1
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Zhang T, Chen X, Tao C, Huang H, Luo Z, Liu M, Cui W, Wang W. Structural and mechanistic insight into the phosphorylation reaction catalyzed by mpox virus thymidine kinase. Antiviral Res 2025; 237:106125. [PMID: 40020877 DOI: 10.1016/j.antiviral.2025.106125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/24/2025] [Accepted: 02/25/2025] [Indexed: 03/03/2025]
Abstract
Mpox virus (MPXV) is the etiological agent of mpox, which is a major threat to human health. The identification of potential drug targets and the development of effective antiviral therapies are still urgently needed. The thymidine kinase (TK) encoded by MPXV initiates the deoxythymidine triphosphate (dTTP) salvage synthesis pathway and facilitates viral DNA replication. MPXV without TK presents significant replication defects. MPXV TK is also responsible for the activation of nucleos(t)ide analogs, which are an important class of antivirals. Despite its importance in the viral life cycle and antiviral development, the structure and catalytic mechanism of MPXV TK are not fully understood. Here, we determined the three-dimensional structure of an MPXV TK variant, in which the glutamic acid at position 83 was substituted with alanine. MPXV TK consists of two domains and forms a tetramer. One protomer binds dTTP with two lassos and a P-loop, while the other protomers are captured in apo-form. Mutation of residues near the dTTP-binding site significantly reduces the catalytic activity of MPXV TK, indicating the importance of these residues in substrate binding and/or catalysis. Specifically, E83 is found to play a crucial role in stabilizing dTTP and lasso II. A biochemical assay confirmed that dTTP functions as a feedback inhibitor of MPXV TK and its inhibitory potency was evaluated. These results may facilitate the discovery of specific inhibitors targeting TK to mitigate MPXV infections.
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Affiliation(s)
- Tenan Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Xiang Chen
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Chengcheng Tao
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Haojun Huang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Zhi Luo
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Center for Novel Target and Therapeutic Intervention, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Mengmeng Liu
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.
| | - Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.
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2
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Rasri N, Kornyanee C, Srisanga K, Nutho B, Chanarat S, Kuhaudomlarp S, Tinikul R, Pakotiprapha D. Biochemical characterization and inhibitor potential of African swine fever virus thymidine kinase. Int J Biol Macromol 2025; 293:139391. [PMID: 39743116 DOI: 10.1016/j.ijbiomac.2024.139391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 12/25/2024] [Accepted: 12/29/2024] [Indexed: 01/04/2025]
Abstract
African Swine Fever (ASF) is a highly contagious disease affecting both domestic pigs and wild boars. In domestic pigs, ASF is a rapidly-progressing disease with a mortality rate reaching 100 %, causing tremendous economic loss in affected areas. ASFV is caused by African Swine Fever Virus (ASFV), which is a large, enveloped double-stranded DNA virus belonging to the Asfarviridae family. ASFV has a remarkably large genome size that encodes more than 150 open reading frames. Among the virally encoded enzymes, thymidine kinase (ASFV-TK) has been shown to be critical for the efficient replication and virulence of ASFV. Here, we report the bioinformatics analysis and biochemical characterization of ASFV-TK. Amino acid sequence analysis revealed that ASFV-TK can be classified as a type II thymidine kinase. Kinetics characterization revealed a maximum velocity (Vmax) and Michaelis constants (Km) that are within the same range as previously characterized type II enzymes. ASFV-TK is competitively inhibited by the feedback inhibitor thymidine 5'-triphosphate and can use 3'-azido-3'-deoxythymidine (AZT) as a substrate with kinetics parameters comparable to those obtained with natural substrates, suggesting that nucleosides and nucleotide analogs could be explored as anti-ASFV agents.
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Affiliation(s)
- Natchaya Rasri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Chayakul Kornyanee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kitima Srisanga
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sakonwan Kuhaudomlarp
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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3
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Makurat S, Cournia Z, Rak J. Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:142-149. [PMID: 34919400 PMCID: PMC8757434 DOI: 10.1021/acs.jcim.1c01157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 11/28/2022]
Abstract
Despite its importance in the nucleoside (and nucleoside prodrug) metabolism, the structure of the active conformation of human thymidine kinase 1 (hTK1) remains elusive. We perform microsecond molecular dynamics simulations of the inactive enzyme form bound to a bisubstrate inhibitor that was shown experimentally to activate another TK1-like kinase, Thermotoga maritima TK (TmTK). Our results are in excellent agreement with the experimental findings for the TmTK closed-to-open state transition. We show that the inhibitor induces an increase of the enzyme radius of gyration due to the expansion on one of the dimer interfaces; the structural changes observed, including the active site pocket volume increase and the decrease in the monomer-monomer buried surface area and of the number of hydrogen bonds (as compared to the inactive enzyme control simulation), indicate that the catalytically competent (open) conformation of hTK1 can be assumed in the presence of an activating ligand.
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Affiliation(s)
- Samanta Makurat
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Janusz Rak
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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4
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Khan N, Shah PP, Ban D, Trigo-Mouriño P, Carneiro MG, DeLeeuw L, Dean WL, Trent JO, Beverly LJ, Konrad M, Lee D, Sabo TM. Solution structure and functional investigation of human guanylate kinase reveals allosteric networking and a crucial role for the enzyme in cancer. J Biol Chem 2019; 294:11920-11933. [PMID: 31201273 DOI: 10.1074/jbc.ra119.009251] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/12/2019] [Indexed: 01/13/2023] Open
Abstract
Human guanylate kinase (hGMPK) is the only known enzyme responsible for cellular GDP production, making it essential for cellular viability and proliferation. Moreover, hGMPK has been assigned a critical role in metabolic activation of antiviral and antineoplastic nucleoside-analog prodrugs. Given that hGMPK is indispensable for producing the nucleotide building blocks of DNA, RNA, and cGMP and that cancer cells possess elevated GTP levels, it is surprising that a detailed structural and functional characterization of hGMPK is lacking. Here, we present the first high-resolution structure of hGMPK in the apo form, determined with NMR spectroscopy. The structure revealed that hGMPK consists of three distinct regions designated as the LID, GMP-binding (GMP-BD), and CORE domains and is in an open configuration that is nucleotide binding-competent. We also demonstrate that nonsynonymous single-nucleotide variants (nsSNVs) of the hGMPK CORE domain distant from the nucleotide-binding site of this domain modulate enzymatic activity without significantly affecting hGMPK's structure. Finally, we show that knocking down the hGMPK gene in lung adenocarcinoma cell lines decreases cellular viability, proliferation, and clonogenic potential while not altering the proliferation of immortalized, noncancerous human peripheral airway cells. Taken together, our results provide an important step toward establishing hGMPK as a potential biomolecular target, from both an orthosteric (ligand-binding sites) and allosteric (location of CORE domain-located nsSNVs) standpoint.
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Affiliation(s)
- Nazimuddin Khan
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Parag P Shah
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Pablo Trigo-Mouriño
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marta G Carneiro
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lynn DeLeeuw
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - William L Dean
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - John O Trent
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Levi J Beverly
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Manfred Konrad
- Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
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5
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Jagiello K, Makurat S, Pereć S, Rak J, Puzyn T. Molecular features of thymidine analogues governing the activity of human thymidine kinase. Struct Chem 2018. [DOI: 10.1007/s11224-018-1124-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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6
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Lin Y, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Sci 2017; 26:2187-2194. [PMID: 28801928 PMCID: PMC5654858 DOI: 10.1002/pro.3270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
We have previously shown that monomeric globular αβ-proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β-strand backbone interactions were structurally confirmed through x-ray crystallography and small-angle X-ray scattering (SAXS). In contrast, C3-C5 designed homo-oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo-oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.
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Affiliation(s)
- Yu‐Ru Lin
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
| | - Nobuyasu Koga
- Research Center of Integrative Molecular SystemsInstitute for Molecular Science, National Institute of Natural Sciences (NINS)Okazaki 444‐8585Japan
- JST, PRESTOKawaguchiSaitama 332‐0012Japan
| | - Sergey M. Vorobiev
- Department of Biological ScienceNortheast Structural Genomics Consortium, Columbia UniversityNew YorkNew York
| | - David Baker
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
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7
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Jiao W, Blackmore NJ, Nazmi AR, Parker EJ. Quaternary structure is an essential component that contributes to the sophisticated allosteric regulation mechanism in a key enzyme from Mycobacterium tuberculosis. PLoS One 2017; 12:e0180052. [PMID: 28665948 PMCID: PMC5493349 DOI: 10.1371/journal.pone.0180052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2017] [Indexed: 01/26/2023] Open
Abstract
The first enzyme of the shikimate pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), adopts a range of distinct allosteric regulation mechanisms in different organisms, related to different quaternary assemblies. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) is a homotetramer, with the allosteric sites in close proximity to the interfaces. Here we examine the importance of the quaternary structure on catalysis and regulation, by amino acid substitution targeting the tetramer interface of MtuDAH7PS. Using only single amino acid substitutions either in, or remote from the interface, two dimeric variants of MtuDAH7PS (MtuDAH7PSF227D and MtuDAH7PSG232P) were successfully generated. Both dimeric variants maintained activity due to the distance between the sites of amino acid substitution and the active sites, but attenuated catalytic efficiency was observed. Both dimeric variants showed significantly disrupted allosteric regulation with greatly impaired binding affinity for one of the allosteric ligands. Molecular dynamics simulations revealed changes in protein dynamics and average conformations in the dimeric variant caused by amino acid substitution remote to the tetramer interface (MtuDAH7PSG232P), which are consistent with the observed reduction in catalytic efficiency and loss of allosteric response.
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Affiliation(s)
- Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola J. Blackmore
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Ali Reza Nazmi
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- * E-mail:
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8
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Valente M, Timm J, Castillo-Acosta VM, Ruiz-Pérez LM, Balzarini T, Nettleship JE, Bird LE, Rada H, Wilson KS, González-Pacanowska D. Cell cycle regulation and novel structural features of thymidine kinase, an essential enzyme in Trypanosoma brucei. Mol Microbiol 2016; 102:365-385. [PMID: 27426054 DOI: 10.1111/mmi.13467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 11/28/2022]
Abstract
Thymidine kinase (TK) is a key enzyme in the pyrimidine salvage pathway which catalyzes the transfer of the γ-phosphate of ATP to 2'-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). Unlike other type II TKs, the Trypanosoma brucei enzyme (TbTK) is a tandem protein with two TK homolog domains of which only the C-terminal one is active. In this study, we establish that TbTK is essential for parasite viability and cell cycle progression, independently of extracellular pyrimidine concentrations. We show that expression of TbTK is cell cycle regulated and that depletion of TbTK leads to strongly diminished dTTP pools and DNA damage indicating intracellular dThd to be an essential intermediate metabolite for the synthesis of thymine-derived nucleotides. In addition, we report the X-ray structure of the catalytically active domain of TbTK in complex with dThd and dTMP at resolutions up to 2.2 Å. In spite of the high conservation of the active site residues, the structures reveal a widened active site cavity near the nucleobase moiety compared to the human enzyme. Our findings strongly support TbTK as a crucial enzyme in dTTP homeostasis and identify structural differences within the active site that could be exploited in the process of rational drug design.
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Affiliation(s)
- Maria Valente
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jennifer Timm
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Víctor M Castillo-Acosta
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Luis M Ruiz-Pérez
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tom Balzarini
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Joanne E Nettleship
- The Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, R92 Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Louise E Bird
- The Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, R92 Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Heather Rada
- The Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, R92 Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain.
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9
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Bhattacharya A, Wang Z, White T, Buffone C, Nguyen LA, Shepard CN, Kim B, Demeler B, Diaz-Griffero F, Ivanov DN. Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect. Sci Rep 2016; 6:31353. [PMID: 27511536 PMCID: PMC4980677 DOI: 10.1038/srep31353] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/18/2016] [Indexed: 12/30/2022] Open
Abstract
SAMHD1, a dNTP triphosphohydrolase, contributes to interferon signaling and restriction of retroviral replication. SAMHD1-mediated retroviral restriction is thought to result from the depletion of cellular dNTP pools, but it remains controversial whether the dNTPase activity of SAMHD1 is sufficient for restriction. The restriction ability of SAMHD1 is regulated in cells by phosphorylation on T592. Phosphomimetic mutations of T592 are not restriction competent, but appear intact in their ability to deplete cellular dNTPs. Here we use analytical ultracentrifugation, fluorescence polarization and NMR-based enzymatic assays to investigate the impact of phosphomimetic mutations on SAMHD1 tetramerization and dNTPase activity in vitro. We find that phosphomimetic mutations affect kinetics of tetramer assembly and disassembly, but their effects on tetramerization equilibrium and dNTPase activity are insignificant. In contrast, the Y146S/Y154S dimerization-defective mutant displays a severe dNTPase defect in vitro, but is indistinguishable from WT in its ability to deplete cellular dNTP pools and to restrict HIV replication. Our data suggest that the effect of T592 phosphorylation on SAMHD1 tetramerization is not likely to explain the retroviral restriction defect, and we hypothesize that enzymatic activity of SAMHD1 is subject to additional cellular regulatory mechanisms that have not yet been recapitulated in vitro.
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Affiliation(s)
- Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Zhonghua Wang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Tommy White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura A Nguyen
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Caitlin N Shepard
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA.,School of Pharmacy, Kyunghee University, Seoul, South Korea
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dmitri N Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
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10
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Agarwal HK, Khalil A, Ishita K, Yang W, Nakkula RJ, Wu LC, Ali T, Tiwari R, Byun Y, Barth RF, Tjarks W. Synthesis and evaluation of thymidine kinase 1-targeting carboranyl pyrimidine nucleoside analogs for boron neutron capture therapy of cancer. Eur J Med Chem 2015; 100:197-209. [PMID: 26087030 DOI: 10.1016/j.ejmech.2015.05.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 10/23/2022]
Abstract
A library of sixteen 2nd generation amino- and amido-substituted carboranyl pyrimidine nucleoside analogs, designed as substrates and inhibitors of thymidine kinase 1 (TK1) for potential use in boron neutron capture therapy (BNCT) of cancer, was synthesized and evaluated in enzyme kinetic-, enzyme inhibition-, metabolomic-, and biodistribution studies. One of these 2nd generation carboranyl pyrimidine nucleoside analogs (YB18A [3]), having an amino group directly attached to a meta-carborane cage tethered via ethylene spacer to the 3-position of thymidine, was approximately 3-4 times superior as a substrate and inhibitor of hTK1 than N5-2OH (2), a 1st generation carboranyl pyrimidine nucleoside analog. Both 2 and 3 appeared to be 5'-monophosphorylated in TK1(+) RG2 cells, both in vitro and in vivo. Biodistribution studies in rats bearing intracerebral RG2 glioma resulted in selective tumor uptake of 3 with an intratumoral concentration that was approximately 4 times higher than that of 2. The obtained results significantly advance the understanding of the binding interactions between TK1 and carboranyl pyrimidine nucleoside analogs and will profoundly impact future design strategies for these agents.
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Affiliation(s)
- Hitesh K Agarwal
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Ahmed Khalil
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Keisuke Ishita
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Weilian Yang
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Robin J Nakkula
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Lai-Chu Wu
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Tehane Ali
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Rohit Tiwari
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Youngjoo Byun
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Rolf F Barth
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Werner Tjarks
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH, USA.
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11
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Structural and Kinetic Characterization of Thymidine Kinase from Leishmania major. PLoS Negl Trop Dis 2015; 9:e0003781. [PMID: 25978379 PMCID: PMC4433323 DOI: 10.1371/journal.pntd.0003781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/23/2015] [Indexed: 01/17/2023] Open
Abstract
Leishmania spp. is a protozoan parasite and the causative agent of leishmaniasis. Thymidine kinase (TK) catalyses the transfer of the γ-phosphate of ATP to 2’-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). L. major Type II TK (LmTK) has been previously shown to be important for infectivity of the parasite and therefore has potential as a drug target for anti-leishmanial therapy. In this study, we determined the enzymatic properties and the 3D structures of holo forms of the enzyme. LmTK efficiently phosphorylates dThd and dUrd and has high structural homology to TKs from other species. However, it significantly differs in its kinetic properties from Trypanosoma brucei TK since purines are not substrates of the enzyme and dNTPs such as dUTP inhibit LmTK. The enzyme had Km and kcat values for dThd of 1.1 μM and 2.62 s-1 and exhibits cooperative binding for ATP. Additionally, we show that the anti-retroviral prodrug zidovudine (3-azido-3-deoxythymidine, AZT) and 5’-modified dUrd can be readily phosphorylated by LmTK. The production of recombinant enzyme at a level suitable for structural studies was achieved by the construction of C-terminal truncated versions of the enzyme and the use of a baculoviral expression system. The structures of the catalytic core of LmTK in complex with dThd, the negative feedback regulator dTTP and the bi-substrate analogue AP5dT, were determined to 2.74, 3.00 and 2.40 Å, respectively, and provide the structural basis for exclusion of purines and dNTP inhibition. The results will aid the process of rational drug design with LmTK as a potential target for anti-leishmanial drugs. The DNA within the genome of an organism encodes all the information, firstly for reproduction and secondly for translation into proteins—the workhorses of a biological cell. Proteins carry out a host of essential biological activities within the cell. A full understanding of a protein now requires determination of a wide range of its properties in solution in the cell and in vitro in solution, but in addition, its 3D structure usually determined by X-ray crystallography. Leishmania species are a family of protozoan parasites of humans and the causative agent of leishmaniasis, a major health concern in the developing world. Selective inhibition of key enzymes in these parasites is a key route for combating these diseases. We have focused our work on thymidine kinase, an important enzyme from Leishmania major, and a potential target for the development of new drugs. We have carried out kinetic studies of the enzyme’s activity in solution and determined its 3D crystal structure, enabling rational drug design.
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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: 0.9] [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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Abstract
The compound class of 3-carboranyl thymidine analogues (3CTAs) are boron delivery agents for boron neutron capture therapy (BNCT), a binary treatment modality for cancer. Presumably, these compounds accumulate selectively in tumor cells via intracellular trapping, which is mediated by hTK1. Favorable in vivo biodistribution profiles of 3CTAs led to promising results in preclinical BNCT of rats with intracerebral brain tumors. This review presents an overview on the design, synthesis, and biological evaluation of first- and second-generation 3CTAs. Boronated nucleosides developed prior to 3CTAs for BNCT and non-boronated N3-substituted thymidine conjugates for other areas of cancer therapy and imaging are also described. In addition, basic features of carborane clusters, which are used as boron moieties in the design and synthesis of 3CTAs, and the biological and structural features of TK1-like enzymes, which are the molecular targets of 3CTAs, are discussed.
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KAY-2-41, a novel nucleoside analogue inhibitor of orthopoxviruses in vitro and in vivo. Antimicrob Agents Chemother 2013; 58:27-37. [PMID: 24126587 DOI: 10.1128/aac.01601-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The availability of adequate treatments for poxvirus infections would be valuable not only for human use but also for veterinary use. In the search for novel antiviral agents, a 1'-methyl-substituted 4'-thiothymidine nucleoside, designated KAY-2-41, emerged as an efficient inhibitor of poxviruses. In vitro, KAY-2-41 was active in the micromolar range against orthopoxviruses (OPVs) and against the parapoxvirus orf. The compound preserved its antiviral potency against OPVs resistant to the reference molecule cidofovir. KAY-2-41 had no noticeable toxicity on confluent monolayers, but a cytostatic effect was seen on growing cells. Genotyping of vaccinia virus (VACV), cowpox virus, and camelpox virus selected for resistance to KAY-2-41 revealed a nucleotide deletion(s) close to the ATP binding site or a nucleotide substitution close to the substrate binding site in the viral thymidine kinase (TK; J2R) gene. These mutations resulted in low levels of resistance to KAY-2-41 ranging from 2.7- to 6.0-fold and cross-resistance to 5-bromo-2'-deoxyuridine (5-BrdU) but not to cidofovir. The antiviral effect of KAY-2-41 relied, at least in part, on activation (phosphorylation) by the viral TK, as shown through enzymatic assays. The compound protected animals from disease and mortality after a lethal challenge with VACV, reduced viral loads in the serum, and abolished virus replication in tissues. In conclusion, KAY-2-41 is a promising nucleoside analogue for the treatment of poxvirus-induced diseases. Our findings warrant the evaluation of additional 1'-carbon-substituted 4'-thiothymidine derivatives as broad-spectrum antiviral agents, since this molecule also showed antiviral potency against herpes simplex virus 1 in earlier studies.
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Mutahir Z, Clausen AR, Andersson KM, Wisen SM, Munch-Petersen B, Piškur J. Thymidine kinase 1 regulatory fine-tuning through tetramer formation. FEBS J 2013; 280:1531-41. [PMID: 23351158 DOI: 10.1111/febs.12154] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 11/30/2022]
Abstract
Thymidine kinase 1 (TK1) provides a crucial precursor, deoxythymidine monophosphate, for nucleic acid synthesis, and the activity of TK1 increases by up to 200-fold during the S-phase of cell division in humans. An important part of the regulatory checkpoints is the ATP and enzyme concentration-dependent transition of TK1 from a dimer with low catalytic efficiency to a tetramer with high catalytic efficiency. This regulatory fine-tuning serves as an additional control to provide a balanced pool of nucleic acid precursors in the cell. We subcloned and over-expressed 10 different TK1s, originating from widely different organisms, and characterized their kinetic and oligomerization properties. Whilst bacteria, plants and Dictyostelium only exhibited dimeric TK1, we found that all animals had a tetrameric TK1. However, a clear ATP-dependent switch between dimer and tetramer was found only in higher vertebrates and was especially pronounced in mammalian and bird TK1s. We suggest that the dimer form is the original form and that the tetramer originated in the animal lineage after the split of Dictyostelium and the lineages leading to invertebrates and vertebrates. The efficient switching mechanism was probably first established in warm-blooded animals when they separated from the rest of the vertebrates.
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Agarwal HK, McElroy CA, Sjuvarsson E, Eriksson S, Darby MV, Tjarks W. Synthesis of N3-substituted carboranyl thymidine bioconjugates and their evaluation as substrates of recombinant human thymidine kinase 1. Eur J Med Chem 2012; 60:456-68. [PMID: 23318906 DOI: 10.1016/j.ejmech.2012.11.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/23/2012] [Accepted: 11/29/2012] [Indexed: 01/19/2023]
Abstract
Four different libraries of overall twenty three N3-substituted thymidine (dThd) analogues, including eleven 3-carboranyl thymidine analogues (3CTAs), were synthesized. The latter are potential agents for Boron Neutron Capture Therapy (BNCT) of cancer. Linker between the dThd scaffold and the m-carborane cluster at the N3-position of the 3CTAs contained amidinyl-(3e and 3f), guanidyl-(7e-7g), tetrazolylmethyl-(9b1/2-9d1/2), or tetrazolyl groups (11b1/2-11d1/2) to improve human thymidine kinase 1 (hTK1) substrate characteristics and water solubilities compared with 1st generation 3CTAs, such as N5 and N5-2OH. The amidinyl- and guanidyl-type N3-substitued dThd analogues (3a-3f and 7a-7g) had hTK1 phosphorylation rates of <30% relative to that of dThd, the endogenous hTK1 substrate, whereas the tetrazolyl-type N3-substitued dThd analogues (9a, 9b1/2-9d1/2 and 11a, 11b1/2-11d1/2) had relative phosphorylation rates (rPRs) of >40%. Compounds 9a, 9b1/2-9d1/2 and 11a, 11b1/2-11d1/2 were subjected to in-depth enzyme kinetics studies and the obtained rk(cat)/K(m) (k(cat)/K(m) relative to that of dThd) ranged from 2.5 to 26%. The tetrazolyl-type N3-substitued dThd analogues 9b1/2 and 11d1/2 were the best substrates of hTK1 with rPRs of 52.4% and 42.5% and rk(cat)/K(m) values of 14.9% and 19.7% respectively. In comparison, the rPR and rk(cat)/K(m) values of N5-2OH in this specific study were 41.5% and 10.8%, respectively. Compounds 3e and 3f were >1900 and >1500 times, respectively, better soluble in PBS (pH 7.4) than N5-2OH whereas solubilities for 9b1/2-9d1/2 and 11b1/2-11d1/2 were only 1.3-13 times better.
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Affiliation(s)
- Hitesh K Agarwal
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
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Hanan S, Jagarlamudi KK, Liya W, Ellen H, Staffan E. Quaternary structures of recombinant, cellular, and serum forms of thymidine kinase 1 from dogs and humans. BMC BIOCHEMISTRY 2012; 13:12. [PMID: 22741536 PMCID: PMC3411398 DOI: 10.1186/1471-2091-13-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/28/2012] [Indexed: 12/29/2022]
Abstract
Background Thymidine kinase 1 (TK1) is a salvage enzyme involved in DNA precursor synthesis, and its expression is proliferation dependent. A serum form of TK1 has been used as a biomarker in human medicine for many years and more recently to monitor canine lymphoma. Canine TK1 has not been cloned and studied. Therefore, dog and human TK1 cDNA were cloned and expressed, and the recombinant enzymes characterized. The serum and cellular forms of canine and human TK1 were studied by size-exclusion chromatography and the level of TK1 protein was determined using polyclonal and monoclonal anti-TK1 antibodies. Results Canine TK1 phosphorylated the thymidine (dThd) analog 3'-azido-thymidine (AZT) as efficiently as it did dThd, whereas AZT phosphorylation by human TK1 was less efficient than that of dThd. Dog TK1 was also more thermostable and pH tolerant than the human enzyme. Oligomeric forms were observed with both enzymes in addition to the tetrameric and dimeric forms. Cellular TK1 was predominantly seen in dimeric and tetrameric forms, in the case of both dog TK1 from MDCK cells and human TK1 from CEM cells. Active serum TK1 was found mainly in a high molecular weight form, and treatment with a reducing agent shifted the high molecular weight complex to lower molecular weight forms with reduced total activity. Western blot analysis demonstrated a polypeptide of 26 kDa (dog) and 25 kDa (human) for cellular and serum TK1. There was no direct correlation between serum TK1 activity and protein level. It appears that a substantial fraction of serum TK1 is not enzymatically active. Conclusions These results suggest that the serum TK1 protein differs from cellular or recombinant forms, is more active in high molecular weight complexes, and is sensitive to reducing agents. The results presented here provide important information for the future development and use of serum TK1 as a diagnostic biomarker in human and veterinary medicine.
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Affiliation(s)
- Sharif Hanan
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, BMC, 575, Uppsala, S-751 23, Sweden
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Tiwari R, Toppino A, Agarwal HK, Huo T, Byun Y, Gallucci J, Hasabelnaby S, Khalil A, Goudah A, Baiocchi RA, Darby MV, Barth RF, Tjarks W. Synthesis, biological evaluation, and radioiodination of halogenated closo-carboranylthymidine analogues. Inorg Chem 2011; 51:629-39. [PMID: 22175713 DOI: 10.1021/ic202150b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis and initial biological evaluation of 3-carboranylthymidine analogues (3CTAs) that are (radio)halogenated at the closo-carborane cluster are described. Radiohalogenated 3CTAs have the potential to be used in the radiotherapy and imaging of cancer because they may be selectively entrapped in tumor cells through monophosphorylation by human thymidine kinase 1 (hTK1). Two strategies for the synthesis of a (127)I-labeled form of a specific 3CTA, previously designated as N5, are described: (1) direct iodination of N5 with iodine monochloride and aluminum chloride to obtain N5-(127)I and (2) initial monoiodination of o-carborane to 9-iodo-o-carborane followed by its functionalization to N5-(127)I. The former strategy produced N5-(127)I in low yields along with di-, tri-, and tetraiodinated N5 as well as decomposition products, whereas the latter method produced only N5-(127)I in high yields. N5-(127)I was subjected to nucleophilic halogen- and isotope-exchange reactions using Na(79/81)Br and Na(125)I, respectively, in the presence of Herrmann's catalyst to obtain N5-(79/81)Br and N5-(125)I, respectively. Two intermediate products formed using the second strategy, 1-(tert-butyldimethylsilyl)-9-iodo-o-carborane and 1-(tert-butyldimethylsilyl)-12-iodo-o-carborane, were subjected to X-ray diffraction studies to confirm that substitution at a single carbon atom of 9-iodo-o-carborane resulted in the formation of two structural isomers. To the best of our knowledge, this is the first report of halogen- and isotope-exchange reactions of B-halocarboranes that have been conjugated to a complex biomolecule. Human TK1 phosphorylation rates of N5, N5-(127)I, and N5-(79/81)Br ranged from 38.0% to 29.6% relative to that of thymidine, the endogenous hTK1 substrate. The in vitro uptake of N5, N5-(127)I, and N5-(79/81)Br in L929 TK1(+) cells was 2.0, 1.8, and 1.4 times greater than that in L929 TK1(-) cells.
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Affiliation(s)
- Rohit Tiwari
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, USA
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Dauter M, Dauter Z. Deprotonated imidodiphosphate in AMPPNP-containing protein structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:1073-5. [PMID: 22120745 PMCID: PMC3225179 DOI: 10.1107/s0907444911046105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/02/2011] [Indexed: 11/10/2022]
Abstract
Many different proteins utilize the chemical energy provided by the cofactor adenosine triphosphate (ATP) for their proper function. A number of structures in the Protein Data Bank (PDB) contain adenosine 5'-(β,γ-imido)triphosphate (AMPPNP), a nonhydrolysable analog of ATP in which the bridging O atom between the two terminal phosphate groups is substituted by the imido function. Under mild conditions imides do not have acidic properties and thus the imide nitrogen should be protonated. However, an analysis of protein structures containing AMPPNP reveals that the imide group is deprotonated in certain complexes if the negative charges of the phosphate moieties in AMPPNP are in part neutralized by coordinating divalent metals or a guanidinium group of an arginine.
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Affiliation(s)
- Miroslawa Dauter
- Basic Research Program, SAIC-Frederick Inc., Argonne National Laboratory, Argonne, IL 60439, USA.
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Deville-Bonne D, El Amri C, Meyer P, Chen Y, Agrofoglio LA, Janin J. Human and viral nucleoside/nucleotide kinases involved in antiviral drug activation: structural and catalytic properties. Antiviral Res 2010; 86:101-20. [PMID: 20417378 DOI: 10.1016/j.antiviral.2010.02.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/31/2010] [Accepted: 02/01/2010] [Indexed: 12/11/2022]
Abstract
Antiviral nucleoside and nucleotide analogs, essential for the treatment of viral infections in the absence of efficient vaccines, are prodrug forms of the active compounds that target the viral DNA polymerase or reverse transcriptase. The activation process requires several successive phosphorylation steps catalyzed by different kinases, which are present in the host cell or encoded by some of the viruses. These activation reactions often are rate-limiting steps and are thus open to improvement. We review here the structural and enzymatic properties of the enzymes that carry out the activation of analogs used in therapy against human immunodeficiency virus and against DNA viruses such as hepatitis B, herpes and poxviruses. Four major classes of drugs are considered: thymidine analogs, non-natural L-nucleosides, acyclic nucleoside analogs and acyclic nucleoside phosphonate analogs. Their efficiency as drugs depends both on the low specificity of the viral polymerase that allows their incorporation into DNA, but also on the ability of human/viral kinases to provide the activated triphosphate active forms at a high concentration at the right place. Two distinct modes of action are considered, depending on the origin of the kinase (human or viral). If the human kinases are house-keeping enzymes that belong to the metabolic salvage pathway, herpes and poxviruses encode for related enzymes. The structures, substrate specificities and catalytic properties of each of these kinases are discussed in relation to drug activation.
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Affiliation(s)
- Dominique Deville-Bonne
- Enzymologie Moléculaire et Fonctionnelle, UR4 Université Pierre et Marie Curie, 7 quai St Bernard, 75252 Paris Cedex 05, France.
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Zander J, Hartenfeller M, Hähnke V, Proschak E, Besier S, Wichelhaus T, Schneider G. Multistep Virtual Screening for Rapid and Efficient Identification of Non-Nucleoside Bacterial Thymidine Kinase Inhibitors. Chemistry 2010; 16:9630-7. [DOI: 10.1002/chem.201001347] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Lutz S, Liu L, Liu Y. Engineering Kinases to Phosphorylate Nucleoside Analogs for Antiviral and Cancer Therapy. Chimia (Aarau) 2009; 63:737-744. [PMID: 20305804 DOI: 10.2533/chimia.2009.737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Enzyme engineering by directed evolution presents a powerful strategy for tailoring the function and physicochemical properties of biocatalysts to therapeutic and industrial applications. Our laboratory's research focuses on developing novel molecular tools for protein engineering, as well as on utilizing these methods to customize enzymes and to study fundamental aspects of their structure and function. Specifically, we are interested in nucleoside and nucleotide kinases which are responsible for the intracellular phosphorylation of nucleoside analog (NA) prodrugs to their biologically active triphosphates. The high substrate specificity of the cellular kinases often interferes with prodrug activation and consequently lowers the potency of NAs as antiviral and cancer therapeutics. A working solution to the problem is the co-adminstration of a promiscuous kinase from viruses, bacteria, and other mammals. However, further therapeutic enhancements of NAs depend on the selective and efficient prodrug phosphorylation. In the absence of true NA kinases in nature, we are pursuing laboratory evolution strategies to generate efficient phosphoryl-transfer catalysts. This review summarizes some of our recent work in the field and outlines future challenges.
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Munch-Petersen B. Reversible tetramerization of human TK1 to the high catalytic efficient form is induced by pyrophosphate, in addition to tripolyphosphates, or high enzyme concentration. FEBS J 2008; 276:571-80. [DOI: 10.1111/j.1742-4658.2008.06804.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
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Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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Desbouis D, Struthers H, Spiwok V, Küster T, Schibli R. Synthesis, In Vitro, and In Silico Evaluation of Organometallic Technetium and Rhenium Thymidine Complexes with Retained Substrate Activity toward Human Thymidine Kinase Type 1. J Med Chem 2008; 51:6689-98. [PMID: 18837546 DOI: 10.1021/jm800530p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dominique Desbouis
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland, Center for Radiopharmaceutical Science, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland, Department of Structure and Function of Saccharides, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 84538 Bratislava, Slovak Republic
| | - Harriet Struthers
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland, Center for Radiopharmaceutical Science, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland, Department of Structure and Function of Saccharides, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 84538 Bratislava, Slovak Republic
| | - Vojtech Spiwok
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland, Center for Radiopharmaceutical Science, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland, Department of Structure and Function of Saccharides, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 84538 Bratislava, Slovak Republic
| | - Tatiana Küster
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland, Center for Radiopharmaceutical Science, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland, Department of Structure and Function of Saccharides, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 84538 Bratislava, Slovak Republic
| | - Roger Schibli
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland, Center for Radiopharmaceutical Science, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland, Department of Structure and Function of Saccharides, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 84538 Bratislava, Slovak Republic
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