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Backer N, Kumar A, Singh AK, Singh H, Narasimhan B, Kumar P. Medicinal chemistry aspects of uracil containing dUTPase inhibitors targeting colorectal cancer. Drug Discov Today 2024; 29:103853. [PMID: 38070703 DOI: 10.1016/j.drudis.2023.103853] [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: 09/04/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Deoxyuridine-5'-triphosphate nucleotidohydrolase (dUTPase), a vital enzyme in pyrimidine metabolism, is a prime target for treating colorectal cancer. Uracil shares structural traits with DNA/RNA bases, prompting exploration by medicinal chemists for pharmacological modifications. Some existing drugs, including thymidylate synthase (TS) and dUTPase inhibitors, incorporate uracil moieties. These derivatives hinder crucial cell proliferation pathways encompassing TS, dUTPases, dihydropyrimidine dehydrogenase, and uracil-DNA glycosylase. This review compiles uracil derivatives that have served as dUTPase inhibitors across various organisms, forming a library for targeting human dUTPase. Insights into their structural requisites for human applications and comparative analyses of binding pockets are provided for analyzing the compounds against human dUTPase.
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Affiliation(s)
- Nabeel Backer
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Harshwardhan Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | | | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India.
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2
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Sanz-Frasquet C, Ciges-Tomas JR, Alite C, Penadés JR, Marina A. The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases. Microbiol Spectr 2023; 11:e0323222. [PMID: 36622213 PMCID: PMC9927489 DOI: 10.1128/spectrum.03232-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/18/2022] [Indexed: 01/10/2023] Open
Abstract
Stl, the master repressor of the Staphylococcus aureus pathogenicity islands (SaPIs), targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. To activate their cycle, some SaPI Stls target both phage dimeric and phage trimeric dUTPases (Duts) as antirepressors, which are structurally unrelated proteins that perform identical functions for the phage. This intimate link between the SaPI's repressor and the phage inducer has imposed an evolutionary optimization of Stl that allows the interaction with Duts from unrelated organisms. In this work, we structurally characterize this sophisticated mechanism of specialization by solving the structure of the prototypical SaPIbov1 Stl in complex with a prokaryotic and a eukaryotic trimeric Dut. The heterocomplexes with Mycobacterium tuberculosis and Homo sapiens Duts show the molecular strategy of Stl to target trimeric Duts from different kingdoms. Our structural results confirm the participation of the five catalytic motifs of trimeric Duts in Stl binding, including the C-terminal flexible motif V that increases the affinity by embracing Stl. In silico and in vitro analyses with a monomeric Dut support the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor in the different kingdoms of life. IMPORTANCE Stl, the Staphylococcus aureus pathogenicity island (SaPI) master repressor, targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. This fascinating phage-SaPI arms race is exemplified by the Stl from SaPIbov1 which targets phage dimeric and trimeric dUTPases (Duts), structurally unrelated proteins with identical functions in the phages. By solving the structure of the Stl in complex with a prokaryotic (M. tuberculosis) and a eukaryotic (human) trimeric Dut, we showed that Stl has developed a sophisticated substrate mimicry strategy to target trimeric Duts. Since all these Duts present identical catalytic mechanisms, Stl is able to interact with Duts from different kingdoms. In addition, in silico modeling with monomeric Dut supports the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor.
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Affiliation(s)
- Carla Sanz-Frasquet
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - J. Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
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3
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Kósa N, Zolcsák Á, Voszka I, Csík G, Horváti K, Horváth L, Bősze S, Herenyi L. Comparison of the Efficacy of Two Novel Antitubercular Agents in Free and Liposome-Encapsulated Formulations. Int J Mol Sci 2021; 22:ijms22052457. [PMID: 33671100 PMCID: PMC7957691 DOI: 10.3390/ijms22052457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis is one of the top ten causes of death worldwide, and due to the appearance of drug-resistant strains, the development of new antituberculotic agents is a pressing challenge. Employing an in silico docking method, two coumaran (2,3-dihydrobenzofuran) derivatives-TB501 and TB515-were determined, with promising in vitro antimycobacterial activity. To enhance their effectiveness and reduce their cytotoxicity, we used liposomal drug carrier systems. Two types of small unilamellar vesicles (SUV) were prepared: multicomponent pH-sensitive stealth liposome (SUVmixed) and monocomponent conventional liposome. The long-term stability of our vesicles was obtained by the examination of particle size distribution with dynamic light scattering. Encapsulation efficiency (EE) of the two drugs was determined from absorption spectra before and after size exclusion chromatography. Cellular uptake and cytotoxicity were determined on human MonoMac-6 cells by flow cytometry. The antitubercular effect was characterized by the enumeration of colony-forming units on Mycobacterium tuberculosis H37Rv infected MonoMac-6 cultures. We found that SUVmixed + TB515 has the best long-term stability. TB515 has much higher EE in both types of SUVs. Cellular uptake for native TB501 is extremely low, but if it is encapsulated in SUVmixed it appreciably increases; in the case of TB515, quasi total uptake is accessible. It is concluded that SUVmixed + TB501 seems to be the most efficacious antitubercular formulation given the presented experiments; to find the most promising antituberculotic formulation for therapy further in vivo investigations are needed.
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Affiliation(s)
- Nikoletta Kósa
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (N.K.); (Á.Z.); (I.V.); (G.C.)
| | - Ádám Zolcsák
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (N.K.); (Á.Z.); (I.V.); (G.C.)
| | - István Voszka
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (N.K.); (Á.Z.); (I.V.); (G.C.)
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (N.K.); (Á.Z.); (I.V.); (G.C.)
| | - Kata Horváti
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Hungarian Academy of Sciences, 1518 Budapest, Hungary; (K.H.); (L.H.)
- Institute of Chemistry, Eötvös Loránd University, 1518 Budapest, Hungary
| | - Lilla Horváth
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Hungarian Academy of Sciences, 1518 Budapest, Hungary; (K.H.); (L.H.)
- Institute of Chemistry, Eötvös Loránd University, 1518 Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Hungarian Academy of Sciences, 1518 Budapest, Hungary; (K.H.); (L.H.)
- Correspondence: (S.B.); (L.H.)
| | - Levente Herenyi
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (N.K.); (Á.Z.); (I.V.); (G.C.)
- Correspondence: (S.B.); (L.H.)
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4
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Liang R, Wang G, Zhang D, Ye G, Li M, Shi Y, Shi J, Chen H, Peng G. Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development. J Biol Chem 2021; 296:100015. [PMID: 33139328 PMCID: PMC7948977 DOI: 10.1074/jbc.ra120.014005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 11/06/2022] Open
Abstract
African swine fever, caused by the African swine fever virus (ASFV), is among the most significant swine diseases. There are currently no effective treatments against ASFV. ASFV contains a gene encoding a dUTPase (E165R), which is required for viral replication in swine macrophages, making it an attractive target for inhibitor development. However, the full structural details of the ASFV dUTPase and those of the comparable swine enzyme are not available, limiting further insights. Herein, we determine the crystal structures of ASFV dUTPase and swine dUTPase in both their ligand-free and ligand-bound forms. We observe that the swine enzyme employs a classical dUTPase architecture made up of three-subunit active sites, whereas the ASFV enzyme employs a novel two-subunit active site. We then performed a comparative analysis of all dUTPase structures uploaded in the Protein Data Bank (PDB), which showed classical and non-classical types were mainly determined by the C-terminal β-strand orientation, and the difference was mainly related to the four amino acids behind motif IV. Thus, our study not only explains the reason for the structural diversity of dUTPase but also reveals how to predict dUTPase type, which may have implications for the dUTPase family. Finally, we tested two dUTPase inhibitors developed for the Plasmodium falciparum dUTPase against the swine and ASFV enzymes. One of these compounds inhibited the ASFV dUTPase at low micromolar concentrations (Kd = 15.6 μM) and with some selectivity (∼2x) over swine dUTPase. In conclusion, our study expands our understanding of the dUTPase family and may aid in the development of specific ASFV inhibitors.
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Affiliation(s)
- Rui Liang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Gang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Ding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Gang Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Mengxia Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China.
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5
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Zang K, Li F, Ma Q. The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner. J Biol Chem 2017; 293:1088-1099. [PMID: 29187596 DOI: 10.1074/jbc.m117.815266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/14/2017] [Indexed: 01/04/2023] Open
Abstract
dUTPases are essential enzymes for maintaining genome integrity and have recently been shown to play moonlighting roles when containing extra sequences. Interestingly, the trimeric dUTPase of white spot syndrome virus (wDUT) harbors a sequence insert at the position preceding the C-terminal catalytic motif V (pre-V insert), rarely seen in other dUTPases. However, whether this extra sequence endows wDUT with additional properties is unknown. Herein, we present the crystal structures of wDUT in both ligand-free and ligand-bound forms. We observed that the pre-V insert in wDUT forms an unusual β-hairpin structure in the domain-swapping region and thereby facilitates a unique orientation of the adjacent C-terminal segment, positioning the catalytic motif V onto the active site of its own subunit instead of a third subunit. Consequently, wDUT employs two-subunit active sites, unlike the widely accepted paradigm that the active site of trimeric dUTPase is contributed by all three subunits. According to results from local structural comparisons, the active-site configuration of wDUT is similar to that of known dUTPases. However, we also found that residues in the second-shell region of the active site are reconfigured in wDUT as an adaption to its unique C-terminal orientation. We also show that deletion of the pre-V insert significantly reduces wDUT's enzymatic activity and thermal stability. We hypothesize that this rare structural arrangement confers additional functionality to wDUT. In conclusion, our study expands the structural diversity in the conserved dUTPase family and illustrates how sequence insertion and amino acid substitution drive protein evolution cooperatively.
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Affiliation(s)
- Kun Zang
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
| | - Qingjun Ma
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China, .,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
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6
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Nagy GN, Suardíaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Tóth J, Vértessy BG, Rosta E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. J Am Chem Soc 2016; 138:15035-15045. [PMID: 27740761 DOI: 10.1021/jacs.6b09012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all of the above properties; all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the γ-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained on the basis of the unique chemistry performed by the pyrophosphatase dUTPases.
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Affiliation(s)
- Gergely N Nagy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Reynier Suardíaz
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Anna Lopata
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Olivér Ozohanics
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Károly Vékey
- Core Technologies Centre, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Rockville, Maryland 10892-9314, United States
| | - Ibolya Leveles
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Beata G Vértessy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
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7
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Lopata A, Leveles I, Bendes ÁÁ, Viskolcz B, Vértessy BG, Jójárt B, Tóth J. A Hidden Active Site in the Potential Drug Target Mycobacterium tuberculosis dUTPase Is Accessible through Small Amplitude Protein Conformational Changes. J Biol Chem 2016; 291:26320-26331. [PMID: 27815500 DOI: 10.1074/jbc.m116.734012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 11/04/2016] [Indexed: 11/06/2022] Open
Abstract
dUTPases catalyze the hydrolysis of dUTP into dUMP and pyrophosphate to maintain the proper nucleotide pool for DNA metabolism. Recent evidence suggests that dUTPases may also represent a selective drug target in mycobacteria because of the crucial role of these enzymes in maintaining DNA integrity. Nucleotide-hydrolyzing enzymes typically harbor a buried ligand-binding pocket at interdomain or intersubunit clefts, facilitating proper solvent shielding for the catalyzed reaction. The mechanism by which substrate binds this hidden pocket and product is released in dUTPases is unresolved because of conflicting crystallographic and spectroscopic data. We sought to resolve this conflict by using a combination of random acceleration molecular dynamics (RAMD) methodology and structural and biochemical methods to study the dUTPase from Mycobacterium tuberculosis In particular, the RAMD approach used in this study provided invaluable insights into the nucleotide dissociation process that reconciles all previous experimental observations. Specifically, our data suggest that nucleotide binding takes place as a small stretch of amino acids transiently slides away and partially uncovers the active site. The in silico data further revealed a new dUTPase conformation on the pathway to a relatively open active site. To probe this model, we developed the Trp21 reporter and collected crystallographic, spectroscopic, and kinetic data that confirmed the interaction of Trp21 with the active site shielding C-terminal arm, suggesting that the RAMD method is effective. In summary, our computational simulations and spectroscopic results support the idea that small loop movements in dUTPase allow the shuttlingof the nucleotides between the binding pocket and the solvent.
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Affiliation(s)
- Anna Lopata
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Ibolya Leveles
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Ábris Ádám Bendes
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Béla Viskolcz
- the Institute of Chemistry, University of Miskolc, Miskolc, Hungary H3529
| | - Beáta G Vértessy
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117.,the Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary H1111, and
| | - Balázs Jójárt
- Department of Chemical Informatics, University of Szeged, Szeged, Hungary H6725
| | - Judit Tóth
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117,
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8
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Benedek A, Horváth A, Hirmondó R, Ozohanics O, Békési A, Módos K, Révész Á, Vékey K, Nagy GN, Vértessy BG. Potential steps in the evolution of a fused trimeric all-β dUTPase involve a catalytically competent fused dimeric intermediate. FEBS J 2016; 283:3268-86. [PMID: 27380921 DOI: 10.1111/febs.13800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 06/08/2016] [Accepted: 07/04/2016] [Indexed: 12/15/2022]
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is essential for genome integrity. Interestingly, this enzyme from Drosophila virilis has an unusual form, as three monomer repeats are merged with short linker sequences, yielding a fused trimer-like dUTPase fold. Unlike homotrimeric dUTPases that are encoded by a single repeat dut gene copy, the three repeats of the D. virilis dut gene are not identical due to several point mutations. We investigated the potential evolutionary pathway that led to the emergence of this extant fused trimeric dUTPase in D. virilis. The herein proposed scenario involves two sequential gene duplications followed by sequence divergence amongst the dut repeats. This pathway thus requires the existence of a transient two-repeat-containing fused dimeric dUTPase intermediate. We identified the corresponding ancestral dUTPase single repeat enzyme together with its tandem repeat evolutionary intermediate and characterized their enzymatic function and structural stability. We additionally engineered and characterized artificial single or tandem repeat constructs from the extant enzyme form to investigate the influence of the emergent residue alterations on the formation of a functional assembly. The observed severely impaired stability and catalytic activity of these latter constructs provide a plausible explanation for evolutionary persistence of the extant fused trimeric D. virilis dUTPase form. For the ancestral homotrimeric and the fused dimeric intermediate forms, we observed strong catalytic and structural competence, verifying viability of the proposed evolutionary pathway. We conclude that the progression along the herein described evolutionary trajectory is determined by the retained potential of the enzyme for its conserved three-fold structural symmetry.
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Affiliation(s)
- András Benedek
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - András Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Angéla Békési
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Módos
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ágnes Révész
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Vékey
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
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9
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Inoguchi N, Chaiseeda K, Yamanishi M, Kim MK, Jang Y, Bajaj M, Chia CP, Becker DF, Moriyama H. Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation. BMC Res Notes 2015; 8:784. [PMID: 26666293 PMCID: PMC4678481 DOI: 10.1186/s13104-015-1760-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) hydrolyzes dUTP to dUMP and pyrophosphate to maintain the cellular thymine-uracil ratio. dUTPase is also a target for cancer chemotherapy. However, the mechanism defining its substrate affinity remains unclear. Sequence comparisons of various dUTPases revealed that Arabidopsis thaliana dUTPase has a unique tryptophan at position 93, which potentially contributes to its degree of substrate affinity. To better understand the roles of tryptophan 93, A. thaliana dUTPase was studied. RESULTS Enzyme assays showed that A. thaliana dUTPase belongs to a high-affinity group of isozymes, which also includes the enzymes from Escherichia coli and Mycobacterium tuberculosis. Enzymes from Homo sapiens and Saccharomyces cerevisiae are grouped as low-affinity dUTPases. The structure of the homo-trimeric A. thaliana dUTPase showed three active sites, each with a different set of ligand interactions between the amino acids and water molecules. On an α-helix, tryptophan 93 appears to keep serine 89 in place via a water molecule and to specifically direct the ligand. Upon being oriented in the active site, the C-terminal residues close the active site to promote the reaction. CONCLUSIONS In the high-affinity group, the prefixed direction of the serine residues was oriented by a positively charged residue located four amino acids away, while low-affinity enzymes possess small hydrophobic residues at the corresponding sites.
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Affiliation(s)
- Noriko Inoguchi
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | | | - Mamoru Yamanishi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Moon Ki Kim
- School of Mechanical Engineering, Sungkyunkwan University, 300 Cheoncheon, Suwon, South Korea.
| | - Yunho Jang
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA, USA. .,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Mamta Bajaj
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Catherine P Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Donald F Becker
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
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10
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Lopata A, Jambrina PG, Sharma PK, Brooks BR, Toth J, Vertessy BG, Rosta E. Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction. ACS Catal 2015. [DOI: 10.1021/cs502087f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Anna Lopata
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Pablo G. Jambrina
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Pankaz K. Sharma
- College
of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892-9314, United States
| | - Judit Toth
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Beata G. Vertessy
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest H1111, Hungary
| | - Edina Rosta
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
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11
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Horváti K, Bacsa B, Szabó N, Fodor K, Balka G, Rusvai M, Kiss É, Mező G, Grolmusz V, Vértessy B, Hudecz F, Bősze S. Antimycobacterial activity of peptide conjugate of pyridopyrimidine derivative against Mycobacterium tuberculosis in a series of in vitro and in vivo models. Tuberculosis (Edinb) 2015; 95 Suppl 1:S207-11. [PMID: 25728610 DOI: 10.1016/j.tube.2015.02.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
New pyridopyrimidine derivatives were defined using a novel HTS in silico docking method (FRIGATE). The target protein was a dUTPase enzyme (EC 3.6.1.23; Rv2697) which plays a key role in nucleotide biosynthesis of Mycobacterium tuberculosis (Mtb). Top hit molecules were assayed in vitro for their antimycobacterial effect on Mtb H37Rv culture. In order to enhance the cellular uptake rate, the TB820 compound was conjugated to a peptid-based carrier and a nanoparticle type delivery system (polylactide-co-glycolide, PLGA) was applied. The conjugate had relevance to in vitro antitubercular activity with low in vitro and in vivo toxicity. In a Mtb H37Rv infected guinea pig model the in vivo efficacy of orally administrated PLGA encapsulated compound was proven: animals maintained a constant weight gain and no external clinical signs of tuberculosis were observed. All tissue homogenates from lung, liver and kidney were found negative for Mtb, and diagnostic autopsy showed that no significant malformations on the tissues occurred.
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Affiliation(s)
- Kata Horváti
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary
| | - Bernadett Bacsa
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary
| | - Nóra Szabó
- Laboratory of Bacteriology, Korányi National Institute for Tuberculosis and Respiratory Medicine, Budapest, Hungary
| | - Kinga Fodor
- Department of State Veterinary Medicine and Agricultural Economics, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - Gyula Balka
- Department of Pathology and Forensic Veterinary Medicine, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - Miklós Rusvai
- Department of Pathology and Forensic Veterinary Medicine, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - Éva Kiss
- Laboratory of Interfaces and Nanostructures, Eötvös L. University, Budapest, Hungary
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary
| | - Vince Grolmusz
- Protein Information Technology Group, Eötvös L. University, Budapest, Hungary
| | - Beáta Vértessy
- Institute of Enzimology, Hungarian Academy of Science, Budapest, Hungary
| | - Ferenc Hudecz
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary; Department of Organic Chemistry, Eötvös L. University, Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary.
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12
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Leveles I, Németh V, Szabó JE, Harmat V, Nyíri K, Bendes ÁÁ, Papp-Kádár V, Zagyva I, Róna G, Ozohanics O, Vékey K, Tóth J, Vértessy BG. Structure and enzymatic mechanism of a moonlighting dUTPase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2298-308. [PMID: 24311572 DOI: 10.1107/s0907444913021136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/29/2013] [Indexed: 02/08/2023]
Abstract
Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a ϕ11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small β-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of ϕ11 phage dUTPase.
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Affiliation(s)
- Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 29 Karolina Street, 1113 Budapest, Hungary
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13
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Pecsi I, Hirmondo R, Brown AC, Lopata A, Parish T, Vertessy BG, Tóth J. The dUTPase enzyme is essential in Mycobacterium smegmatis. PLoS One 2012; 7:e37461. [PMID: 22655049 PMCID: PMC3360063 DOI: 10.1371/journal.pone.0037461] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/20/2012] [Indexed: 02/06/2023] Open
Abstract
Thymidine biosynthesis is essential in all cells. Inhibitors of the enzymes involved in this pathway (e.g. methotrexate) are thus frequently used as cytostatics. Due to its pivotal role in mycobacterial thymidylate synthesis dUTPase, which hydrolyzes dUTP into the dTTP precursor dUMP, has been suggested as a target for new antitubercular agents. All mycobacterial genomes encode dUTPase with a mycobacteria-specific surface loop absent in the human dUTPase. Using Mycobacterium smegmatis as a fast growing model for Mycobacterium tuberculosis, we demonstrate that dUTPase knock-out results in lethality that can be reverted by complementation with wild-type dUTPase. Interestingly, a mutant dUTPase gene lacking the genus-specific loop was unable to complement the knock-out phenotype. We also show that deletion of the mycobacteria-specific loop has no major effect on dUTPase enzymatic properties in vitro and thus a yet to be identified loop-specific function seems to be essential within the bacterial cell context. In addition, here we demonstrated that Mycobacterium tuberculosis dUTPase is fully functional in Mycobacterium smegmatis as it rescues the lethal knock-out phenotype. Our results indicate the potential of dUTPase as a target for antitubercular drugs and identify a genus-specific surface loop on the enzyme as a selective target.
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Affiliation(s)
- Ildiko Pecsi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Rita Hirmondo
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Amanda C. Brown
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Anna Lopata
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tanya Parish
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Beata G. Vertessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
- * E-mail: (BGV); (JT)
| | - Judit Tóth
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail: (BGV); (JT)
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14
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Horváti K, Bacsa B, Szabó N, Dávid S, Mező G, Grolmusz V, Vértessy B, Hudecz F, Bősze S. Enhanced cellular uptake of a new, in silico identified antitubercular candidate by peptide conjugation. Bioconjug Chem 2012; 23:900-7. [PMID: 22515329 DOI: 10.1021/bc200221t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis is a successful pathogen, and it can survive in infected macrophages in dormant phase for years and decades. The therapy of tuberculosis takes at least six months, and the slow-growing bacterium is resistant to many antibiotics. The development of novel antimicrobials to counter the emergence of bacteria resistant to current therapies is urgently needed. In silico docking methods and structure-based drug design are useful bioinformatics tools for identifying new agents. A docking experiment to M. tuberculosis dUTPase enzyme, which plays a key role in the bacterial metabolism, has resulted in 10 new antitubercular drug candidates. The uptake of antituberculars by infected macrophages is limited by extracellular diffusion. The optimization of the cellular uptake by drug delivery systems can decrease the used dosages and the length of the therapy, and it can also enhance the bioavailability of the drug molecule. In this study, improved in vitro efficacy was achieved by attaching the TB5 antitubercular drug candidate to peptide carriers. As drug delivery components, (i) an antimicrobial granulysin peptide and (ii) a receptor specific tuftsin peptide were used. An efficient synthetic approach was developed to conjugate the in silico identified TB5 coumarone derivative to the carrier peptides. The compounds were effective on M. tuberculosis H37Rv culture in vitro; the chemical linkage did not affect the antimycobacterial activity. Here, we show that the OT20 tuftsin and GranF2 granulysin peptide conjugates have dramatically enhanced uptake into human MonoMac6 cells. The TB5-OT20 tuftsin conjugate exhibited significant antimycobacterial activity on M. tuberculosis H37Rv infected MonoMac6 cells and inhibited intracellular bacteria.
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Affiliation(s)
- Kata Horváti
- Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University , Budapest, Hungary
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15
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Site-directed mutagenesis provides insights into the selective binding of trityl derivatives to Plasmodium falciparum dUTPase. Eur J Med Chem 2011; 46:3309-14. [PMID: 21600680 DOI: 10.1016/j.ejmech.2011.04.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/13/2011] [Accepted: 04/19/2011] [Indexed: 11/21/2022]
Abstract
We have previously identified a series of triphenylmethane derivatives of deoxyuridine with antimalarial activity in vitro which selectively inhibit Plasmodium falciparum deoxyuridine triphosphate nucleotidohydrolase (PfdUTPase) compared to the human enzyme. The crystal structure of PfdUTPase in complex with one of these inhibitors suggested that the triphenylmethane derivative was selective due to a series of interactions between the trityl group and the side chains of residues Phe(46), Ile(117) and Lys(96) located in a hydrophobic pocket distinct from the phosphate binding site. Here we show by site-directed mutagenesis that the hydrophobic nature of the trityl binding site and in particular aromatic interactions established between the inhibitor and residue Phe(46) contribute significantly to the binding of uracil-based derivatives containing trityl groups in the 5'-position. Thus, changing Phe(46) for alanine resulted in increased K(i) values for all compounds tested. Conversely, substitution of the polar residue Lys(96) for Ala results in smaller K(i) values and an increase in selectivity with regard to human dUTPase. This information will aid in the design of inhibitors with improved activity against the Plasmodium enzyme.
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