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The Trypanosoma cruzi TcrNT2 Nucleoside Transporter Is a Conduit for the Uptake of 5-F-2'-Deoxyuridine and Tubercidin Analogues. Molecules 2022; 27:molecules27228045. [PMID: 36432150 PMCID: PMC9693223 DOI: 10.3390/molecules27228045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Among the scarce validated drug targets against Chagas disease (CD), caused by Trypanosoma cruzi, the parasite's nucleoside salvage system has recently attracted considerable attention. Although the trypanocidal activity of tubercidin (7-deazapurine) has long been known, the identification of a class of 7-substituted tubercidin analogs with potent in vitro and in vivo activity and much-enhanced selectivity has made nucleoside analogs among the most promising lead compounds against CD. Here, we investigate the recently identified TcrNT2 nucleoside transporter and its potential role in antimetabolite chemotherapy. TcrNT2, expressed in a Leishmania mexicana cell line lacking the NT1 nucleoside transporter locus, displayed very high selectivity and affinity for thymidine with a Km of 0.26 ± 0.05 µM. The selectivity was explained by interactions of 2-oxo, 4-oxo, 5-Me, 3'-hydroxy and 5'-hydroxy with the transporter binding pocket, whereas a hydroxy group at the 2' position was deleterious to binding. This made 5-halogenated 2'-deoxyuridine analogues good substrates but 5-F-2'-deoxyuridine displayed disappointing activity against T. cruzi trypomastigotes. By comparing the EC50 values of tubercidin and its 7-substituted analogues against L. mexicana Cas9, Cas9ΔNT1 and Cas9ΔNT1+TcrNT2 it was shown that TcrNT2 can take up tubercidin and, at a minimum, a subset of the analogs.
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2
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Decreased glutamate transport in acivicin resistant Leishmania tarentolae. PLoS Negl Trop Dis 2021; 15:e0010046. [PMID: 34914690 PMCID: PMC8718007 DOI: 10.1371/journal.pntd.0010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/30/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Studies of drug resistance in the protozoan parasites of the genus Leishmania have been helpful in revealing biochemical pathways as potential drug targets. The chlorinated glutamine analogue acivicin has shown good activity against Leishmania cells and was shown to target several enzymes containing amidotransferase domains. We selected a Leishmania tarentolae clone for acivicin resistance. The genome of this resistant strain was sequenced and the gene coding for the amidotransferase domain-containing GMP synthase was found to be amplified. Episomal expression of this gene in wild-type L. tarentolae revealed a modest role in acivicin resistance. The most prominent defect observed in the resistant mutant was reduced uptake of glutamate, and through competition experiments we determined that glutamate and acivicin, but not glutamine, share the same transporter. Several amino acid transporters (AATs) were either deleted or mutated in the resistant cells. Some contributed to the acivicin resistance phenotype although none corresponded to the main glutamate transporter. Through sequence analysis one AAT on chromosome 22 corresponded to the main glutamate transporter. Episomal expression of the gene coding for this transporter in the resistant mutant restored glutamate transport and acivicin susceptibility. Its genetic knockout led to reduced glutamate transport and acivicin resistance. We propose that acivicin binds covalently to this transporter and as such leads to decreased transport of glutamate and acivicin thus leading to acivicin resistance. Studies of drug resistance in the protozoan parasites of the genus Leishmania have been helpful in revealing biochemical pathways as potential drug targets. Here we report on the characterization at the genomics and metabolomics levels of a L. tarentolae strain made resistant to acivicin, an analogue of glutamine with activity against this parasite. We found that resistance to acivicin is accompanied by a reduced uptake and intracellular levels of glutamate and that both are expected to share the same transporter. Through gene overexpression and disruption studies we identified the main amino acid transporter responsible for glutamate uptake.
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3
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Natto MJ, Miyamoto Y, Munday JC, AlSiari TA, Al-Salabi MI, Quashie NB, Eze AA, Eckmann L, De Koning HP. Comprehensive characterization of purine and pyrimidine transport activities in Trichomonas vaginalis and functional cloning of a trichomonad nucleoside transporter. Mol Microbiol 2021; 116:1489-1511. [PMID: 34738285 PMCID: PMC8688338 DOI: 10.1111/mmi.14840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/30/2021] [Accepted: 10/30/2021] [Indexed: 11/30/2022]
Abstract
Trichomoniasis is a common and widespread sexually-transmitted infection, caused by the protozoan parasite Trichomonas vaginalis. T. vaginalis lacks the biosynthetic pathways for purines and pyrimidines, making nucleoside metabolism a drug target. Here we report the first comprehensive investigation into purine and pyrimidine uptake by T. vaginalis. Multiple carriers were identified and characterized with regard to substrate selectivity and affinity. For nucleobases, a high-affinity adenine transporter, a possible guanine transporter and a low affinity uracil transporter were found. Nucleoside transporters included two high affinity adenosine/guanosine/uridine/cytidine transporters distinguished by different affinities to inosine, a lower affinity adenosine transporter, and a thymidine transporter. Nine Equilibrative Nucleoside Transporter (ENT) genes were identified in the T. vaginalis genome. All were expressed equally in metronidazole-resistant and -sensitive strains. Only TvagENT2 was significantly upregulated in the presence of extracellular purines; expression was not affected by co-culture with human cervical epithelial cells. All TvagENTs were cloned and separately expressed in Trypanosoma brucei. We identified the main broad specificity nucleoside carrier, with high affinity for uridine and cytidine as well as purine nucleosides including inosine, as TvagENT3. The in-depth characterization of purine and pyrimidine transporters provides a critical foundation for the development of new anti-trichomonal nucleoside analogues.
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Affiliation(s)
- Manal J. Natto
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Yukiko Miyamoto
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jane C. Munday
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Tahani A. AlSiari
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mohammed I. Al-Salabi
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Neils B. Quashie
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, University of Ghana
| | - Anthonius A. Eze
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Current affiliation: Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Lars Eckmann
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Harry P. De Koning
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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4
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Steketee PC, Dickie EA, Iremonger J, Crouch K, Paxton E, Jayaraman S, Alfituri OA, Awuah-Mensah G, Ritchie R, Schnaufer A, Rowan T, de Koning HP, Gadelha C, Wickstead B, Barrett MP, Morrison LJ. Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition. PLoS Pathog 2021; 17:e1009734. [PMID: 34310651 PMCID: PMC8384185 DOI: 10.1371/journal.ppat.1009734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/24/2021] [Accepted: 06/21/2021] [Indexed: 11/18/2022] Open
Abstract
Animal African Trypanosomiasis (AAT) is a debilitating livestock disease prevalent across sub-Saharan Africa, a main cause of which is the protozoan parasite Trypanosoma congolense. In comparison to the well-studied T. brucei, there is a major paucity of knowledge regarding the biology of T. congolense. Here, we use a combination of omics technologies and novel genetic tools to characterise core metabolism in T. congolense mammalian-infective bloodstream-form parasites, and test whether metabolic differences compared to T. brucei impact upon sensitivity to metabolic inhibition. Like the bloodstream stage of T. brucei, glycolysis plays a major part in T. congolense energy metabolism. However, the rate of glucose uptake is significantly lower in bloodstream stage T. congolense, with cells remaining viable when cultured in concentrations as low as 2 mM. Instead of pyruvate, the primary glycolytic endpoints are succinate, malate and acetate. Transcriptomics analysis showed higher levels of transcripts associated with the mitochondrial pyruvate dehydrogenase complex, acetate generation, and the glycosomal succinate shunt in T. congolense, compared to T. brucei. Stable-isotope labelling of glucose enabled the comparison of carbon usage between T. brucei and T. congolense, highlighting differences in nucleotide and saturated fatty acid metabolism. To validate the metabolic similarities and differences, both species were treated with metabolic inhibitors, confirming that electron transport chain activity is not essential in T. congolense. However, the parasite exhibits increased sensitivity to inhibition of mitochondrial pyruvate import, compared to T. brucei. Strikingly, T. congolense exhibited significant resistance to inhibitors of fatty acid synthesis, including a 780-fold higher EC50 for the lipase and fatty acid synthase inhibitor Orlistat, compared to T. brucei. These data highlight that bloodstream form T. congolense diverges from T. brucei in key areas of metabolism, with several features that are intermediate between bloodstream- and insect-stage T. brucei. These results have implications for drug development, mechanisms of drug resistance and host-pathogen interactions.
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Affiliation(s)
- Pieter C Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily A Dickie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - James Iremonger
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn Crouch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Edith Paxton
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharth Jayaraman
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Omar A Alfituri
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ryan Ritchie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Rowan
- Global Alliance for Livestock Veterinary Medicines, Edinburgh, United Kingdom
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Liam J Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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5
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Yagüe-Capilla M, Castillo-Acosta VM, Bosch-Navarrete C, Ruiz-Pérez LM, González-Pacanowska D. A Mitochondrial Orthologue of the dNTP Triphosphohydrolase SAMHD1 Is Essential and Controls Pyrimidine Homeostasis in Trypanosoma brucei. ACS Infect Dis 2021; 7:318-332. [PMID: 33417760 DOI: 10.1021/acsinfecdis.0c00551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The maintenance of deoxyribonucleotide triphosphate (dNTP) homeostasis through synthesis and degradation is critical for accurate genomic and mitochondrial DNA replication fidelity. Trypanosoma brucei makes use of both the salvage and de novo pathways for the provision of pyrimidine dNTPs. In this respect, the sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) appears to be the most relevant dNTPase controlling dNTP/deoxynucleoside homeostasis in mammalian cells. Here, we have characterized the role of a unique trypanosomal SAMHD1 orthologue denominated TbHD52. Our results show that TbHD52 is a mitochondrial enzyme essential in bloodstream forms of T. brucei. Knockout cells are pyrimidine auxotrophs that exhibit strong defects in genomic integrity, cell cycle progression, and nuclear DNA and kinetoplast segregation in the absence of extracellular thymidine. The lack of TbHD52 can be counteracted by the overexpression of human dCMP deaminase, an enzyme that is directly involved in dUMP formation yet absent in trypanosomes. Furthermore, the cellular dNTP quantification and metabolomic analysis of TbHD52 null mutants revealed perturbations in the nucleotide metabolism with a substantial accumulation of dCTP and cytosine-derived metabolites while dTTP formation was significantly reduced. We propose that this HD-domain-containing protein unique to kinetoplastids plays an essential role in pyrimidine dNTP homeostasis and contributes to the provision of deoxycytidine required for cellular dTTP biosynthesis.
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Affiliation(s)
- Miriam Yagüe-Capilla
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Víctor M. Castillo-Acosta
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Cristina Bosch-Navarrete
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
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6
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Campagnaro GD, de Koning HP. Purine and pyrimidine transporters of pathogenic protozoa - conduits for therapeutic agents. Med Res Rev 2020; 40:1679-1714. [PMID: 32144812 DOI: 10.1002/med.21667] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Abstract
Purines and pyrimidines are essential nutrients for any cell. Most organisms are able to synthesize their own purines and pyrimidines, but this ability was lost in protozoans that adapted to parasitism, leading to a great diversification in transporter activities in these organisms, especially for the acquisition of amino acids and nucleosides from their hosts throughout their life cycles. Many of these transporters have been shown to have sufficiently different substrate affinities from mammalian transporters, making them good carriers for therapeutic agents. In this review, we summarize the knowledge obtained on purine and pyrimidine activities identified in protozoan parasites to date and discuss their importance for the survival of these parasites and as drug carriers, as well as the perspectives of developments in the field.
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Affiliation(s)
- Gustavo D Campagnaro
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, UK
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, UK
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7
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Auletta S, Caravan W, Persaud JK, Thuilot SF, Brown DG, Parkin DW, Stockman BJ. Discovery of Ligand-Efficient Scaffolds for the Design of Novel Trichomonas vaginalis Uridine Nucleoside Ribohydrolase Inhibitors Using Fragment Screening. ACS OMEGA 2019; 4:16226-16232. [PMID: 31592163 PMCID: PMC6777076 DOI: 10.1021/acsomega.9b02472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
Trichomoniasis is caused by the parasitic protozoan Trichomonas vaginalis. The increasing prevalence of strains resistant to the current 5-nitroimidazole treatments creates the need for novel therapies. T. vaginalis cannot synthesize purine and pyrimidine rings and requires salvage pathway enzymes to obtain them from host nucleosides. The uridine nucleoside ribohydrolase was screened using an 19F NMR-based activity assay against a 2000-compound fragment diversity library. Several series of inhibitors were identified including scaffolds based on acetamides, cyclic ureas or ureas, pyridines, and pyrrolidines. A number of potent singleton compounds were identified, as well. Eighteen compounds with IC50 values of 20 μM or lower were identified, including some with ligand efficiency values of 0.5 or greater. Detergent and jump-dilution counter screens validated all scaffold classes as target-specific, reversible inhibitors. Identified scaffolds differ substantially from 5-nitroimidazoles. Medicinal chemistry using the structure-activity relationship emerging from the fragment hits is being pursued to discover nanomolar inhibitors.
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Affiliation(s)
- Shannon Auletta
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
| | - Wagma Caravan
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
| | - Julia K. Persaud
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
| | - Samantha F. Thuilot
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
| | - Dean G. Brown
- Hit
Discovery, Discovery Sciences, IMED Biotech
Unit, AstraZeneca, 35
Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David W. Parkin
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
| | - Brian J. Stockman
- Department
of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, Unites States
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8
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Zhang L, Jiang Y, Pang X, Hua P, Gao X, Li Q, Li Z. Simultaneous Optimization of Ultrasound-Assisted Extraction for Flavonoids and Antioxidant Activity of Angelica keiskei Using Response Surface Methodology (RSM). Molecules 2019; 24:E3461. [PMID: 31554203 PMCID: PMC6804174 DOI: 10.3390/molecules24193461] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 02/02/2023] Open
Abstract
Angelica keiskei Koidzumi (A. keiskei), as a Japanese edible herbal plant, enjoys a variety of biological activities due to the presence of numerous active compounds, especially flavonoids. This study aims for the optimization of ultrasound-assisted extraction (UAE) for flavonoids in A. keiskei and their antioxidant activity by using the response surface methodology (RSM). Single-factor experiments and a four-factor three-level Box-Behnken design (BBD) were performed to explore the effects of the following parameters on flavonoid extraction and antioxidant activity evaluation: ultrasonic temperature (X1), ultrasonic time (X2), ethanol concentration (X3) and liquid-solid ratio (X4). The optimum conditions of the combination of total flavonoid content (TFC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity (DPPH-RSC) and ferric-reducing antioxidant power (FRAP) were as follows: X1 = 80 °C, X2 = 4 min, X3 = 78%, X4 = 35 mL/g, respectively. The experimental results provide a theoretical basis for the extensive utilization of A. keiskei and flavonoids extraction from A. keiskei as a potential source of antioxidants.
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Affiliation(s)
- Lei Zhang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
| | - Yuhuan Jiang
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Xuening Pang
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Puyue Hua
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Xiang Gao
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Qun Li
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
| | - Zichao Li
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
- Qingdao Balanson Biotech Co., Ltd., Qingdao 266071, China.
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9
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Khandazhinskaya AL, Matyugina ES, Solyev PN, Wilkinson M, Buckheit KW, Buckheit RW, Chernousova LN, Smirnova TG, Andreevskaya SN, Alzahrani KJ, Natto MJ, Kochetkov SN, de Koning HP, Seley-Radtke KL. Investigation of 5'-Norcarbocyclic Nucleoside Analogues as Antiprotozoal and Antibacterial Agents. Molecules 2019; 24:E3433. [PMID: 31546633 PMCID: PMC6804079 DOI: 10.3390/molecules24193433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022] Open
Abstract
Carbocyclic nucleosides have long played a role in antiviral, antiparasitic, and antibacterial therapies. Recent results from our laboratories from two structurally related scaffolds have shown promising activity against both Mycobacterium tuberculosis and several parasitic strains. As a result, a small structure activity relationship study was designed to further probe their activity and potential. Their synthesis and the results of the subsequent biological activity are reported herein.
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Affiliation(s)
- Anastasia L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Maggie Wilkinson
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Karen W. Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Robert W. Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Larisa N. Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Tatiana G. Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Sofya N. Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Khalid J. Alzahrani
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
- Department of Clinical Laboratory, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | - Manal J. Natto
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Harry P. de Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
| | - Katherine L. Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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10
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Veale CGL, Hoppe HC. Screening of the Pathogen Box reveals new starting points for anti-trypanosomal drug discovery. MEDCHEMCOMM 2018; 9:2037-2044. [PMID: 30647879 PMCID: PMC6301270 DOI: 10.1039/c8md00319j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/30/2018] [Indexed: 12/16/2022]
Abstract
This study aimed to uncover new starting points for anti-trypansomal drug discovery through the screening of the Pathogen Box against Trypanosoma brucei brucei. Our study identified compounds 35, 39, 46, 53 and 56 whose activity and selectivity highlighted them as promising candidates with potential for further study and optimisation.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics , Pietermaritzburg Campus , University of KwaZulu-Natal , Private Bag X01 , Scottsville , 3209 , South Africa . ; Tel: +27 33 260 6365
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology , Rhodes University , Grahamstown , 6140 , South Africa . ; Tel: +27 46 603 8262
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11
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Alam R, Barbarovich AT, Caravan W, Ismail M, Barskaya A, Parkin DW, Stockman BJ. Druggability of the guanosine/adenosine/cytidine nucleoside hydrolase from Trichomonas vaginalis. Chem Biol Drug Des 2018; 92:1736-1742. [PMID: 29808562 DOI: 10.1111/cbdd.13341] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/28/2018] [Accepted: 05/06/2018] [Indexed: 12/15/2022]
Abstract
Trichomonas vaginalis infects approximately 300 million people worldwide annually. Infected individuals have a higher susceptibility to more serious conditions such as cervical and prostate cancer. The parasite has developed increasing resistance to current drug therapies, with an estimated 5% of clinical cases resulting from resistant strains, creating the need for new therapeutic strategies with novel mechanisms of action. Nucleoside salvage pathway enzymes represent novel drug targets as these pathways are essential for the parasite's survival. The guanosine/adenosine/cytidine nucleoside hydrolase (GACNH) may be particularly important as its expression is upregulated under glucose-limiting conditions mimicking those that occur during infection establishment. GACNH was screened against the NIH Clinical Collection to explore its druggability. Seven compounds were identified with IC50 values <20 μM. Extensive overlap was found between inhibitors of GACNH and the adenosine/guanosine nucleoside hydrolase (AGNH), but no overlap was found with inhibitors of the uridine nucleoside hydrolase. The guanosine analog ribavirin was the only compound found to be specific for GACNH. Compounds that inhibit both AGNH and GACNH purine salvage pathway enzymes may prove critical given the role that GACNH appears to play in the early stages of infection.
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Affiliation(s)
- Rayyan Alam
- Department of Chemistry, Adelphi University, Garden City, New York
| | | | - Wagma Caravan
- Department of Chemistry, Adelphi University, Garden City, New York
| | - Mirna Ismail
- Department of Chemistry, Adelphi University, Garden City, New York
| | - Angela Barskaya
- Department of Chemistry, Adelphi University, Garden City, New York
| | - David W Parkin
- Department of Chemistry, Adelphi University, Garden City, New York
| | - Brian J Stockman
- Department of Chemistry, Adelphi University, Garden City, New York
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12
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Fresh insights into the pyrimidine metabolism in the trypanosomatids. Parasit Vectors 2018; 11:87. [PMID: 29422065 PMCID: PMC5803862 DOI: 10.1186/s13071-018-2660-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/18/2018] [Indexed: 11/26/2022] Open
Abstract
The trypanosomatid parasites continue their killing spree resulting in significant annual mortality due to the lack of effective treatments and the prominence of these diseases in poorer countries. These dimorphic parasites thrive unchecked in the host system, outsmarting the immune mechanisms. An understanding of biology of these parasitic forms will help in the management and elimination of these fatal diseases. Investigation of various metabolic pathways in these parasites has shed light in the understanding of the unique biology of the trypansomatids. An understanding of these pathways have helped in tracing the soft targets in the metabolic pathways, which could be used as effective drug targets which would further impact the therupeutic implications. Pyrimidine pathway is a vital metabolic pathway which yields in the formation of pyrimidines, which are then integrated in nucleic acids (DNA and RNA) in sugars (UDP sugars) and lipids (CDP lipids). A wealth of data and information has been generated in the past decades by in-depth analyses of pyrimidine pathway in the trypanosomatid parasites, which can aid in the identification of anomalies between the parasitic and host counterpart which could be further harnessed to develop therapeutic interventions for the treatment of parasitic diseases. This review presents an updated and comprehensive detailing of the pyrimidine metabolism in the trypansomatids, their uniqueness and their distinctions, and its possible outcomes that would aid in the eradication of these parasitic diseases.
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13
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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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14
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Alzahrani KJH, Ali JAM, Eze AA, Looi WL, Tagoe DNA, Creek DJ, Barrett MP, de Koning HP. Functional and genetic evidence that nucleoside transport is highly conserved in Leishmania species: Implications for pyrimidine-based chemotherapy. Int J Parasitol Drugs Drug Resist 2017; 7:206-226. [PMID: 28453984 PMCID: PMC5407577 DOI: 10.1016/j.ijpddr.2017.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 11/28/2022]
Abstract
Leishmania pyrimidine salvage is replete with opportunities for therapeutic intervention with enzyme inhibitors or antimetabolites. Their uptake into cells depends upon specific transporters; therefore it is essential to establish whether various Leishmania species possess similar pyrimidine transporters capable of drug uptake. Here, we report a comprehensive characterization of pyrimidine transport in L. major and L. mexicana. In both species, two transporters for uridine/adenosine were detected, one of which also transported uracil and the antimetabolites 5-fluoruracil (5-FU) and 5F,2'deoxyuridine (5F,2'dUrd), and was designated uridine-uracil transporter 1 (UUT1); the other transporter mediated uptake of adenosine, uridine, 5F,2'dUrd and thymidine and was designated Nucleoside Transporter 1 (NT1). To verify the reported L. donovani model of two NT1-like genes encoding uridine/adenosine transporters, and an NT2 gene encoding an inosine transporter, we cloned the corresponding L. major and L. mexicana genes, expressing each in T. brucei. Consistent with the L. donovani reports, the NT1-like genes of either species mediated the adenosine-sensitive uptake of [3H]-uridine but not of [3H]-inosine. Conversely, the NT2-like genes mediated uptake of [3H]-inosine but not [3H]-uridine. Among pyrimidine antimetabolites tested, 5-FU and 5F,2'dUrd were the most effective antileishmanials; resistance to both analogs was induced in L. major and L. mexicana. In each case it was found that the resistant cells had lost the transport capacity for the inducing drug. Metabolomics analysis found that the mechanism of action of 5-FU and 5F-2'dUrd was similar in both Leishmania species, with major changes in deoxynucleotide metabolism. We conclude that the pyrimidine salvage system is highly conserved in Leishmania species - essential information for the development of pyrimidine-based chemotherapy.
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Affiliation(s)
- Khalid J H Alzahrani
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Department of Clinical Laboratory, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Juma A M Ali
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Al Jabal Al Gharbi University, Gharyan, Libya
| | - Anthonius A Eze
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Department of Medical Biochemistry, College of Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Wan Limm Looi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel N A Tagoe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Darren J Creek
- Department of Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Michael P Barrett
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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15
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Evaluation of the antiprotozoan properties of 5′-norcarbocyclic pyrimidine nucleosides. Bioorg Med Chem Lett 2017; 27:3081-3086. [DOI: 10.1016/j.bmcl.2017.05.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
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16
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Biochemical characterization of dihydroorotase of Leishmania donovani: Understanding pyrimidine metabolism through its inhibition. Biochimie 2016; 131:45-53. [DOI: 10.1016/j.biochi.2016.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/15/2016] [Indexed: 11/22/2022]
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17
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The Open Form Inducer Approach for Structure-Based Drug Design. PLoS One 2016; 11:e0167078. [PMID: 27893848 PMCID: PMC5125662 DOI: 10.1371/journal.pone.0167078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023] Open
Abstract
Many open form (OF) structures of drug targets were obtained a posteriori by analysis of co-crystals with inhibitors. Therefore, obtaining the OF structure of a drug target a priori will accelerate development of potent inhibitors. In addition to its small active site, Trypanosoma cruzi dihydroorotate dehydrogenase (TcDHODH) is fully functional in its monomeric form, making drug design approaches targeting the active site and protein-protein interactions unrealistic. Therefore, a novel a priori approach was developed to determination the TcDHODH active site in OF. This approach consists of generating an "OF inducer" (predicted in silico) to bind the target and cause steric repulsion with flexible regions proximal to the active site that force it open. We provide the first proof-of-concept of this approach by predicting and crystallizing TcDHODH in complex with an OF inducer, thereby obtaining the OF a priori with its subsequent use in designing potent and selective inhibitors. Fourteen co-crystal structures of TcDHODH with the designed inhibitors are presented herein. This approach has potential to encourage drug design against diseases where the molecular targets are such difficult proteins possessing small AS volume. This approach can be extended to study open/close conformation of proteins in general, the identification of allosteric pockets and inhibitors for other drug targets where conventional drug design approaches are not applicable, as well as the effective exploitation of the increasing number of protein structures deposited in Protein Data Bank.
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18
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Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PLoS Pathog 2016; 12:e1006010. [PMID: 27820863 PMCID: PMC5098729 DOI: 10.1371/journal.ppat.1006010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/18/2016] [Indexed: 01/17/2023] Open
Abstract
The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK) catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD), which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA), which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5'-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5'-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug.
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Affiliation(s)
- Christopher Leija
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Filipa Rijo-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Lisa N. Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zeping Hu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
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19
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Dewar S, Sienkiewicz N, Ong HB, Wall RJ, Horn D, Fairlamb AH. The Role of Folate Transport in Antifolate Drug Action in Trypanosoma brucei. J Biol Chem 2016; 291:24768-24778. [PMID: 27703008 PMCID: PMC5114424 DOI: 10.1074/jbc.m116.750422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/14/2016] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to identify and characterize mechanisms of resistance to antifolate drugs in African trypanosomes. Genome-wide RNAi library screens were undertaken in bloodstream form Trypanosoma brucei exposed to the antifolates methotrexate and raltitrexed. In conjunction with drug susceptibility and folate transport studies, RNAi knockdown was used to validate the functions of the putative folate transporters. The transport kinetics of folate and methotrexate were further characterized in whole cells. RNA interference target sequencing experiments identified a tandem array of genes encoding a folate transporter family, TbFT1-3, as major contributors to antifolate drug uptake. RNAi knockdown of TbFT1-3 substantially reduced folate transport into trypanosomes and reduced the parasite's susceptibly to the classical antifolates methotrexate and raltitrexed. In contrast, knockdown of TbFT1-3 increased susceptibly to the non-classical antifolates pyrimethamine and nolatrexed. Both folate and methotrexate transport were inhibited by classical antifolates but not by non-classical antifolates or biopterin. Thus, TbFT1-3 mediates the uptake of folate and classical antifolates in trypanosomes, and TbFT1-3 loss-of-function is a mechanism of antifolate drug resistance.
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Affiliation(s)
- Simon Dewar
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Natasha Sienkiewicz
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Han B Ong
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Richard J Wall
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - David Horn
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Alan H Fairlamb
- From the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
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20
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Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt SK, Burgess KEV, Breitling R, Watson DG, Bringaud F, Barrett MP. Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathog 2015; 11:e1004689. [PMID: 25775470 PMCID: PMC4361558 DOI: 10.1371/journal.ppat.1004689] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/19/2015] [Indexed: 01/21/2023] Open
Abstract
Metabolomics coupled with heavy-atom isotope-labelled glucose has been used to probe the metabolic pathways active in cultured bloodstream form trypomastigotes of Trypanosoma brucei, a parasite responsible for human African trypanosomiasis. Glucose enters many branches of metabolism beyond glycolysis, which has been widely held to be the sole route of glucose metabolism. Whilst pyruvate is the major end-product of glucose catabolism, its transamination product, alanine, is also produced in significant quantities. The oxidative branch of the pentose phosphate pathway is operative, although the non-oxidative branch is not. Ribose 5-phosphate generated through this pathway distributes widely into nucleotide synthesis and other branches of metabolism. Acetate, derived from glucose, is found associated with a range of acetylated amino acids and, to a lesser extent, fatty acids; while labelled glycerol is found in many glycerophospholipids. Glucose also enters inositol and several sugar nucleotides that serve as precursors to macromolecule biosynthesis. Although a Krebs cycle is not operative, malate, fumarate and succinate, primarily labelled in three carbons, were present, indicating an origin from phosphoenolpyruvate via oxaloacetate. Interestingly, the enzyme responsible for conversion of phosphoenolpyruvate to oxaloacetate, phosphoenolpyruvate carboxykinase, was shown to be essential to the bloodstream form trypanosomes, as demonstrated by the lethal phenotype induced by RNAi-mediated downregulation of its expression. In addition, glucose derivatives enter pyrimidine biosynthesis via oxaloacetate as a precursor to aspartate and orotate. In this work we have followed the distribution of carbon derived from glucose in bloodstream form trypanosomes, the causative agent of African trypanosomiasis, revealing it to enter a diverse range of metabolites. The work involved using 13C-labelled glucose and following the fate of the labelled carbon with an LC-MS based metabolomics platform. Beyond glycolysis and the oxidative branch of the pentose phosphate pathway the label entered lipid biosynthesis both through glycerol 3-phosphate and also acetate. Glucose derived carbon also entered nucleotide synthesis through ribose and pyrimidine synthesis through oxaloacetate-derived aspartate. Appreciable quantities of the carboxylic acids succinate and malate were identified, although labelling patterns indicate they are not TCA cycle derived. Amino sugars and sugar nucleotides were also labelled as was inositol used in protein modification but not in inositol phospholipid headgroup production. We confirm active and essential oxaloacetate production in bloodstream form trypanosomes and show that phosphoenolpyruvate carboxykinase is essential to these parasites using RNA interference. The amount of glucose entering these metabolites is minor compared to the quantity that enters pyruvate excreted from the cell, but the observation that enzymes contributing to the metabolism of glucose beyond glycolysis can be essential offers potential new targets for chemotherapy against trypanosomiasis.
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Affiliation(s)
- Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, Parkville, Victoria, Australia
| | - Muriel Mazet
- Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Fiona Achcar
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jana Anderson
- Department of Public Health, Institute of Health and Wellbeing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Ruwida Kamour
- Department of Medicinal and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tripoli, Tripoli, Libya
| | - Pauline Morand
- Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Yoann Millerioux
- Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Achuthanunni Chokkathukalam
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, Garscube Campus, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Stefan K. Weidt
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, Garscube Campus, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karl E. V. Burgess
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, Garscube Campus, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Michael P. Barrett
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, Garscube Campus, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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21
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Ong HB, Lee WS, Patterson S, Wyllie S, Fairlamb AH. Homoserine and quorum-sensing acyl homoserine lactones as alternative sources of threonine: a potential role for homoserine kinase in insect-stage Trypanosoma brucei. Mol Microbiol 2014; 95:143-56. [PMID: 25367138 PMCID: PMC4460637 DOI: 10.1111/mmi.12853] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2014] [Indexed: 12/29/2022]
Abstract
De novo synthesis of threonine from aspartate occurs via the β-aspartyl phosphate pathway in plants, bacteria and fungi. However, the Trypanosoma brucei genome encodes only the last two steps in this pathway: homoserine kinase (HSK) and threonine synthase. Here, we investigated the possible roles for this incomplete pathway through biochemical, genetic and nutritional studies. Purified recombinant TbHSK specifically phosphorylates L-homoserine and displays kinetic properties similar to other HSKs. HSK null mutants generated in bloodstream forms displayed no growth phenotype in vitro or loss of virulence in vivo. However, following transformation into procyclic forms, homoserine, homoserine lactone and certain acyl homoserine lactones (AHLs) were found to substitute for threonine in growth media for wild-type procyclics, but not HSK null mutants. The tsetse fly is considered to be an unlikely source of these nutrients as it feeds exclusively on mammalian blood. Bioinformatic studies predict that tsetse endosymbionts possess part (up to homoserine in Wigglesworthia glossinidia) or all of the β-aspartyl phosphate pathway (Sodalis glossinidius). In addition S. glossinidius is known to produce 3-oxohexanoylhomoserine lactone which also supports trypanosome growth. We propose that T. brucei has retained HSK and threonine synthase in order to salvage these nutrients when threonine availability is limiting.
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Affiliation(s)
- Han B Ong
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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22
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Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C. Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Mol Microbiol 2014; 94:307-26. [PMID: 25145465 PMCID: PMC4285177 DOI: 10.1111/mmi.12764] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2014] [Indexed: 01/14/2023]
Abstract
African trypanosomes are an excellent system for quantitative modelling of post-transcriptional mRNA control. Transcription is constitutive and polycistronic; individual mRNAs are excised by trans splicing and polyadenylation. We here measure mRNA decay kinetics in two life cycle stages, bloodstream and procyclic forms, by transcription inhibition and RNASeq. Messenger RNAs with short half-lives tend to show initial fast degradation, followed by a slower phase; they are often stabilized by depletion of the 5′–3′ exoribonuclease XRNA. Many longer-lived mRNAs show initial slow degradation followed by rapid destruction: we suggest that the slow phase reflects gradual deadenylation. Developmentally regulated mRNAs often show regulated decay, and switch their decay pattern. Rates of mRNA decay are good predictors of steady state levels for short mRNAs, but mRNAs longer than 3 kb show unexpectedly low abundances. Modelling shows that variations in splicing and polyadenylation rates can contribute to steady-state mRNA levels, but this is completely dependent on competition between processing and co-transcriptional mRNA precursor destruction.
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Affiliation(s)
- Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
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23
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The role of the de novo pyrimidine biosynthetic pathway in Cryptococcus neoformans high temperature growth and virulence. Fungal Genet Biol 2014; 70:12-23. [PMID: 25011011 DOI: 10.1016/j.fgb.2014.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/09/2014] [Accepted: 06/14/2014] [Indexed: 11/21/2022]
Abstract
Fungal infections are often difficult to treat due to the inherent similarities between fungal and animal cells and the resulting host toxicity from many antifungal compounds. Cryptococcus neoformans is an opportunistic fungal pathogen of humans that causes life-threatening disease, primarily in immunocompromised patients. Since antifungal therapy for this microorganism is limited, many investigators have explored novel drug targets aim at virulence factors, such as the ability to grow at mammalian physiological temperature (37°C). To address this issue, we used the Agrobacterium tumefaciens gene delivery system to create a random insertion mutagenesis library that was screened for altered growth at elevated temperatures. Among several mutants unable to grow at 37°C, we explored one bearing an interruption in the URA4 gene. This gene encodes dihydroorotase (DHOase) that is involved in the de novo synthesis of pyrimidine ribonucleotides. Loss of the C. neoformans Ura4 protein, by targeted gene interruption, resulted in an expected uracil/uridine auxotrophy and an unexpected high temperature growth defect. In addition, the ura4 mutant displayed phenotypic defects in other prominent virulence factors (melanin, capsule and phospholipase) and reduced stress response compared to wild type and reconstituted strains. Accordingly, this mutant had a decreased survival rate in macrophages and attenuated virulence in a murine model of cryptococcal infection. Quantitative PCR analysis suggests that this biosynthetic pathway is induced during the transition from 30°C to 37°C, and that transcriptional regulation of de novo and salvage pyrimidine pathway are under the control of the Ura4 protein.
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Ritt JF, Raymond F, Leprohon P, Légaré D, Corbeil J, Ouellette M. Gene amplification and point mutations in pyrimidine metabolic genes in 5-fluorouracil resistant Leishmania infantum. PLoS Negl Trop Dis 2013; 7:e2564. [PMID: 24278495 PMCID: PMC3836990 DOI: 10.1371/journal.pntd.0002564] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/15/2013] [Indexed: 12/02/2022] Open
Abstract
Background The human protozoan parasites Leishmania are prototrophic for pyrimidines with the ability of both de novo biosynthesis and uptake of pyrimidines. Methodology/Principal Findings Five independent L. infantum mutants were selected for resistance to the pyrimidine analogue 5-fluorouracil (5-FU) in the hope to better understand the metabolism of pyrimidine in Leishmania. Analysis of the 5-FU mutants by comparative genomic hybridization and whole genome sequencing revealed in selected mutants the amplification of DHFR-TS and a deletion of part of chromosome 10. Point mutations in uracil phosphorybosyl transferase (UPRT), thymidine kinase (TK) and uridine phosphorylase (UP) were also observed in three individual resistant mutants. Transfection experiments confirmed that these point mutations were responsible for 5-FU resistance. Transport studies revealed that one resistant mutant was defective for uracil and 5-FU import. Conclusion/Significance This study provided further insights in pyrimidine metabolism in Leishmania and confirmed that multiple mutations can co-exist and lead to resistance in Leishmania. The human protozoan parasites Leishmania present the ability of both de novo biosynthesis and uptake of pyrimidines. The pyrimidine pathway is not well understood in these parasites. In the hope to better understand the pyrimidine pathway in Leishmania, five independent L. infantum mutants were selected for resistance to the pyrimidine analogue 5-fluorouracil (5-FU). Analysis of the 5-FU mutants by comparative genomic hybridization and whole genome sequencing revealed the amplification of the main target enzyme DHFR-TS, and point mutations in three important metabolic enzymes. Transfection experiments confirmed that these point mutations were responsible for 5-FU resistance. Transport studies also revealed that one resistant mutant was defective for uracil and 5-FU import. Overall, this study provided further insights in pyrimidine metabolism in Leishmania and confirmed that multiple mutations can co-exist and lead to resistance in these protozoa.
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Affiliation(s)
- Jean-François Ritt
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
| | - Frédéric Raymond
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
| | - Danielle Légaré
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
| | - Jacques Corbeil
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de recherche en Infectiologie du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Québec City, Québec, Canada
- * E-mail:
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Ong HB, Sienkiewicz N, Wyllie S, Patterson S, Fairlamb AH. Trypanosoma brucei (UMP synthase null mutants) are avirulent in mice, but recover virulence upon prolonged culture in vitro while retaining pyrimidine auxotrophy. Mol Microbiol 2013; 90:443-55. [PMID: 23980694 PMCID: PMC3868941 DOI: 10.1111/mmi.12376] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2013] [Indexed: 11/30/2022]
Abstract
African trypanosomes are capable of both de novo synthesis and salvage of pyrimidines. The last two steps in de novo synthesis are catalysed by UMP synthase (UMPS) – a bifunctional enzyme comprising orotate phosphoribosyl transferase (OPRT) and orotidine monophosphate decarboxylase (OMPDC). To investigate the essentiality of pyrimidine biosynthesis in Trypanosoma brucei, we generated a umps double knockout (DKO) line by gene replacement. The DKO was unable to grow in pyrimidine-depleted medium in vitro, unless supplemented with uracil, uridine, deoxyuridine or UMP. DKO parasites were completely resistant to 5-fluoroorotate and hypersensitive to 5-fluorouracil, consistent with loss of UMPS, but remained sensitive to pyrazofurin indicating that, unlike mammalian cells, the primary target of pyrazofurin is not OMPDC. The null mutant was unable to infect mice indicating that salvage of host pyrimidines is insufficient to support growth. However, following prolonged culture in vitro, parasites regained virulence in mice despite retaining pyrimidine auxotrophy. Unlike the wild-type, both pyrimidine auxotrophs secreted substantial quantities of orotate, significantly higher in the virulent DKO line. We propose that this may be responsible for the recovery of virulence in mice, due to host metabolism converting orotate to uridine, thereby bypassing the loss of UMPS in the parasite.
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Affiliation(s)
- Han B Ong
- Divisional of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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Soysa R, Wilson ZN, Elferich J, Forquer I, Shinde U, Riscoe MK, Yates PA, Ullman B. Substrate inhibition of uracil phosphoribosyltransferase by uracil can account for the uracil growth sensitivity of Leishmania donovani pyrimidine auxotrophs. J Biol Chem 2013; 288:29954-64. [PMID: 23986453 DOI: 10.1074/jbc.m113.478826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pathogenic protozoan parasite Leishmania donovani is capable of both de novo pyrimidine biosynthesis and salvage of pyrimidines from the host milieu. Genetic analysis has authenticated L. donovani uracil phosphoribosyltransferase (LdUPRT), an enzyme not found in mammalian cells, as the focal enzyme of pyrimidine salvage because all exogenous pyrimidines that can satisfy the requirement of the parasite for pyrimidine nucleotides are funneled to uracil and then phosphoribosylated to UMP in the parasite by LdUPRT. To characterize this unique parasite enzyme, LdUPRT was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. Kinetic analysis revealed apparent Km values of 20 and 99 μM for the natural substrates uracil and phosphoribosylpyrophosphate, respectively, as well as apparent Km values 6 and 7 μM for the pyrimidine analogs 5-fluorouracil and 4-thiouracil, respectively. Size exclusion chromatography revealed the native LdUPRT to be tetrameric and retained partial structure and activity in high concentrations of urea. L. donovani mutants deficient in de novo pyrimidine biosynthesis, which require functional LdUPRT for growth, are hypersensitive to high concentrations of uracil, 5-fluorouracil, and 4-thiouracil in the growth medium. This hypersensitivity can be explained by the observation that LdUPRT is substrate-inhibited by uracil and 4-thiouracil, but 5-fluorouracil toxicity transpires via an alternative mechanism. This substrate inhibition of LdUPRT provides a protective mechanism for the parasite by facilitating purine and pyrimidine nucleotide pool balance and by sparing phosphoribosylpyrophosphate for consumption by the nutritionally indispensable purine salvage process.
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Affiliation(s)
- Radika Soysa
- From the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098 and
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