1
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Wagner AG, Eskandari R, Schramm VL. An enzyme-coupled microplate assay for activity and inhibition of hmdUMP hydrolysis by DNPH1. Anal Biochem 2023; 672:115171. [PMID: 37142196 PMCID: PMC10334339 DOI: 10.1016/j.ab.2023.115171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
2'-Deoxynucleoside 5'-monophosphate N-glycosidase 1 (DNPH1) hydrolyzes the epigenetically modified nucleotide 5-hydroxymethyl 2'-deoxyuridine 5'-monophosphate (hmdUMP) derived from DNA metabolism. Published assays of DNPH1 activity are low throughput, use high concentrations of DNPH1, and have not incorporated or characterized reactivity with the natural substrate. We describe the enzymatic synthesis of hmdUMP from commercially available materials and define its steady-state kinetics with DNPH1 using a sensitive, two-pathway enzyme coupled assay. This continuous absorbance-based assay works in 96-well plate format using nearly 500-fold less DNPH1 than previous methods. With a Z prime value of 0.92, the assay is suitable for high-throughput assays, screening of DNPH1 inhibitors, or characterization of other deoxynucleotide monophosphate hydrolases.
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Affiliation(s)
- Andrew G Wagner
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States
| | - Roozbeh Eskandari
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, United States.
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2
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El Kouni MH. Pyrimidine metabolism in schistosomes: A comparison with other parasites and the search for potential chemotherapeutic targets. Comp Biochem Physiol B Biochem Mol Biol 2017; 213:55-80. [PMID: 28735972 PMCID: PMC5593796 DOI: 10.1016/j.cbpb.2017.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/18/2022]
Abstract
Schistosomes are responsible for the parasitic disease schistosomiasis, an acute and chronic parasitic ailment that affects >240 million people in 70 countries worldwide. It is the second most devastating parasitic disease after malaria. At least 200,000 deaths per year are associated with the disease. In the absence of the availability of vaccines, chemotherapy is the main stay for combating schistosomiasis. The antischistosomal arsenal is currently limited to a single drug, Praziquantel, which is quite effective with a single-day treatment and virtually no host-toxicity. Recently, however, the question of reduced activity of Praziquantel has been raised. Therefore, the search for alternative antischistosomal drugs merits the study of new approaches of chemotherapy. The rational design of a drug is usually based on biochemical and physiological differences between pathogens and host. Pyrimidine metabolism is an excellent target for such studies. Schistosomes, unlike most of the host tissues, require a very active pyrimidine metabolism for the synthesis of DNA and RNA. This is essential for the production of the enormous numbers of eggs deposited daily by the parasite to which the granulomas response precipitates the pathogenesis of schistosomiasis. Furthermore, there are sufficient differences between corresponding enzymes of pyrimidine metabolism from the host and the parasite that can be exploited to design specific inhibitors or "subversive substrates" for the parasitic enzymes. Specificities of pyrimidine transport also diverge significantly between parasites and their mammalian host. This review deals with studies on pyrimidine metabolism in schistosomes and highlights the unique characteristic of this metabolism that could constitute excellent potential targets for the design of safe and effective antischistosomal drugs. In addition, pyrimidine metabolism in schistosomes is compared with that in other parasites where studies on pyrimidine metabolism have been more elaborate, in the hope of providing leads on how to identify likely chemotherapeutic targets which have not been looked at in schistosomes.
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Affiliation(s)
- Mahmoud H El Kouni
- Department of Pharmacology and Toxicology, Center for AIDS Research, Comprehensive Cancer Center, General Clinical Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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3
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Orozco Rodriguez JM, Nesrini M, Christiansen LS, Knecht W. Expression of tomato thymidine kinase 1 by means of the baculovirus expression vector system. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:691-698. [PMID: 27906616 DOI: 10.1080/15257770.2016.1139126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tomato thymidine kinase 1 (ToTK1) is a deoxyribonucleoside kinase (dNK) that has been subject to study because of its potential to phosphorylate the nucleoside analogue 3-azido-2,3-dideoxythymidine (azidothymidine, AZT) equally well as its natural substrate thymidine (dThd). The combination of ToTK1 and AZT has been tested in two animal studies for its efficiency and use in suicide gene therapy for malignant glioma. The determination of the 3D structure of ToTK1 might shed light on the structure-function relationships of nucleoside activation by this enzyme and thereby show routes toward further improvement of ToTK1 and other TK1-like dNKs for suicide gene therapy. Here we report the successful expression of both full-length ToTK1 and a C-terminal truncated ToTK1 in Spodoptera frugiperda and Trichoplusia ni insect cells using the baculovirus expression vector system. This constitutes a further step on the road to determine the 3D structure of the first TK1 of plant origin, but also an enzyme with great potential for dNK-mediated suicide gene therapy.
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Affiliation(s)
| | - Mohamad Nesrini
- a Department of Biology and Lund Protein Production Platform , Lund University , Lund , Sweden
| | | | - Wolfgang Knecht
- a Department of Biology and Lund Protein Production Platform , Lund University , Lund , Sweden
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4
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Christiansen LS, van Zanten G, Berenstein D, Lauridsen M, Kjærulff S, Søndergaard L, Munch-Petersen B. Isolation of a novel protein, P12-from adult Drosophila melanogaster that inhibits deoxyribonucleoside and protein kinase activities and activates 3'-5'- exonuclease activity. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:699-706. [PMID: 27906621 DOI: 10.1080/15257770.2015.1131295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We have previously found that Drosophila melanogaster only has one deoxyribonucleoside kinase, Dm-dNK, however, capable to phosphorylate all four natural deoxyribonucleosides. Dm-dNK was originally isolated from an embryonic cell line. We wanted to study the expression of Dm-dNK during development from embryonic cells to adult flies and found declining Dm-dNK activity during development and no activity in adult flies. Surprisingly, the extract from adult flies exhibited a strong inhibitory effect on deoxyribonucloside kinase activity. The dNK-inhibitor was precipitable with ammonium sulfate, and was purified to a high degree by gel-filtration as indicated by LC-MS/MS analysis. Since the inhibitor eluted from G-200 gel-filtration with a size of 10-13 kDa, we named it P12. We tested the purified fraction for specificity towards various enzymes and found that both mammalian and bacterial dNKs were inhibited, whereas there was no effect on hexokinase and pyruvate kinases and acidic phosphatase. However, when tested against cyclin B-dependent kinase, we found a strong inhibitory effect. Both with human Cdk1/CycB and S. pombe Cdc2/B-type cyclin the purified fraction from Superdex 200 that inhibited Dm-dNK, also inhibited the two protein kinases to the same degree. Furthermore, testing P12 in a DNA polymerase based assay we found that the 3'-5'-exonuclease part of the DNA polymerase (Klenow polymerase) was activated.
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Affiliation(s)
| | - Gabriella van Zanten
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Dvora Berenstein
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Marianne Lauridsen
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Søren Kjærulff
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
| | - Leif Søndergaard
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
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5
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Mutahir Z, Christiansen LS, Clausen AR, Berchtold MW, Gojkovic Z, Munch-Petersen B, Knecht W, Piškur J. Gene duplications and losses among vertebrate deoxyribonucleoside kinases of the non-TK1 Family. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:677-690. [PMID: 27906638 DOI: 10.1080/15257770.2016.1143557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK). In this study, we characterized a family of dCK/deoxyguanosine kinase (dGK)-like enzymes from a frog Xenopus laevis and a bird Gallus gallus. We showed that X. laevis has a duplicated dCK gene and a dGK gene, whereas G. gallus has a duplicated dCK gene but has lost the dGK gene. We cloned, expressed, purified, and subsequently determined the kinetic parameters of the dCK/dGK enzymes encoded by these genes. The two dCK enzymes in G. gallus have broader substrate specificity than their human or X. laevis counterparts. Additionally, the duplicated dCK enzyme in G. gallus might have become mitochondria. Based on our study we postulate that changing and adapting substrate specificities and subcellular localization are likely the drivers behind the evolution of vertebrate dNKs.
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Affiliation(s)
| | - Louise Slot Christiansen
- a Department of Biology , Lund University , Lund , Sweden.,e Lund Protein Production Platform, Lund University , Lund , Sweden
| | | | - Martin W Berchtold
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
| | | | - Birgitte Munch-Petersen
- a Department of Biology , Lund University , Lund , Sweden.,d Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Wolfgang Knecht
- a Department of Biology , Lund University , Lund , Sweden.,e Lund Protein Production Platform, Lund University , Lund , Sweden
| | - Jure Piškur
- a Department of Biology , Lund University , Lund , Sweden
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6
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Slot Christiansen L, Munch-Petersen B, Knecht W. Non-Viral Deoxyribonucleoside Kinases--Diversity and Practical Use. J Genet Genomics 2015; 42:235-48. [PMID: 26059771 DOI: 10.1016/j.jgg.2015.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/04/2015] [Accepted: 01/05/2015] [Indexed: 12/30/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) phosphorylate deoxyribonucleosides to their corresponding monophosphate compounds. dNks also phosphorylate deoxyribonucleoside analogues that are used in the treatment of cancer or viral infections. The study of the mammalian dNKs has therefore always been of great medical interest. However, during the last 20 years, research on dNKs has gone into non-mammalian organisms. In this review, we focus on non-viral dNKs, in particular their diversity and their practical applications. The diversity of this enzyme family in different organisms has proven to be valuable in studying the evolution of enzymes. Some of these newly discovered enzymes have been useful in numerous practical applications in medicine and biotechnology, and have contributed to our understanding of the structural basis of nucleoside and nucleoside analogue activation.
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Affiliation(s)
| | - Birgitte Munch-Petersen
- Department of Biology, Lund University, Lund 22362, Sweden; Department of Science, Systems and Models, Roskilde University, Roskilde 4000, Denmark
| | - Wolfgang Knecht
- Department of Biology, Lund University, Lund 22362, Sweden; Lund Protein Production Platform, Lund University, Lund 22362, Sweden.
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7
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Konrad A, Lai J, Mutahir Z, Piškur J, Liberles DA. The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa. J Mol Evol 2014; 78:202-16. [PMID: 24500774 DOI: 10.1007/s00239-014-9611-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/21/2014] [Indexed: 12/22/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) carry out the rate-determining step in the nucleoside salvage pathway within all domains of life where the pathway is present, and, hence, are an indication on whether or not a species/genus retains the ability to salvage deoxyribonucleosides. Here, a phylogenetic tree is constructed for the thymidine kinase 2-like dNK gene family in metazoa. Each enzyme class (deoxycytidine, deoxyguanosine, and deoxythymidine kinases, as well as the multisubstrate dNKs) falls into a monophyletic clade. However, in vertebrates, dCK contains an apparent duplication with one paralog lost in mammals, and a number of crustacean genomes (like Caligus rogercresseyi and Lepeophtheirus salmonis) unexpectedly contain not only the multisubstrate dNKs, related to Drosophila multisubstrate dNK, but also a TK2-like kinase. Additionally, crustaceans (Daphnia, Caligus, and Lepeophtheirus) and some insects (Tribolium, Danaus, Pediculus, and Acyrthosiphon) contain several multisubstrate dNK-like enzymes which group paraphyletically within the arthropod clade. This might suggest that the multisubstrate dNKs underwent multiple rounds of duplications with differential retention of duplicate copies between insect families and more complete retention within some crustaceans and insects. Genomes of several basal animalia contain more than one dNK-like sequence, some of which group outside the remaining eukaryotes (both plants and animals) and/or with bacterial dNKs. Within the vertebrates, the mammalian genomes do not contain the second dCK, while birds, fish, and amphibians do retain it. Phasianidae (chicken and turkey) have lost dGK, while it has been retained in other bird lineages, like zebra finch. Reconstruction of the ancestral sequence between the multisubstrate arthropod dNKs and the TK2 clade of vertebrates followed by homology modeling and discrete molecular dynamics calculations on this sequence were performed to examine the evolutionary path which led to the two different enzyme classes. The structural models showed that the carboxyl terminus of the ancestral sequence is more helical than dNK, in common with TK2, although any implications of this for enzyme specificity will require biochemical validation. Finally, rate-shift and conservation-shift analysis between clades with different specificities uncovered candidate residues outside the active site pocket which may have contributed to differentiation in substrate specificity between enzyme clades.
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Affiliation(s)
- Anke Konrad
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA,
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8
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Naguib FN, el Kouni MH. Nucleoside kinases in adult Schistosoma mansoni: Phosphorylation of pyrimidine nucleosides. Mol Biochem Parasitol 2014; 194:53-5. [DOI: 10.1016/j.molbiopara.2014.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 04/19/2014] [Accepted: 04/21/2014] [Indexed: 11/28/2022]
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9
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Cassera MB, Ho MC, Merino EF, Burgos ES, Rinaldo-Matthis A, Almo SC, Schramm VL. A high-affinity adenosine kinase from Anopheles gambiae. Biochemistry 2011; 50:1885-93. [PMID: 21247194 DOI: 10.1021/bi101921w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome analysis revealed a mosquito orthologue of adenosine kinase in Anopheles gambiae (AgAK; the most important vector for the transmission of Plasmodium falciparum in Africa). P. falciparum are purine auxotrophs and do not express an adenosine kinase but rely on their hosts for purines. AgAK was kinetically characterized and found to have the highest affinity for adenosine (K(m) = 8.1 nM) of any known adenosine kinase. AgAK is specific for adenosine at the nucleoside site, but several nucleotide triphosphate phosphoryl donors are tolerated. The AgAK crystal structure with a bound bisubstrate analogue Ap(4)A (2.0 Å resolution) reveals interactions for adenosine and ATP and the geometry for phosphoryl transfer. The polyphosphate charge is partly neutralized by a bound Mg(2+) ion and an ion pair to a catalytic site Arg. The AgAK structure consists of a large catalytic core in a three-layer α/β/α sandwich, and a small cap domain in contact with adenosine. The specificity and tight binding for adenosine arise from hydrogen bond interactions of Asn14, Leu16, Leu40, Leu133, Leu168, Phe168, and Thr171 and the backbone of Ile39 and Phe168 with the adenine ring as well as through hydrogen bond interactions between Asp18, Gly64, and Asn68 and the ribosyl 2'- and 3'-hydroxyl groups. The structure is more similar to that of human adenosine kinase (48% identical) than to that of AK from Toxoplasma gondii (31% identical). With this extraordinary affinity for AgAK, adenosine is efficiently captured and converted to AMP at near the diffusion limit, suggesting an important role for this enzyme in the maintenance of the adenine nucleotide pool. mRNA analysis verifies that AgAK transcripts are produced in the adult insects.
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Affiliation(s)
- María B Cassera
- Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York 10461, United States
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10
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Zhang Y, Luo M, Schramm VL. Transition states of Plasmodium falciparum and human orotate phosphoribosyltransferases. J Am Chem Soc 2009; 131:4685-94. [PMID: 19292447 PMCID: PMC2669657 DOI: 10.1021/ja808346y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Orotate phosphoribosyltransferases (OPRT) catalyze the formation of orotidine 5'-monophosphate (OMP) from alpha-D-phosphoribosylpyrophosphate (PRPP) and orotate, an essential step in the de novo biosynthesis of pyrimidines. Pyrimidine de novo biosynthesis is required in Plasmodium falciparum , and thus OPRT of the parasite (PfOPRT) is a target for antimalarial drugs. De novo biosynthesis of pyrimidines is also a feature of rapidly proliferating cancer cells. Human OPRT (HsOPRT) is therefore a target for neoplastic and autoimmune diseases. One approach to the inhibition of OPRTs is through analogues that mimic the transition states of PfOPRT and HsOPRT. The transition state structures of these OPRTs were analyzed by kinetic isotope effects (KIEs), substrate specificity, and computational chemistry. With phosphonoacetic acid (PA), an analogue of pyrophosphate, the intrinsic KIEs of [1'-(14)C], [1, 3-(15)N(2)], [3-(15)N], [1'-(3)H], [2'-(3)H], [4'-(3)H], and [5'-(3)H(2)] are 1.034, 1.028, 0.997, 1.261, 1.116, 0.974, and 1.013 for PfOPRT and 1.035, 1.025, 0.993, 1.199, 1.129, 0.962, and 1.019 for HsOPRT, respectively. Transition state structures of PfOPRT and HsOPRT were determined computationally by matching the calculated and intrinsic KIEs. The enzymes form late associative D(N)*A(N)(double dagger) transition states with complete orotate loss and partially associative nucleophile. The C1'-O(PA) distances are approximately 2.1 A at these transition states. The modest [1'-(14)C] KIEs and large [1'-(3)H] KIEs are characteristic of D(N)*A(N)(double dagger) transition states. The large [2'-(3)H] KIEs indicate a ribosyl 2'-C-endo conformation at the transition states. p-Nitrophenyl beta-D-ribose 5'-phosphate is a poor substrate of PfOPRT and HsOPRT but is a nanomolar inhibitor, supporting a reaction coordinate with strong leaving group activation.
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Affiliation(s)
- Yong Zhang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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11
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Knecht W, Mikkelsen NE, Clausen AR, Willer M, Eklund H, Gojković Z, Piskur J. Drosophila melanogaster deoxyribonucleoside kinase activates gemcitabine. Biochem Biophys Res Commun 2009; 382:430-3. [PMID: 19285960 DOI: 10.1016/j.bbrc.2009.03.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 03/07/2009] [Indexed: 11/15/2022]
Abstract
Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2A resolution structure of Dm-dNK in complex with gemcitabine shows that the residues Tyr70 and Arg105 play a crucial role in the firm positioning of gemcitabine by extra interactions made by the fluoride atoms. This explains why gemcitabine is a good substrate for Dm-dNK.
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Affiliation(s)
- Wolfgang Knecht
- BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
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12
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Knecht W, Rozpedowska E, Le Breton C, Willer M, Gojkovic Z, Sandrini MPB, Joergensen T, Hasholt L, Munch-Petersen B, Piskur J. Drosophila deoxyribonucleoside kinase mutants with enhanced ability to phosphorylate purine analogs. Gene Ther 2007; 14:1278-86. [PMID: 17581598 DOI: 10.1038/sj.gt.3302982] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transduced deoxyribonucleoside kinases (dNK) can be used to kill recipient cells in combination with nucleoside prodrugs. The Drosophila melanogaster multisubstrate dNK (Dm-dNK) displays a superior turnover rate and has a great plasticity regarding its substrates. We used directed evolution to create Dm-dNK mutants with increased specificity for several nucleoside analogs (NAs) used as anticancer or antiviral drugs. Four mutants were characterized for the ability to sensitize Escherichia coli toward analogs and for their substrate specificity and kinetic parameters. The mutants had a reduced ability to phosphorylate pyrimidines, while the ability to phosphorylate purine analogs was relatively similar to the wild-type enzyme. We selected two mutants, for expression in the osteosarcoma 143B, the glioblastoma U-87M-G and the breast cancer MCF7 cell lines. The sensitivities of the transduced cell lines in the presence of the NAs fludarabine (F-AraA), cladribine (CdA), vidarabine and cytarabine were compared to the parental cell lines. The sensitivity of 143B cells was increased by 470-fold in the presence of CdA and of U-87M-G cells by 435-fold in the presence of F-AraA. We also show that a choice of the selection and screening system plays a crucial role when optimizing suicide genes by directed evolution.
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Affiliation(s)
- W Knecht
- BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
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13
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Dictyostelium discoideum Salvages Purine Deoxyribonucleosides by Highly Specific Bacterial-like Deoxyribonucleoside Kinases. J Mol Biol 2007; 369:653-64. [DOI: 10.1016/j.jmb.2007.03.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/13/2007] [Accepted: 03/13/2007] [Indexed: 11/23/2022]
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14
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Gerth ML, Lutz S. Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. J Mol Biol 2007; 370:742-51. [PMID: 17543337 PMCID: PMC1986717 DOI: 10.1016/j.jmb.2007.05.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Revised: 04/29/2007] [Accepted: 05/02/2007] [Indexed: 11/26/2022]
Abstract
In antiviral and cancer therapy, deoxyribonucleoside kinases (dNKs) are often the rate-limiting step in activating nucleoside analog (NA) prodrugs into their cytotoxic, phosphorylated forms. We have constructed libraries of hybrid enzymes by non-homologous recombination of the pyrimidine-specific human thymidine kinase 2 and the broad-specificity dNK from Drosophila melanogaster; their low sequence identity has precluded engineering by conventional, homology-dependent shuffling techniques. From these libraries, we identified chimeras that phosphorylate nucleoside analogs with higher activity than either parental enzyme, and that possess new activity towards the anti-HIV prodrug 2',3'-didehydro-3'-deoxythymidine (d4T). These results demonstrate the potential of non-homologous recombination within the dNK family for creating enzymes with new and improved activities towards nucleoside analogs. In addition, our results exposed a previously unknown role for the C-terminal regions of these dNKs in determining substrate selectivity.
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15
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Gerth ML, Lutz S. Mutagenesis of non-conserved active site residues improves the activity and narrows the specificity of human thymidine kinase 2. Biochem Biophys Res Commun 2007; 354:802-7. [PMID: 17266931 PMCID: PMC1853344 DOI: 10.1016/j.bbrc.2007.01.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 01/16/2007] [Indexed: 11/26/2022]
Abstract
Human thymidine kinase 2 (TK2) is critical for the nucleotide salvage pathway and phosphorylation of nucleoside analog prodrugs in vivo; however, it remains poorly studied because of difficulties in expressing it heterologously. TK2 is strictly pyrimidine-specific, whereas its phylogenetic relative, the Drosophila melanogaster deoxyribonucleoside kinase (DmdNK), shows higher activity and broader specificity towards both pyrimidines and purines. These differences are counterintuitive, as only two of 29 active site residues differ in the two enzymes: F80 and M118 in DmdNK are L78 and L116 in TK2. In addition to reporting an optimized protocol for the expression and purification of TK2, we have used site-directed mutagenesis to introduce the DmdNK-like amino acids into TK2, and characterized the three resulting enzymes (L78F-TK2, L116M-TK2, and L78F/L116M-TK2). These mutations improve the K(M) for thymidine, increasing the catalytic activity of L78F/L116M-TK2 4.4-fold, yet leaving the activity for deoxycytidine or the purine nucleosides unchanged.
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Affiliation(s)
- Monica L Gerth
- Chemistry Department, Emory University, Atlanta, GA 30322, USA
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16
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Breuer M, De Loof A, Balzarini J, Huybrechts R. Insecticidal activity of the pyrimidine nucleoside analogue (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU). PEST MANAGEMENT SCIENCE 2005; 61:737-741. [PMID: 15838935 DOI: 10.1002/ps.1053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The insecticidal activity of the antiherpetic agent (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) was assessed in in vivo assays against the fall armyworm, Spodoptera frugiperda (JE Smith) (Lepidoptera, Noctuidae). BVDU, mixed into an artificial diet, caused a variety of effects, depending on the concentration used. Compared with controls, food intake was lower, larval growth was retarded and larval development was prolonged. The treated larvae formed smaller pupae and the hatching moths often showed morphogenetic defects. A higher mortality could be found in larval and pupal stages and was generally caused by moult disruption. A choice assay showed that BVDU has very slight feeding-deterrent properties, which only partly explain the toxic effects. The agent most probably acts through its cytostatic activity that has been described previously using cell lines of different insect species.
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Affiliation(s)
- Michael Breuer
- Zoological Institute, Katholieke Universiteit Leuven, Naamsestraat 59, B-3000 Leuven, Belgium.
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Piskur J, Sandrini MPB, Knecht W, Munch-Petersen B. Animal deoxyribonucleoside kinases: ‘forward’ and ‘retrograde’ evolution of their substrate specificity1. FEBS Lett 2004; 560:3-6. [PMID: 14987989 DOI: 10.1016/s0014-5793(04)00081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/19/2004] [Accepted: 01/19/2004] [Indexed: 10/26/2022]
Abstract
Deoxyribonucleoside kinases, which catalyse the phosphorylation of deoxyribonucleosides, are present in several copies in most multicellular organisms and therefore represent an excellent model to study gene duplication and specialisation of the duplicated copies through partitioning of substrate specificity. Recent studies suggest that in the animal lineage one of the progenitor kinases, the so-called dCK/dGK/TK2-like gene, was duplicated prior to separation of the insect and mammalian lineages. Thereafter, insects lost all but one kinase, dNK (EC 2.7.1.145), which subsequently, through remodelling of a limited number of amino acid residues, gained a broad substrate specificity.
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Affiliation(s)
- Jure Piskur
- BioCentrum-DTU, Eukaryote Molecular Biology Group, Building 301, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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