthesis were found throughout T. spiralis and C. elegans developmental cycles, including developmentally arrested forms, that is, T. spiralis muscle larva and C. elegans dauer larva. As ThyA activity is characteristic for cells that left the G0 phase of the cell cycle, an exceptional regulation of the cell cycle in nematodes is suggested, manifested by a global cell cycle arrest in developmentally arrested larvae of the two species. ThyA immunolocalization during development of T. spiralis and C. elegans revealed the presence of high enzyme levels not only in the developing embryos, where it was expected, but also in gonad primordia, egg and sperm cells, nerve ring and secretory cells, opening to T. spiralis esophagus and C. elegans pharynx, where it may point to those cell populations remaining cell cycle arrested.
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Affiliation(s)
- Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Barbara Gołos
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | | | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Patrycja Wińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tadeusz Moczoń
- Institute of Parasitology, Polish Academy of Sciences, Warszawa, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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Dowierciał A, Wilk P, Rypniewski W, Frączyk T, Jarmuła A, Banaszak K, Dąbrowska M, Cieśla J, Rode W. Crystal structures of thymidylate synthase from nematodes, Trichinella spiralis and Caenorhabditis elegans, as a potential template for species-specific drug design. Pteridines 2013. [DOI: 10.1515/pterid-2013-0011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Crystal structures were solved of the binary complexes Trichinella spiralis and Caenorhabditis elegans thymidylate synthases with deoxyuridine monophosphate (dUMP), with crystals obtained by the vapor diffusion method in hanging drops. For the T. spiralis thymidylate synthase-dUMP complex, the diffraction data were collected at the BESSY Synchrotron to 1.9 Å resolution. The crystal belongs to the space group P1 with two dimers in the asymmetric unit (ASU). For the C. elegans TS-dUMP complex crystal, the diffraction data were collected at the BESSY Synchrotron to 2.48 Å resolution, and the crystal belongs to the space group P 32 2 1, with two monomers (one dimer) in the ASU. Structural comparisons were made of both structures and each of them with the corresponding mouse thymidylate synthase complex.
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Affiliation(s)
- Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Frączyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Joanna Cieśla
- 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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Dowierciał A, Jarmuła A, Wilk P, Rypniewski W, Kierdaszuk B, Rode W. Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate. Pteridines 2013. [DOI: 10.1515/pterid-2013-0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
To solve the inhibition mechanism of thymidylate synthase (TS) by N4-hydroxy-dCMP (N4-OH-dCMP), crystallographic studies were undertaken. Structures of three mouse TS (mTS) complexes with the inhibitor were solved, based on crystals formed by the enzyme protein in the presence of either only N4-OH-dCMP [crystal A, belonging to the space group C 1 2 1, with two monomers in asymmetric unit (ASU), measured to 1.75 Å resolution] or both N4-OH-dCMP and N5,10
-methylenetetrahydrofolate (mTHF) (crystals B and C, both belonging to the space group C 2 2 21, each with a single monomer in ASU, measured to resolution of 1.35 Å and 1.17 Å, respectively). Whereas crystal A-based structure revealed the mTS-N4-OH-dCMP binary complex, as expected, crystals B- and C-based structures showed the enzyme to be involved in a ternary complex with N4-OH-dCMP and noncovalently bound dihydrofolate (DHF), instead of expected mTHF, suggesting the inhibition to be a consequence of an abortive enzyme-catalyzed reaction, involving a transfer of the one-carbon group to a hitherto unknown site and oxidation of THF to DHF. Moreover, both C(5) and C(6) inhibitor atoms showed sp3 hybridization, suggesting C(5) reduction, with no apparent indication of C(5) proton release. In accordance with our previous results, in all subunits of these structures the inhibitor molecule was identified as the anti rotamer of imino tautomer, forming, similar to deoxyuridine monophosphate, two hydrogen bonds with a conservative asparagine (mouse Asn220) side chain.
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Affiliation(s)
- Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Borys Kierdaszuk
- Warsaw University, Institute of Experimental Physics, Warsaw, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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Affiliation(s)
- Joanna Nizioł
- Bioorganic Chemistry Laboratory,
Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Avenue, 35-959 Rzeszów,
Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw,
Poland
| | - Barbara Laskowska
- The State Higher School of Technology and Economics, 16 Czarnieckiego
Street, 37-500 Jarosław, Poland
| | - Tomasz Ruman
- Bioorganic Chemistry Laboratory,
Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Avenue, 35-959 Rzeszów,
Poland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dabrowska M, Skoneczny M, Rode W. Functional gene expression profile underlying methotrexate-induced senescence in human colon cancer cells. Tumour Biol 2011; 32:965-76. [PMID: 21678067 PMCID: PMC3156317 DOI: 10.1007/s13277-011-0198-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/27/2011] [Indexed: 11/21/2022] Open
Abstract
Cellular functions accompanying establishment of premature senescence in methotrexate-treated human colon cancer C85 cells are deciphered in the present study from validated competitive expression microarray data, analyzed with the use of Ingenuity Pathways Analysis (IPA) software. The nitrosative/oxidative stress, inferred from upregulated expression of inducible nitric oxide synthase (iNOS) and mitochondrial dysfunction-associated genes, including monoamine oxidases MAOA and MAOB, β-amyloid precursor protein (APP) and presenilin 1 (PSEN1), is identified as the main determinant of signaling pathways operating during senescence establishment. Activation of p53-signaling pathway is found associated with both apoptotic and autophagic components contributing to this process. Activation of nuclear factor κB (NF-κB), resulting from interferon γ (IFNγ), integrin, interleukin 1β (IL-1β), IL-4, IL-13, IL-22, Toll-like receptors (TLRs) 1, 2 and 3, growth factors and tumor necrosis factor (TNF) superfamily members signaling, is found to underpin inflammatory properties of senescent C85 cells. Upregulation of p21-activated kinases (PAK2 and PAK6), several Rho molecules and myosin regulatory light chains MYL12A and MYL12B, indicates acquisition of motility by those cells. Mitogen-activated protein kinase p38 MAPK β, extracellular signal-regulated kinases ERK2 and ERK5, protein kinase B AKT1, as well as calcium, are identified as factors coordinating signaling pathways in senescent C85 cells.
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Affiliation(s)
- Magdalena Dabrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093, Warsaw, Poland.
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Cieśla J, Frączyk T, Rode W. Phosphorylation of basic amino acid residues in proteins: important but easily missed. Acta Biochim Pol 2011; 58:137-148. [PMID: 21623415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Revised: 04/05/2011] [Accepted: 04/30/2011] [Indexed: 05/30/2023]
Abstract
Reversible phosphorylation is the most widespread posttranslational protein modification, playing regulatory role in almost every aspect of cell life. The majority of protein phosphorylation research has been focused on serine, threonine and tyrosine that form acid-stable phosphomonoesters. However, protein histidine, arginine and lysine residues also may undergo phosphorylation to yield acid-labile phosphoramidates, most often remaining undetected in conventional studies of protein phosphorylation. It has become increasingly evident that acid-labile protein phosphorylations play important roles in signal transduction and other regulatory processes. Beside acting as high-energy intermediates in the transfer of the phosphoryl group from donor to acceptor molecules, phosphohistidines have been found so far in histone H4, heterotrimeric G proteins, ion channel KCa3.1, annexin 1, P-selectin and myelin basic protein, as well as in recombinant thymidylate synthase expressed in bacterial cells. Phosphoarginines occur in histone H3, myelin basic protein and capsidic protein VP12 of granulosis virus, whereas phospholysine in histone H1. This overview of the current knowledge on phosphorylation of protein basic amino-acid residues takes into consideration its proved or possible roles in cell functioning. Specific requirements of studies on acid-labile protein phosphorylation are also indicated.
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Affiliation(s)
- Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
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Abstract
Reversible phosphorylation is the most widespread posttranslational protein modification, playing regulatory role in almost every aspect of cell life. The majority of protein phosphorylation research has been focused on serine, threonine and tyrosine that form acid-stable phosphomonoesters. However, protein histidine, arginine and lysine residues also may undergo phosphorylation to yield acid-labile phosphoramidates, most often remaining undetected in conventional studies of protein phosphorylation. It has become increasingly evident that acid-labile protein phosphorylations play important roles in signal transduction and other regulatory processes. Beside acting as high-energy intermediates in the transfer of the phosphoryl group from donor to acceptor molecules, phosphohistidines have been found so far in histone H4, heterotrimeric G proteins, ion channel KCa3.1, annexin 1, P-selectin and myelin basic protein, as well as in recombinant thymidylate synthase expressed in bacterial cells. Phosphoarginines occur in histone H3, myelin basic protein and capsidic protein VP12 of granulosis virus, whereas phospholysine in histone H1. This overview of the current knowledge on phosphorylation of protein basic amino-acid residues takes into consideration its proved or possible roles in cell functioning. Specific requirements of studies on acid-labile protein phosphorylation are also indicated.
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Fusaro M, Jurkiewicz A, Jarmuła A, Leś A, Rode W. Hypothesis of a proton switch in QM/MM modelling of interaction of dUMP analogues with thymidylate synthase. Molecular Simulation 2010. [DOI: 10.1080/08927022.2010.502938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ruman T, Jarmuła A, Rode W. The aromaticity of 5,6-dihydroborauracil, borauracil and benzoborauracil systems. Bioorg Chem 2010; 38:242-5. [PMID: 20638706 DOI: 10.1016/j.bioorg.2010.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/25/2010] [Accepted: 06/25/2010] [Indexed: 11/16/2022]
Abstract
The nucleus-independent chemical shift (NICS) indices of aromaticity, calculated for four boron compounds, 4-hydroxy-5,6-dihydroborauracil, 4-hydroxyborauracil, borazine and 4-hydroxybenzoborauracil, and parent uracil, were analyzed in parallel with the NMR properties, in order to learn more about the aromaticity of those heterocyclic systems. The existence of a unique solvent-dependent aromaticity of 4-hydroxyborauracil is indicated.
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Affiliation(s)
- Tomasz Ruman
- Rzeszów University of Technology, Department of Biochemistry and Biotechnology, Poland.
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Swiniarska M, Leś A, Rode W, Cieśla J, Millán-Pacheco C, Blake IO, Pastor N. Segmental motions of rat thymidylate synthase leading to half-the-sites behavior. Biopolymers 2010; 93:549-59. [PMID: 20095045 DOI: 10.1002/bip.21393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Thymidylate synthase (TS) is a homodimeric enzyme with two equivalent active sites composed of residues from both subunits. Despite the structural symmetry of the enzyme, certain experimental results are consistent with half-the-sites activity, suggesting negative cooperativity between the active sites. To gain insight into the mechanism behind this phenomenon, we explore segmental motions of rat TS in the absence of ligands, with normal mode analysis as a tool. Using solvent accessible surface area of the active site pocket as a monitor of the degree of opening of the active sites, we classified the first 25 nontrivial normal modes, obtained from the web server of the program ElNémo, according to the behavior of the active sites. We found seven modes that open and close both sites symmetrically and nine that do so in an anticorrelated fashion. We characterized the motions of these modes by visual inspection and through measurement of distances between selected atoms lining the active site pockets. The segments that regulate access to the active site correspond to the loop containing R44, helix K, and a long loop containing residues 103-125, in agreement with a large body of crystallographic studies. These elements can be activated together or in isolation. There are more asymmetric modes than symmetric ones in the set we analyzed, probably accounting for the half-the-sites behavior of the enzyme. Three of the asymmetric modes result in changes at the dimer interface and indicate the endpoints of possible communication pathways between the active sites.
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Jarmuła A, Fraczyk T, Cieplak P, Rode W. Mechanism of influence of phosphorylation on serine 124 on a decrease of catalytic activity of human thymidylate synthase. Bioorg Med Chem 2010; 18:3361-70. [PMID: 20430630 PMCID: PMC4127429 DOI: 10.1016/j.bmc.2010.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 04/01/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022]
Abstract
Regulation by phosphorylation is a well-established mechanism for controlling biological activity of proteins. Recently, phosphorylation of serine 124 in human thymidylate synthase (hTS) has been shown to lower the catalytic activity of the enzyme. To clarify a possible mechanism of the observed influence, molecular dynamics (MD), essential dynamics (ED) and MM-GBSA studies were undertaken. Structures derived from the MD trajectories reveal incorrect binding alignment between the pyrimidine ring of the substrate, dUMP, and the pterine ring of the cofactor analogue, THF, in the active site of the phosphorylated enzyme. The ED analysis indicates changes in the behavior of collective motions in the phosphorylated enzyme, suggesting that the formation of the closed ternary complex is hindered. Computed free energies, in agreement with structural analysis, predict that the binding of dUMP and THF to hTS is favored in the native compared to phosphorylated state of the enzyme. The paper describes at the structural level how phosphorylation at the distant site influences the ligand binding. We propose that the 'phosphorylation effect' is transmitted from the outside loop of Ser 124 into the active site via a subtle mechanism initiated by the long-range electrostatic repulsion between the phosphate groups of dUMP and Ser124. The mechanism can be described in terms of the interplay between the two groups of amino acids: the link (residues 125-134) and the patch (residues 189-192), resulting in the change of orientation of the pyrimidine ring of dUMP, which, in turn, prevents the correct alignment between the latter ring and the pterin ring of THF.
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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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Ruman T, Długopolska K, Jurkiewicz A, Rut D, Frączyk T, Cieśla J, Leś A, Szewczuk Z, Rode W. Thiophosphorylation of free amino acids and enzyme protein by thiophosphoramidate ions. Bioorg Chem 2010; 38:74-80. [DOI: 10.1016/j.bioorg.2009.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 11/25/2022]
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Fraczyk T, Kubiński K, Masłyk M, Cieśla J, Hellman U, Shugar D, Rode W. Phosphorylation of thymidylate synthase from various sources by human protein kinase CK2 and its catalytic subunits. Bioorg Chem 2010; 38:124-31. [PMID: 20199796 DOI: 10.1016/j.bioorg.2010.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/06/2010] [Accepted: 02/09/2010] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) was found to be a substrate for both catalytic subunits of human CK2, with phosphorylation by CK2alpha and CK2alpha' characterized by similar K(m) values, 4.6microM and 4.2microM, respectively, but different efficiencies, the apparent turnover number with CK2alpha being 10-fold higher. With both catalytic subunits, phosphorylation of human TS, like calmodulin and BID, was strongly inhibited in the presence of the regulatory subunit CK2beta, the holoenzyme being activated by polylysine. Phosphorylation of recombinant human, rat, mouse and Trichinella spiralis TSs proteins was compared, with the human enzyme being apparently a much better substrate than the others. Following hydrolysis and TLC, phosphoserine was detected in human and rat, and phosphotyrosine in T. spiralis, TS, used as substrates for CK2alpha. MALDI-TOF MS analysis led to identification of phosphorylated Ser(124) in human TS, within a sequence LGFS(124)TREEGD, atypical for a CK2 substrate recognition site. The phosphorylation site is located in a region considered important for the catalytic mechanism or regulation of human TS, corresponding to the loop 107-128. Following phosphorylation by CK2alpha, resulting in incorporation of 0.4mol of phosphate per mol of dimeric TS, human TS exhibits unaltered K(m) values for dUMP and N(5,10)-methylenetetrahydrofolate, but a 50% lower turnover number, pointing to a strong influence of Ser(124) phosphorylation on its catalytic efficiency.
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Affiliation(s)
- Tomasz Fraczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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Ruman T, Długopolska K, Jurkiewicz A, Rydel K, Leś A, Rode W. The synthesis and NMR investigation on novel boron derivatives of stavudine. Bioorg Chem 2010; 38:87-91. [PMID: 20074771 DOI: 10.1016/j.bioorg.2009.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
Abstract
Preparation and spectroscopic properties of novel boron-containing derivatives of anti-HIV agent stavudine are presented, The new compounds, (5'-O-(4,4,5,5-tetramethyl-1,3,2-dioxaboronate)-2'-3'-didehydro-2'-3'-dideoxythymidine and 5'-O-(dihydroxyboronate)-2'-3'-didehydro-2'-3'-dideoxythymidine), were prepared by direct reaction between stavudine and reagents containing BH moieties - pinacolborane and borane-dimethylsulfide complexes, respectively. The boron coordination equilibrium of those compounds was analyzed by water titration monitored by NMR. Results of the DFT calculations and NMR experiments pointed to structural and electronic similarity of tetrahedral boron complexes to phosphate group.
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Affiliation(s)
- Tomasz Ruman
- Rzeszów University of Technology, Department of Biochemistry and Biotechnology, Poland.
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Ruman T, Dlugopolska K, Jurkiewicz A, Kramarz D, Fraczyk T, Les A, Rode W. The Synthesis, Reactivity and NMR Investigation on 15N-Thiophosphoramidates (Supplementary Material). LETT ORG CHEM 2009. [DOI: 10.2174/157017809790442943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ruman T, Długopolska K, Kuśnierz A, Rode W. Synthesis and NMR properties of derivatives of 5,6-dihydroborauracil and 5,6-dihydroborathymine. Bioorg Chem 2009; 37:180-4. [PMID: 19674766 DOI: 10.1016/j.bioorg.2009.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/11/2009] [Accepted: 07/13/2009] [Indexed: 11/18/2022]
Abstract
Novel boron compounds, a series of 4-hydroxy-5,6-dihydroborauracil and 4-hydroxy-5,6-dihydroborathymine derivatives containing various substituents at 3-, 5- and 6-positions, is presented. The spectroscopic properties, along with analyses of NMR-controlled boron compound-alcohol and boron compound-amine interactions, proves the existence of sp(3)-hybridized, stable B,B-bis-methoxy-5,6-dihydroborauracils and pyridine-/n-butylamine-5,6-dihydroborauracils ate-complexes in solution.
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Affiliation(s)
- Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Department of Biochemistry and Biotechnology, 35-959 Rzeszów, Poland.
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Ruman T, Długopolska K, Kuśnierz A, Jurkiewicz A, Leś A, Rode W. Synthesis and NMR properties of novel 5,6-dihydroborauracil derivatives. Bioorg Chem 2009; 37:65-9. [DOI: 10.1016/j.bioorg.2009.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 03/12/2009] [Accepted: 03/13/2009] [Indexed: 12/01/2022]
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Dabrowska M, Mosieniak G, Skierski J, Sikora E, Rode W. Methotrexate-induced senescence in human adenocarcinoma cells is accompanied by induction of p21(waf1/cip1) expression and lack of polyploidy. Cancer Lett 2009; 284:95-101. [PMID: 19467772 DOI: 10.1016/j.canlet.2009.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 01/20/2023]
Abstract
Human colorectal adenocarcinoma C85 cells, treated with high dose methotrexate (1 microM; IC(50)=51 nM), undergo accelerated senescence, as the cells (i) are growth arrested at the G(1) and S phases of the cell cycle, (ii) are SA-beta-galactosidase-positive, (iii) show induced expression of p21(waf1/cip1) and decreased expression of p16(INK4a), and (iv) show DNA synthesis continued at the reduced level. The fraction of C85 cells with DNA content higher than 4N is maintained at the same level (14%) in cells untreated, as well as regrown after the treatment. Multinucleation is found as the main karyotypic abnormality.
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Affiliation(s)
- Magdalena Dabrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., Warsaw 02-093, Poland.
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Humeniuk R, Menon LG, Mishra PJ, Gorlick R, Sowers R, Rode W, Pizzorno G, Cheng YC, Kemeny N, Bertino JR, Banerjee D. Decreased levels of UMP kinase as a mechanism of fluoropyrimidine resistance. Mol Cancer Ther 2009; 8:1037-44. [PMID: 19383847 DOI: 10.1158/1535-7163.mct-08-0716] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
5-Fluorouracil (5-FU) continues to be widely used for treatment of gastrointestinal cancers. Because many tumors show primary or acquired resistance, it is important to understand the molecular basis underlying the mechanism of resistance to 5-FU. In addition to its effect on thymidylate synthase inhibition and DNA synthesis, 5-FU may also influence RNA metabolism. Our previous studies revealed that colorectal cancer cells resistant to bolus 5-FU (HCT-8/4hFU) showed significantly decreased incorporation of the drug into RNA. Resistance to bolus 5-FU was associated with lower expression of UMP kinase (UMPK), an enzyme that plays an important role in the activation of 5-FU to 5-FUTP and its incorporation into RNA. Activities of other 5-FU-metabolizing enzymes (e.g., thymidine kinase, uridine phosphorylase, thymidine phosphorylase, and orotate phosphoribosyltransferase) remained unchanged between sensitive and resistant cell lines. Herein, we show that UMPK down-regulation in 5-FU-sensitive cells (HCT-8/P) induces resistance to bolus 5-FU treatment. Moreover, HCT-8/4hFU cells are even more cross-resistant to treatment with 5-fluorouridine, consistent with the current understanding of 5-fluorouridine as a RNA-directed drug. Importantly, colorectal cancer hepatic metastases isolated from patients clinically resistant to weekly bolus 5-FU/leucovorin treatment exhibited decreased mRNA expression of UMPK but not thymidylate synthase or dihydropyrimidine dehydrogenase compared with tumor samples of patients not previously exposed to 5-FU. Our findings provide new insights into the mechanisms of acquired resistance to 5-FU in colorectal cancer and implicate UMPK as an important mechanism of clinical resistance to pulse 5-FU treatment in some patients.
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Affiliation(s)
- Rita Humeniuk
- The Graduate School of Biomedical Sciences, Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08903, USA
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Abstract
Nurse cell (NC), formed from skeletal muscle cells upon infection with parasitic nematode trichina, presents a rare system of long-term suspension in the cell cycle. Signaling pathways and general biological functions of Trichinella spiralis NC, inferred from network analysis of competitive expression microarray data (NC vs. C2C12 myoblasts and myotubes), performed in Ingenuity Pathways Analysis (IPA) software and confirmed by Real-Time PCR, are presented. Assuming 4N DNA content in NC nuclei, its cell cycle arrest is identified herein as a hypermitogenic of G(1)-like type, accompanied by induction of senescence, underpinned by increased expression of p15, p16 and p57 cell cycle inhibitors, as well as overexpression of senescence-associated, beta-galactosidase and numerous secretory factors. Growth factor signaling, with predominant role of EGF, cytokine signaling and G-protein-coupled receptor signaling, are suggested as dominant NC signal transduction pathways. Fos, FosB, STAT6, CREBL2, ID4 and retinoic acid dependent nuclear receptors appear to be the main factors determining NC specific gene transcription. Antigen presentation, complement signaling and beta-amyloid processing pathways are also identified as operating in NC. In general, NC pathology is found to pertain to cancer, as well as other, including immunological and neurological, disorders.
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Affiliation(s)
- Magdalena Dabrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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Jarmuła A, Dowierciał A, Rode W. A molecular modeling study of the interaction of 2'-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase. Bioorg Med Chem Lett 2008; 18:2701-8. [PMID: 18362071 DOI: 10.1016/j.bmcl.2008.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 03/03/2008] [Accepted: 03/06/2008] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulations and free energy calculations are presented, exploring previously described experimentally studied interactions of a series of 2'-fluoro-substituted dUMP/FdUMP analogues with thymidylate synthase (TS). The results show the inhibitory behaviors of 2'-F-ara-UMP, 2',2''-diF-dUMP and 2',5-diF-ara-UMP to be dependent upon the binding positions and orientations adopted by the molecules of these compounds in the active site of TS. The binding mode of 2',5-diF-ara-UMP suggests a novel role of the active site residue Trp 80, stabilizing through hydrophobic stacking the binding position of the pyrimidine ring in 2',5-diF-ara-UMP.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warszawa, Poland.
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Ziemkowski P, Felczak K, Poznański J, Kulikowski T, Zieliński Z, Cieśla J, Rode W. Interactions of 2'-fluoro-substituted dUMP analogues with thymidylate synthase. Biochem Biophys Res Commun 2007; 362:37-43. [PMID: 17692822 DOI: 10.1016/j.bbrc.2007.07.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 07/19/2007] [Indexed: 11/22/2022]
Abstract
A series of 2'-fluoro-substituted dUMP/FdUMP analogues were synthesized, their interaction with human recombinant thymidylate synthase investigated, and structural (1)H and (19)F NMR study of the corresponding nucleosides performed. While 2'-F-dUMP (fluorine in the "down" configuration), in striking contrast to 2'-F-ara-UMP (fluorine in the "up" configuration) and 2',2''-diF-dUMP, showed substrate activity, 2'-F-ara-UMP and 2',2''-diF-dUMP were classic inhibitors, and 2',5-diF-ara-UMP behaved as a strong slow-binding inhibitor, suggesting the 2'-F substituent in the "up" position to interfere with the active center cysteine thiol addition to the pyrimidine C(6) and the pyrimidine C(5)-F to prevent this interference. In support, the direct through space heteronuclear coupling J(HF) was observed for the fluorine "up" derivatives, 2'-F-ara-U and 2',5-diF-ara-U, causing the splitting of the H(6) resonance lines. The absence of such splitting in 2',2''-diF-dUrd, indicating an unusual orientation of the base in relation to the furanose, was associated with an exceptionally weak interaction with the enzyme.
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Affiliation(s)
- Przemysław Ziemkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Krzysztof Felczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Tadeusz Kulikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland.
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Cieśla J, Jagielska E, Skopiński T, Dabrowska M, Maley F, Rode W. Binding and repression of translation of the cognate mRNA by Trichinella spiralis thymidylate synthase differ from the corresponding interactions of the human enzyme. Biochem J 2007; 402:601. [PMID: 17326266 PMCID: PMC1863577 DOI: 10.1042/bj4020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jarmuła A, Cieplak P, Krygowski TM, Rode W. The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: molecular modeling and QSAR. Bioorg Med Chem 2007; 15:2346-58. [PMID: 17275316 DOI: 10.1016/j.bmc.2007.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 12/24/2006] [Accepted: 01/17/2007] [Indexed: 11/20/2022]
Abstract
Thymidylate synthase (TS) is a target enzyme for a number of anticancer agents including the 5-fluorouracil metabolite, FdUMP. The present paper reports on molecular modeling studies of the effect of substitution at C(5) position in the pyrimidine ring of the TS substrate, dUMP, on the binding affinity for the enzyme. The results of molecular dynamics simulations show that the binding of C(5) analogues of dUMP to TS in the binary complexes does not undergo changes, unless a substituent with a large steric effect, such as the propyl group, is involved. On the other hand, apparent differences in the binding of the TS cofactor, resulting from varying substitution at dUMP C(5), are observed in the modeled structures of the ternary complexes of TS. These binding characteristics are supplemented with a classical QSAR model quantifying the relation between the affinity for TS and the substituent electronic and steric effects of C(5) analogues of dUMP. Based on the findings from the present work, the perspectives for finding promising new C(5) analogues of dUMP as potential agents targeted against TS are discussed.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
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Dabrowska M, Hendrikx PJ, Skierski J, Malinowska M, Bertino JR, Rode W. EGFP fluorescence as an indicator of cancer cells response to methotrexate. Eur J Pharmacol 2006; 555:93-9. [PMID: 17141212 DOI: 10.1016/j.ejphar.2006.10.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 10/11/2006] [Accepted: 10/13/2006] [Indexed: 10/24/2022]
Abstract
Methotrexate action in viable cells was monitored by registering changes in EGFP (Enhanced Green Fluorescent Protein) fluorescence intensity. Treatment with 1 microM methotrexate for 48 h of human colorectal adenocarcinoma C85 cells, stably transfected to express EGFP, caused 5-fold increase in EGFP fluorescence assayed by flow cytometry with no distinct increase in EGFP protein level. This was correlated with morphological changes, including an increase of cell granularity and cell shape flattening, as well as cell cycle G1 phase arrest revealed by DNA content analysis. Methotrexate removal allowed the morphology of the cells in culture to revert in 10 days to normal. The cells that survived methotrexate exposure were propagated as C85r cell subline and displayed kinetics of methotrexate sensitivity parallel to that of the parental C85 line. As the increase in EGFP fluorescence could also be visualized by fluorescence microscopy, this reporter system may be employed to image methotrexate action in cancer cells in living models.
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Affiliation(s)
- Magdalena Dabrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
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