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Eistrikh-Heller PA, Rubinsky SV, Samygina VR, Gabdulkhakov AG, Kovalchuk MV, Mironov AS, Lashkov AA. Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.
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Yang C, Li J, Huang Z, Zhang X, Gao X, Zhu C, Morris PF, Zhang X. Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici. Sci Rep 2020; 10:9051. [PMID: 32493959 PMCID: PMC7271239 DOI: 10.1038/s41598-020-65935-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/08/2020] [Indexed: 11/09/2022] Open
Abstract
Uridine phosphorylase (UP) is a key enzyme of pyrimidine salvage pathways that enables the recycling of endogenous or exogenous-supplied pyrimidines and plays an important intracellular metabolic role. Here, we biochemically and structurally characterized two evolutionarily divergent uridine phosphorylases, PcUP1 and PcUP2 from the oomycete pathogen Phytophthora capsici. Our analysis of other oomycete genomes revealed that both uridine phosphorylases are present in Phytophthora and Pythium genomes, but only UP2 is seen in Saprolegnia spp. which are basal members of the oomycetes. Moreover, uridine phosphorylases are not found in obligate oomycete pathogens such as Hyaloperonospora arabidopsidis and Albugo spp. PcUP1 and PcUP2 are upregulated 300 and 500 fold respectively, within 90 min after infection of pepper leaves. The crystal structures of PcUP1 in ligand-free and in complex with uracil/ribose-1-phosphate, 2'-deoxyuridine/phosphate and thymidine/phosphate were analyzed. Crystal structure of this uridine phosphorylase showed strict conservation of key residues in the binding pocket. Structure analysis of PcUP1 with bound ligands, and site-directed mutagenesis of key residues provide additional support for the "push-pull" model of catalysis. Our study highlights the importance of pyrimidine salvage during the earliest stages of infection.
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Affiliation(s)
- Cancan Yang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Jing Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Zhenling Huang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Xuefa Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Xiaolei Gao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Chunyuang Zhu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China
| | - Paul F Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - XiuGuo Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271000, China.
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Il’icheva IA, Polyakov KM, Mikhailov SN. Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases. Biomolecules 2020; 10:E552. [PMID: 32260512 PMCID: PMC7226091 DOI: 10.3390/biom10040552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022] Open
Abstract
Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 5'-deoxy-5'-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N↔S interconversion. In most of the complexes, the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn ↔ anti transitions. Such conformations of nucleosides in complexes are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme-substrate complex formation for this enzyme group.
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Affiliation(s)
| | | | - Sergey N. Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (I.A.I.); (K.M.P.)
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Rocha JA, Rego NCS, Carvalho BTS, Silva FI, Sousa JA, Ramos RM, Passos ING, de Moraes J, Leite JRSA, Lima FCA. Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties. PLoS One 2018; 13:e0198476. [PMID: 29944674 PMCID: PMC6019389 DOI: 10.1371/journal.pone.0198476] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/18/2018] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis affects million people and its control is widely dependent on a single drug, praziquantel. Computational chemistry has led to the development of new tools that predict molecular properties related to pharmacological potential. We conducted a theoretical study of the imizadole alkaloids of Pilocarpus microphyllus (Rutaceae) with schistosomicidal properties. The molecules of epiisopiloturine, epiisopilosine, isopilosine, pilosine, and macaubine were evaluated using theory models (B3lyp/SDD, B3lyp/6-31+G(d,p), B3lyp/6-311++G(d,p)). Absorption, distribution, metabolization, excretion, and toxicity (ADMET) predictions were used to determine the pharmacokinetic and pharmacodynamic properties of the alkaloids. After optimization, the molecules were submitted to molecular docking calculations with the purine nucleoside phosphorylase, thioredoxin glutathione reductase, methylthioadenosine phosphorylase, arginase, uridine phosphorylase, Cathepsin B1 and histone deacetylase 8 enzymes, which are possible targets of Schistosoma mansoni. The results showed that B3lyp/6-311++G(d,p) was the optimal model to describe the properties studied. Thermodynamic analysis showed that epiisopiloturine and epiisopilosine were the most stable isomers; however, the epiisopilosine ligand achieved a superior interaction with the enzymes studied in the molecular docking experiments, which corroborated the results of previous experimental studies on schistosomiasis.
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Affiliation(s)
- Jefferson A. Rocha
- The Postgraduate Program of the Northeast Network of Biotechnology, RENORBIO, Focal Point UFPI, Teresina, Piauí, Brazil
- Research Group in Natural Sciences and Biotechnology, Federal University of Maranhão, CIENATEC / UFMA, Grajaú, MA, Brazil
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
| | - Nayra C. S. Rego
- The Postgraduate Program of the Northeast Network of Biotechnology, RENORBIO, Focal Point UFPI, Teresina, Piauí, Brazil
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
| | - Bruna T. S. Carvalho
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
| | - Francisco I. Silva
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
| | - Jose A. Sousa
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
| | - Ricardo M. Ramos
- Research Laboratory in Information Systems, Department of Information, Environment, Health and Food Production, Federal Institute of Piauí, LAPESI / IFPI, Teresina, PI, Brazil
| | - Ionara N. G. Passos
- Research Group in Natural Sciences and Biotechnology, Federal University of Maranhão, CIENATEC / UFMA, Grajaú, MA, Brazil
| | - Josué de Moraes
- Research Center for Neglected Diseases, Guarulhos University, NPDN / UNG, Guarulhos, SP, Brazil
| | - Jose R. S. A. Leite
- Area Morphology, Faculty of Medicine, Campus Darcy Ribeiro, University of Brasília, UnB, Brasília, DF, Brazil
| | - Francisco C. A. Lima
- The Postgraduate Program of the Northeast Network of Biotechnology, RENORBIO, Focal Point UFPI, Teresina, Piauí, Brazil
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, GPQQ&PF / UESPI, Teresina, PI, Brazil
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El Kouni MH. Pyrimidine metabolism in schistosomes: A comparison with other parasites and the search for potential chemotherapeutic targets. Comp Biochem Physiol B Biochem Mol Biol 2017; 213:55-80. [PMID: 28735972 PMCID: PMC5593796 DOI: 10.1016/j.cbpb.2017.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/18/2022]
Abstract
Schistosomes are responsible for the parasitic disease schistosomiasis, an acute and chronic parasitic ailment that affects >240 million people in 70 countries worldwide. It is the second most devastating parasitic disease after malaria. At least 200,000 deaths per year are associated with the disease. In the absence of the availability of vaccines, chemotherapy is the main stay for combating schistosomiasis. The antischistosomal arsenal is currently limited to a single drug, Praziquantel, which is quite effective with a single-day treatment and virtually no host-toxicity. Recently, however, the question of reduced activity of Praziquantel has been raised. Therefore, the search for alternative antischistosomal drugs merits the study of new approaches of chemotherapy. The rational design of a drug is usually based on biochemical and physiological differences between pathogens and host. Pyrimidine metabolism is an excellent target for such studies. Schistosomes, unlike most of the host tissues, require a very active pyrimidine metabolism for the synthesis of DNA and RNA. This is essential for the production of the enormous numbers of eggs deposited daily by the parasite to which the granulomas response precipitates the pathogenesis of schistosomiasis. Furthermore, there are sufficient differences between corresponding enzymes of pyrimidine metabolism from the host and the parasite that can be exploited to design specific inhibitors or "subversive substrates" for the parasitic enzymes. Specificities of pyrimidine transport also diverge significantly between parasites and their mammalian host. This review deals with studies on pyrimidine metabolism in schistosomes and highlights the unique characteristic of this metabolism that could constitute excellent potential targets for the design of safe and effective antischistosomal drugs. In addition, pyrimidine metabolism in schistosomes is compared with that in other parasites where studies on pyrimidine metabolism have been more elaborate, in the hope of providing leads on how to identify likely chemotherapeutic targets which have not been looked at in schistosomes.
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Affiliation(s)
- Mahmoud H El Kouni
- Department of Pharmacology and Toxicology, Center for AIDS Research, Comprehensive Cancer Center, General Clinical Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Scortecci JF, Serrão VHB, Cheleski J, Torini JR, Romanello L, DeMarco R, D'Muniz Pereira H. Spectroscopic and calorimetric assays reveal dependence on dCTP and two metals (Zn 2++Mg 2+) for enzymatic activity of Schistosoma mansoni deoxycytidylate (dCMP) deaminase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1326-1335. [PMID: 28807888 DOI: 10.1016/j.bbapap.2017.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/27/2022]
Abstract
The parasite Schistosoma mansoni possess all pathways for pyrimidine biosynthesis, whereby deaminases play an essential role in the thymidylate cycle, a crucial step to controlling the ratio between cytidine and uridine nucleotides. In this study, we heterologously expressed and purified the deoxycytidylate (dCMP) deaminase from S. mansoni to obtain structural, biochemical and kinetic information. Small-angle X-ray scattering of this enzyme showed that it is organized as a hexamer in solution. Isothermal titration calorimetry was used to determine the kinetic constants for dCMP-dUMP conversion and the role of dCTP and dTTP in enzymatic regulation. We evaluated the metals involved in activating the enzyme and show for the first time the dependence of correct folding on the interaction of two metals. This study provides information that may be useful for understanding the regulatory mechanisms involved in the metabolic pathways of S. mansoni. Thus, improving our understanding of the function of these essential pathways for parasite metabolism and showing for the first time the hitherto unknown deaminase function in this parasite.
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Affiliation(s)
| | - Vitor Hugo Balasco Serrão
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Juliana Cheleski
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Juliana Roberta Torini
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Larissa Romanello
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
| | - Ricardo DeMarco
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP CEP 13566-590, Brazil
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Serrão VHB, Romanello L, Cassago A, de Souza JRT, Cheleski J, DeMarco R, Brandão-Neto J, Pereira HD. Structure and kinetics assays of recombinant Schistosoma mansoni dihydrofolate reductase. Acta Trop 2017; 170:190-196. [PMID: 28288799 DOI: 10.1016/j.actatropica.2017.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 10/20/2022]
Abstract
The parasite Schistosoma mansoni possesses all pathways for pyrimidine biosynthesis, in which dihydrofolate reductase (DHFR), thymidylate cycle participants, is essential for nucleotide metabolism to obtain energy and structural nucleic acids. Thus, DHFRs have been widely suggested as therapeutic targets for the treatment of infectious diseases. In this study, we expressed recombinant SmDHFR in a heterologous manner to obtain structural, biochemical and kinetic information. X-ray diffraction of recombinant SmDHFR at 1.95Å resolution showed that the structure exhibited the canonical DHFR fold. Isothermal titration calorimetry was used to determine the kinetic constants for NADP+ and dihydrofolate. Moreover, inhibition assays were performed using the commercial folate analogs methotrexate and aminopterin; these analogs are recognized as folate competitors and are used as chemotherapeutic agents in cancer and autoimmune diseases. This study provides information that may prove useful for the future discovery of novel drugs and for understanding these metabolic steps from this pathway of S. mansoni, thus aiding in our understanding of the function of these essential pathways for parasite metabolism.
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Zeraik AE, Balasco Serrão VH, Romanello L, Torini JR, Cassago A, DeMarco R, Pereira HD. Schistosoma mansoni displays an adenine phosphoribosyltransferase preferentially expressed in mature female gonads and vitelaria. Mol Biochem Parasitol 2017; 214:82-86. [PMID: 28392476 DOI: 10.1016/j.molbiopara.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/14/2022]
Abstract
Schistosoma mansoni depends upon the purine salvage pathway to obtain purine nucleotides; therefore, enzymes from this pathway are essential for parasite survival. Here, we focused on the adenine phosphoribosyltransferase (APRT) enzyme, which catalyzes the condensation reaction between adenine and PRPP (5-phosphoribosylpyrophosphate) to produce AMP and PPi. Kinetic experiments using the heterologously expressed protein of one APRT isoform from S. mansoni indicate that it is catalytically active, and whole-mount in situ hybridization studies indicate that the transcripts of this protein are concentrated in the posterior region of the ovary and vitellaria of female adult worms. Moreover, a phylogenetic analysis has shown that APRT exists in multiple copies originating from gene duplications at the base of the Schistosoma genus. Other enzymes from the purine and pyrimidine salvage pathways have also been found to present multiple copies in schistosomes, suggesting that evolutionary pressure to diversify these genes' families may be related to a specialized role in parasite reproduction.
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Affiliation(s)
- Ana Eliza Zeraik
- São Carlos Institute of Physics, São Paulo University, São Carlos, SP 13563-120, Brazil.
| | | | - Larissa Romanello
- São Carlos Institute of Physics, São Paulo University, São Carlos, SP 13563-120, Brazil
| | | | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, LNNano/CNPEM, Campinas, SP 13083-970, Brazil
| | - Ricardo DeMarco
- São Carlos Institute of Physics, São Paulo University, São Carlos, SP 13563-120, Brazil
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