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Crystallographic approach to fragment-based hit discovery against Schistosoma mansoni purine nucleoside phosphorylase. Biochem J 2021; 478:3655-3670. [PMID: 34529035 DOI: 10.1042/bcj20210041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Several Schistosoma species cause Schistosomiasis, an endemic disease in 78 countries that is ranked second amongst the parasitic diseases in terms of its socioeconomic impact and human health importance. The drug recommended for treatment by the WHO is praziquantel (PZQ), but there are concerns associated with PZQ, such as the lack of information about its exact mechanism of action, its high price, its effectiveness - which is limited to the parasite's adult form - and reports of resistance. The parasites lack the de novo purine pathway, rendering them dependent on the purine salvage pathway or host purine bases for nucleotide synthesis. Thus, the Schistosoma purine salvage pathway is an attractive target for the development of necessary and selective new drugs. In this study, the purine nucleotide phosphorylase II (PNP2), a new isoform of PNP1, was submitted to a high-throughput fragment-based hit discovery using a crystallographic screening strategy. PNP2 was crystallized and crystals were soaked with 827 fragments, a subset of the Maybridge 1000 library. X-ray diffraction data was collected and structures were solved. Out of 827-screened fragments we have obtained a total of 19 fragments that show binding to PNP2. Fourteen of these fragments bind to the active site of PNP2, while five were observed in three other sites. Here we present the first fragment screening against PNP2.
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2
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Oliveira NF, Silva CLM. Unveiling the Potential of Purinergic Signaling in Schistosomiasis Treatment. Curr Top Med Chem 2021; 21:193-204. [PMID: 32972342 DOI: 10.2174/1568026620666200924115113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/15/2020] [Accepted: 08/24/2020] [Indexed: 11/22/2022]
Abstract
Schistosomiasis is a neglected tropical disease. It is related to long-lasting granulomatous fibrosis and inflammation of target organs, and current sub-optimal pharmacological treatment creates global public health concerns. Intravascular worms and eggs release antigens and extracellular vesicles that target host endothelial cells, modulate the immune system, and stimulate the release of damageassociated molecular patterns (DAMPs). ATP, one of the most studied DAMPs, triggers a cascade of autocrine and paracrine actions through purinergic P2X and P2Y receptors, which are shaped by ectonucleotidases (CD39). Both P2 receptor families, and in particular P2Y1, P2Y2, P2Y12, and P2X7 receptors, have been attracting increasing interest in several inflammatory diseases and drug development. Current data obtained from the murine model unveiled a CD39-ADP-P2Y1/P2Y12 receptors signaling pathway linked to the liver and mesenteric exacerbations of schistosomal inflammation. Therefore, we proposed that members of this purinergic signaling could be putative pharmacological targets to reduce schistosomal morbidity.
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Affiliation(s)
- Nathália Ferreira Oliveira
- Laboratory of Molecular and Biochemical Pharmacology, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia Lucia Martins Silva
- Laboratory of Molecular and Biochemical Pharmacology, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Cardoso FJB, Xavier LP, Santos AV, Pereira HD, Santos LDS, Molfetta FAD. Identification of potential inhibitors of Schistosoma mansoni purine nucleoside phosphorylase from neolignan compounds using molecular modelling approaches. J Biomol Struct Dyn 2021; 40:8248-8260. [PMID: 33830889 DOI: 10.1080/07391102.2021.1910073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Schistosomiasis is a parasitic disease that is part of the neglected tropical diseases (NTDs), which cause significant levels of morbidity and mortality in millions of people throughout the world. The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) represents a potential target for discovering new agents, and neolignans stand out as an important class of compounds. In this work, molecular modeling studies and biological assays of a set of neolignans were conducted against the PNP enzymes of the parasite and the human homologue (HssPNP). The results of the molecular docking described that the neolignans showed good complementarity by the active site of SmPNP. Molecular dynamics (MD) studies revealed that both complexes (Sm/HssPNP - neolignan compounds) were stable by analyzing the root mean square deviation (RMSD) values, and the binding free energy values suggest that the selected structures can interact and inhibit the catalytic activity of the SmPNP. Finally, the biological assay indicated that the selected neolignans presented a better molecular profile of inhibition compared to the human enzyme, as these ligands did not have the capacity to inhibit enzymatic activity, indicating that these compounds are promising candidates and that they can be used in future research in chemotherapy for schistosomiasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Agenor Valadares Santos
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Humberto D'Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
| | - Lourivaldo da Silva Santos
- Laboratório de Síntese e Produtos Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém-PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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Torini JR, de Freitas Fernandes A, Balasco Serrão VH, Romanello L, Bird LE, Nettleship JE, Owens RJ, Brandão-Neto J, Zeraik AE, DeMarco R, D'Muniz Pereira H. Characterization of a Schistosoma mansoni NDPK expressed in sexual and digestive organs. Mol Biochem Parasitol 2019; 231:111187. [PMID: 31103556 DOI: 10.1016/j.molbiopara.2019.111187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 12/20/2022]
Abstract
Nucleoside diphosphate kinases (NDPKs) are crucial to keep the high triphosphate nucleotide levels in the biological process. The enzymatic mechanism has been extensively described; however, the structural characteristics and kinetic parameters have never been fully determined. In Schistosoma mansoni, NDPK (SmNDPK) is directly involved in the pyrimidine and purine salvage pathways, being essential for nucleotide metabolism. The SmNDPK enzymatic activity is the highest of the known purine metabolisms when compared to the mammalian NDPKs, suggesting the importance of this enzyme in the worm metabolism. Here, we report the recombinant expression of SmNDPK that resulted in 1.7 and 1.9 Å apo-form structure in different space-groups, as well as the 2.1 Å SmNDPK.ADP complex. The binding and kinetic assays reveal the ATP-dependence for enzyme activation. Moreover, in situ hybridization showed that SmNDPK transcripts are found in reproductive organs and in the esophagus gland of adult worms, which can be intrinsically related with the oviposition and digestive processes. These results will help us fully understand the crucial participation of this enzyme in Schistosoma mansoni and its importance for the pathology of the disease.
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Affiliation(s)
- Juliana Roberta Torini
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
| | - Adriano de Freitas Fernandes
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
| | - Vitor Hugo Balasco Serrão
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil; Department of Medicine Pathobiology, University of Toronto, M5S 1A8, Toronto, Canada.
| | - Larissa Romanello
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
| | - Louise E Bird
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, OX11 0FA, UK
| | - Joanne E Nettleship
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, OX11 0FA, UK
| | - Raymond J Owens
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, OX11 0FA, UK
| | - José Brandão-Neto
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Ana Eliza Zeraik
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
| | - Ricardo DeMarco
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
| | - Humberto D'Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil
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5
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Torini JR, Romanello L, Batista FAH, Serrão VHB, Faheem M, Zeraik AE, Bird L, Nettleship J, Reddivari Y, Owens R, DeMarco R, Borges JC, Brandão-Neto J, Pereira HD. The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs. PLoS One 2018; 13:e0203532. [PMID: 30192840 PMCID: PMC6128611 DOI: 10.1371/journal.pone.0203532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022] Open
Abstract
Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a KD of 27 μM for cytosine, and a KM of 76.3 μM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity.
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Affiliation(s)
- Juliana Roberta Torini
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Larissa Romanello
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Fernanda Aparecida Heleno Batista
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biociências, Campinas, São Paulo, Brazil
| | - Vitor Hugo Balasco Serrão
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Muhammad Faheem
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Federal District, Brazil
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Federal District, Brazil
| | - Ana Eliza Zeraik
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Louise Bird
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Joanne Nettleship
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Yamini Reddivari
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Ray Owens
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Ricardo DeMarco
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Júlio César Borges
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo, Brazil
| | - José Brandão-Neto
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Humberto D’Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
- * E-mail:
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Libby CJ, Tran AN, Scott SE, Griguer C, Hjelmeland AB. The pro-tumorigenic effects of metabolic alterations in glioblastoma including brain tumor initiating cells. Biochim Biophys Acta Rev Cancer 2018; 1869:175-188. [PMID: 29378228 PMCID: PMC6596418 DOI: 10.1016/j.bbcan.2018.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 02/06/2023]
Abstract
De-regulated cellular energetics is an emerging hallmark of cancer with alterations to glycolysis, oxidative phosphorylation, the pentose phosphate pathway, lipid oxidation and synthesis and amino acid metabolism. Understanding and targeting of metabolic reprogramming in cancers may yield new treatment options, but metabolic heterogeneity and plasticity complicate this strategy. One highly heterogeneous cancer for which current treatments ultimately fail is the deadly brain tumor glioblastoma. Therapeutic resistance, within glioblastoma and other solid tumors, is thought to be linked to subsets of tumor initiating cells, also known as cancer stem cells. Recent profiling of glioblastoma and brain tumor initiating cells reveals changes in metabolism, as compiled here, that may be more broadly applicable. We will summarize the profound role for metabolism in tumor progression and therapeutic resistance and discuss current approaches to target glioma metabolism to improve standard of care.
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Affiliation(s)
- Catherine J. Libby
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA 35294
| | - Anh Nhat Tran
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA 35294
| | - Sarah E. Scott
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA 35294
| | - Corinne Griguer
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA 35294
| | - Anita B. Hjelmeland
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA 35294,, corresponding author, Anita Hjelmeland, Ph.D., Assistant Professor, University of Alabama at Birmingham, Department of Cell, Developmental, and Integrative Biology, 1900 University Blvd, THT 979, Birmingham Al 35294,
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FERREIRA LEONARDOG, OLIVA GLAUCIUS, ANDRICOPULO ADRIANOD. From Medicinal Chemistry to Human Health: Current Approaches to Drug Discovery for Cancer and Neglected Tropical Diseases. ACTA ACUST UNITED AC 2018; 90:645-661. [DOI: 10.1590/0001-3765201820170505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022]
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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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Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway. PLoS Negl Trop Dis 2016; 10:e0005178. [PMID: 27935959 PMCID: PMC5147791 DOI: 10.1371/journal.pntd.0005178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 11/22/2022] Open
Abstract
Schistosoma mansoni do not have de novo purine pathways and rely on purine salvage for their purine supply. It has been demonstrated that, unlike humans, the S. mansoni is able to produce adenine directly from adenosine, although the enzyme responsible for this activity was unknown. In the present work we show that S. mansoni 5´-deoxy-5´-methylthioadenosine phosphorylase (MTAP, E.C. 2.4.2.28) is capable of use adenosine as a substrate to the production of adenine. Through kinetics assays, we show that the Schistosoma mansoni MTAP (SmMTAP), unlike the mammalian MTAP, uses adenosine substrate with the same efficiency as MTA phosphorolysis, which suggests that this enzyme is part of the purine pathway salvage in S. mansoni and could be a promising target for anti-schistosoma therapies. Here, we present 13 SmMTAP structures from the wild type (WT), including three single and one double mutant, and generate a solid structural framework for structure description. These crystal structures of SmMTAP reveal that the active site contains three substitutions within and near the active site when compared to it mammalian counterpart, thus opening up the possibility of developing specific inhibitors to the parasite MTAP. The structural and kinetic data for 5 substrates reveal the structural basis for this interaction, providing substract for inteligent design of new compounds for block this enzyme activity. The huge challenge in parasitic chemotherapy development is finding a specific compound to attack the parasite organisms without damaging their host. Schistosoma mansoni, which is the causative agent of schistosomiasis, is one of the major health concerns in the developing world. Purine bases are essential for organisms that make DNA, RNA and energetic molecules during parasitic growth and egg laying. The parasites depend entirely on re-utilizing existing purines, not being able to synthesize them from more simple molecules. The adenosine phosphorylase is an important activity for this process and kinetic assays we performed with this S. mansoni MTAP confirm that it displays this specific activity that is not present in the human metabolism. Therefore, understanding the properties of this enzyme is an important step in achieving an efficient anti-schistosomiasis drug with minimal collateral effects to humans.
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Rodrigues MVN, Barbosa AF, da Silva JF, dos Santos DA, Vanzolini KL, de Moraes MC, Corrêa AG, Cass QB. 9-Benzoyl 9-deazaguanines as potent xanthine oxidase inhibitors. Bioorg Med Chem 2015; 24:226-31. [PMID: 26712096 DOI: 10.1016/j.bmc.2015.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/23/2015] [Accepted: 12/05/2015] [Indexed: 11/28/2022]
Abstract
A novel potent xanthine oxidase inhibitor, 3-nitrobenzoyl 9-deazaguanine (LSPN451), was selected from a series of 10 synthetic derivatives. The enzymatic assays were carried out using an on-flow bidimensional liquid chromatography (2D LC) system, which allowed the screening¸ the measurement of the kinetic inhibition constant and the characterization of the inhibition mode. This compound showed a non-competitive inhibition mechanism with more affinity for the enzyme-substrate complex than for the free enzyme, and inhibition constant of 55.1±9.80 nM, about thirty times more potent than allopurinol. Further details of synthesis and enzymatic studies are presented herein.
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Affiliation(s)
- Marili V N Rodrigues
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, 13148-218 Paulínia, SP, Brazil; Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Alexandre F Barbosa
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Júlia F da Silva
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Deborah A dos Santos
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Kenia L Vanzolini
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Marcela C de Moraes
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil; Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141 Niterói, RJ, Brazil
| | - Arlene G Corrêa
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil.
| | - Quezia B Cass
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil.
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12
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Target-based molecular modeling strategies for schistosomiasis drug discovery. Future Med Chem 2015; 7:753-64. [DOI: 10.4155/fmc.15.21] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Schistosomiasis, a neglected tropical disease caused by worms from the class Trematoda (genus Schistosoma), is a serious chronic condition that has been reported in approximately 80 countries. Nearly 250 million people are affected worldwide, mostly in the sub-Saharan Africa. Praziquantel, the mainstay of treatment, has been used for 30 years, and cases of resistance have been reported. The purpose of this perspective is to discuss current target-based molecular modeling strategies in schistosomiasis drug discovery. Advances in the field and the role played by the integration between computational modeling and experimental validation are also discussed. Finally, recent cases of the contribution of modern approaches in computational medicinal chemistry to the field are explored.
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13
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A comprehensive review on bioactive fused heterocycles as purine-utilizing enzymes inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1295-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Barnett CB, Naidoo KJ. PNP diminishes guanosine glycosidic bond strength through restrictive ring pucker as a precursor to phosphorylation. J Phys Chem B 2013; 117:6019-26. [PMID: 23621450 DOI: 10.1021/jp3109013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Purine nucleoside phosphorylase is a transferase that catalyzes the addition of phosphate and removal of a purine base from guanosine and similar nucleosides. Here the interplay between sugar puckering conformation, the enzyme, and the perceived course of the reaction is examined using QM/MM FEARCF dynamics simulations. The enzyme biases the guanosine sugar ring toward a flattened (4)E conformer as a step that is critical to the success of the phosphorylation reaction. The C4' endo conformer allows the nonbonded ring oxygen orbital to align and donate electrons into the antibonding glycosidic bond orbital, thus weakening the bond. This conformational preference is due to sustained and directed noncovalent interactions anchored by the phosphate nucleophile's hydrogen bonds to the sugar C2' and C3' hydroxyls. In so doing, PNP alters the solution sugar ring pucker preferences as part of its catalytic reaction barrier lowering function.
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Affiliation(s)
- Christopher B Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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15
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de Moraes MC, Cardoso CL, Cass QB. Immobilized purine nucleoside phosphorylase from Schistosoma mansoni for specific inhibition studies. Anal Bioanal Chem 2013; 405:4871-8. [DOI: 10.1007/s00216-013-6872-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/20/2013] [Accepted: 02/25/2013] [Indexed: 11/29/2022]
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16
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de Giuseppe PO, Martins NH, Meza AN, dos Santos CR, Pereira HD, Murakami MT. Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases. PLoS One 2012; 7:e44282. [PMID: 22957058 PMCID: PMC3434127 DOI: 10.1371/journal.pone.0044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 07/31/2012] [Indexed: 01/07/2023] Open
Abstract
The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.
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Affiliation(s)
- Priscila O. de Giuseppe
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Nadia H. Martins
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Andreia N. Meza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila R. dos Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Humberto D’Muniz Pereira
- Instituto de Física de São Carlos, Grupo de Cristalografia, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Mario T. Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- * E-mail:
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17
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Abstract
Drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein–ligand interactions. Structure- (SBDD) and ligand-based drug design (LBDD) approaches bring together the most powerful concepts in modern chemistry and biology, linking medicinal chemistry with structural biology. The definition and assessment of both chemical and biological space have revitalized the importance of exploring the intrinsic complementary nature of experimental and computational methods in drug design. Major challenges in this field include the identification of promising hits and the development of high-quality leads for further development into clinical candidates. It becomes particularly important in the case of neglected tropical diseases (NTDs) that affect disproportionately poor people living in rural and remote regions worldwide, and for which there is an insufficient number of new chemical entities being evaluated owing to the lack of innovation and R&D investment by the pharmaceutical industry. This perspective paper outlines the utility and applications of SBDD and LBDD approaches for the identification and design of new small-molecule agents for NTDs.
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18
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Ferreira RS, Guido RVC, Andricopulo AD, Oliva G. In silicoscreening strategies for novel inhibitors of parasitic diseases. Expert Opin Drug Discov 2011; 6:481-9. [DOI: 10.1517/17460441.2011.563297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Severino RP, Guido RV, Marques EF, Brömme D, da Silva MFDG, Fernandes JB, Andricopulo AD, Vieira PC. Acridone alkaloids as potent inhibitors of cathepsin V. Bioorg Med Chem 2011; 19:1477-81. [DOI: 10.1016/j.bmc.2010.12.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 12/22/2010] [Accepted: 12/27/2010] [Indexed: 10/18/2022]
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20
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Postigo MP, Guido RVC, Oliva G, Castilho MS, da R Pitta I, de Albuquerque JFC, Andricopulo AD. Discovery of new inhibitors of Schistosoma mansoni PNP by pharmacophore-based virtual screening. J Chem Inf Model 2011; 50:1693-705. [PMID: 20695479 DOI: 10.1021/ci100128k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Schistosomiasis is considered the second most important tropical parasitic disease, with severe socioeconomic consequences for millions of people worldwide. Schistosoma mansoni , one of the causative agents of human schistosomiasis, is unable to synthesize purine nucleotides de novo, which makes the enzymes of the purine salvage pathway important targets for antischistosomal drug development. In the present work, we describe the development of a pharmacophore model for ligands of S. mansoni purine nucleoside phosphorylase (SmPNP) as well as a pharmacophore-based virtual screening approach, which resulted in the identification of three thioxothiazolidinones (1-3) with substantial in vitro inhibitory activity against SmPNP. Synthesis, biochemical evaluation, and structure-activity relationship investigations led to the successful development of a small set of thioxothiazolidinone derivatives harboring a novel chemical scaffold as new competitive inhibitors of SmPNP at the low-micromolar range. Seven compounds were identified with IC(50) values below 100 μM. The most potent inhibitors 7, 10, and 17 with IC(50) of 2, 18, and 38 μM, respectively, could represent new potential lead compounds for further development of the therapy of schistosomiasis.
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Affiliation(s)
- Matheus P Postigo
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
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