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Nayeri T, Sarvi S, Daryani A. Effective factors in the pathogenesis of Toxoplasmagondii. Heliyon 2024; 10:e31558. [PMID: 38818168 PMCID: PMC11137575 DOI: 10.1016/j.heliyon.2024.e31558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/11/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Toxoplasma gondii (T. gondii) is a cosmopolitan protozoan parasite in humans and animals. It infects about 30 % of the human population worldwide and causes potentially fatal diseases in immunocompromised hosts and neonates. For this study, five English-language databases (ScienceDirect, ProQuest, Web of Science, PubMed, and Scopus) and the internet search engine Google Scholar were searched. This review was accomplished to draw a global perspective of what is known about the pathogenesis of T. gondii and various factors affecting it. Virulence and immune responses can influence the mechanisms of parasite pathogenesis and these factors are in turn influenced by other factors. In addition to the host's genetic background, the type of Toxoplasma strain, the routes of transmission of infection, the number of passages, and different phases of parasite life affect virulence. The identification of virulence factors of the parasite could provide promising insights into the pathogenesis of this parasite. The results of this study can be an incentive to conduct more intensive research to design and develop new anti-Toxoplasma agents (drugs and vaccines) to treat or prevent this infection. In addition, further studies are needed to better understand the key agents in the pathogenesis of T. gondii.
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Affiliation(s)
- Tooran Nayeri
- Infectious and Tropical Diseases Research Center, Dezful University of Medical Sciences, Dezful, Iran
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shahabeddin Sarvi
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmad Daryani
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Liu Q, Guan XA, Li DF, Zheng YX, Wang S, Xuan XN, Zhao JL, He L. Babesia gibsoni Whole-Genome Sequencing, Assembling, Annotation, and Comparative Analysis. Microbiol Spectr 2023; 11:e0072123. [PMID: 37432130 PMCID: PMC10434002 DOI: 10.1128/spectrum.00721-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
The intracellular protozoan parasite Babesia gibsoni infects canine erythrocytes and causes babesiosis. The hazards to animal health have increased due to the rise of B. gibsoni infections and medication resistance. However, the lack of high-quality full-genome sequencing sets has expanded the obstacles to the development of pathogeneses, drugs, and vaccines. In this study, the whole genome of B. gibsoni was sequenced, assembled, and annotated. The genomic size of B. gibsoni was 7.94 Mbp in total. Four chromosomes with the size of 0.69 Mb, 2.10 Mb, 2.77 Mb, and 2.38 Mb, respectively, 1 apicoplast (28.4 Kb), and 1 mitochondrion (5.9 Kb) were confirmed. KEGG analysis revealed 2,641 putative proteins enriched on 316 pathways, and GO analysis showed 7,571 annotations of the nuclear genome in total. Synteny analysis showed a high correlation between B. gibsoni and B. bovis. A new divergent point of B. gibsoni occurred around 297.7 million years ago, which was earlier than that of B. bovis, B. ovata, and B. bigemina. Orthology analysis revealed 22 and 32 unique genes compared to several Babesia spp. and apicomplexan species. The metabolic pathways of B.gibsoni were characterized, pointing to a minimal size of the genome. A species-specific secretory protein SA1 and 19 homologous genes were identified. Selected specific proteins, including apetala 2 (AP2) factor, invasion-related proteins BgAMA-1 and BgRON2, and rhoptry function proteins BgWH_04g00700 were predicted, visualized, and modeled. Overall, whole-genome sequencing provided molecular-level support for the diagnosis, prevention, clinical treatment, and further research of B. gibsoni. IMPORTANCE The whole genome of B. gibsoni was first sequenced, annotated, and disclosed. The key part of genome composition, four chromosomes, was comparatively analyzed for the first time. A full-scale phylogeny evolution analysis based on the whole-genome-wide data of B. gibsoni was performed, and a new divergent point on the evolutionary path was revealed. In previous reports, molecular studies were often limited by incomplete genomic data, especially in key areas like life cycle regulation, metabolism, and host-pathogen interaction. With the whole-genome sequencing of B. gibsoni, we provide useful genetic data to encourage the exploration of new terrain and make it feasible to resolve the theoretical and practical problems of babesiosis.
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Affiliation(s)
- Qin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Xing-Ai Guan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Dong-Fang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Ya-Xin Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Sen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Xue-Nan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro Hokkaido, Japan
| | - Jun-Long Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, China
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Hyperpolarizing DNA Nucleobases via NMR Signal Amplification by Reversible Exchange. Molecules 2023; 28:molecules28031198. [PMID: 36770865 PMCID: PMC9921525 DOI: 10.3390/molecules28031198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
The present work investigates the potential for enhancing the NMR signals of DNA nucleobases by parahydrogen-based hyperpolarization. Signal amplification by reversible exchange (SABRE) and SABRE in Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) of selected DNA nucleobases is demonstrated with the enhancement (ε) of 1H, 15N, and/or 13C spins in 3-methyladenine, cytosine, and 6-O-guanine. Solutions of the standard SABRE homogenous catalyst Ir(1,5-cyclooctadeine)(1,3-bis(2,4,6-trimethylphenyl)imidazolium)Cl ("IrIMes") and a given nucleobase in deuterated ethanol/water solutions yielded low 1H ε values (≤10), likely reflecting weak catalyst binding. However, we achieved natural-abundance enhancement of 15N signals for 3-methyladenine of ~3300 and ~1900 for the imidazole ring nitrogen atoms. 1H and 15N 3-methyladenine studies revealed that methylation of adenine affords preferential binding of the imidazole ring over the pyrimidine ring. Interestingly, signal enhancements (ε~240) of both 15N atoms for doubly labelled cytosine reveal the preferential binding of specific tautomer(s), thus giving insight into the matching of polarization-transfer and tautomerization time scales. 13C enhancements of up to nearly 50-fold were also obtained for this cytosine isotopomer. These efforts may enable the future investigation of processes underlying cellular function and/or dysfunction, including how DNA nucleobase tautomerization influences mismatching in base-pairing.
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Babai R, Izrael R, Vértessy BG. Characterization of the dynamics of Plasmodium falciparum deoxynucleotide-triphosphate pool in a stage-specific manner. Sci Rep 2022; 12:19926. [PMID: 36402851 PMCID: PMC9675800 DOI: 10.1038/s41598-022-23807-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/06/2022] [Indexed: 11/21/2022] Open
Abstract
Understanding and characterizing the molecular background of the maintenance of genomic integrity might be a major factor in comprehending the exceptional ability of the malaria parasite, Plasmodium falciparum to adapt at a fast pace to antimalarials. A balanced nucleotide pool is an essential factor for high-fidelity replication. The lack of detailed studies on deoxynucleotide-triphosphate (dNTP) pools in various intraerythrocytic stages of Plasmodium falciparum motivated our present study. Here, we focused on the building blocks of DNA and utilized an EvaGreen-based dNTP incorporation assay to successfully measure the temporal dynamics of dNTPs in every intraerythrocytic stage and in drug-treated trophozoites. Our findings show that the ratio of dNTPs in the ring-stage parasites significantly differs from the more mature trophozoite and schizont stages. We were also able to detect dGTP levels that have never been shown before and found it to be the least abundant dNTP in all stages. Treatment with WR99210, a TS-DHFR inhibitor drug, affected not only dTTP, but also dGTP levels, despite its presumed selective action on pyrimidine biosynthesis. Results from our studies might assist in a better understanding of genome integrity mechanisms and may potentially lead to novel drug related aspects involving purine and pyrimidine metabolic targets.
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Affiliation(s)
- Réka Babai
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451George A. Olah Doctoral School of Chemistry and Chemical Technology, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
| | - Richard Izrael
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, 6720 Hungary
| | - Beáta G. Vértessy
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
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Chhibber-Goel J, Shukla A, Shanmugam D, Sharma A. Profiling of metabolic alterations in mice infected with malaria parasites via high-resolution metabolomics. Mol Biochem Parasitol 2022; 252:111525. [PMID: 36209797 DOI: 10.1016/j.molbiopara.2022.111525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Malaria infection can result in distinct clinical outcomes from asymptomatic to severe. The association between patho-physiological changes and molecular changes in the host, and their correlation with severity of malaria progression is not fully understood. METHODS In this study, we addressed mass spectrometry-based temporal profiling of serum metabolite levels from mice infected with Plasmodium berhgei (strain ANKA). RESULTS We show global perturbations and identify changes in specific metabolites in correlation with disease progression. While metabolome-wide changes were apparent in late-stage malaria, a subset of metabolites exhibited highly correlated changes with disease progression. These metabolites changed early on following infection and either continued or maintained the change as mice developed severe disease. Some of these have the potential to be sentinel metabolites for severe malaria. Moreover, glycolytic metabolites, purine nucleotide precursors, tryptophan and its bioactive derivatives were many fold decreased in late-stage disease. Interestingly, uric acid, a metabolic waste reported to be elevated in severe human malaria, increased with disease progression, and subsequently appears to be detoxified into allantoin. This detoxification mechanism is absent in humans as they lack the enzyme uricase. CONCLUSIONS We have identified candidate marker metabolites that may be of relevance in the context of human malaria.
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Affiliation(s)
- Jyoti Chhibber-Goel
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Anurag Shukla
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dhanasekaran Shanmugam
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Amit Sharma
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India; ICMR-National institute of Malaria Research, New Delhi 110077, India.
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Botnar A, Lawrence G, Maher SP, Vantaux A, Witkowski B, Shiau JC, Merino EF, De Vore D, Yang C, Murray C, Cassera MB, Leahy JW, Kyle DE. Alkyne modified purines for assessment of activation of Plasmodium vivax hypnozoites and growth of pre-erythrocytic and erythrocytic stages in Plasmodium spp. Int J Parasitol 2022; 52:733-744. [PMID: 35447149 PMCID: PMC9576819 DOI: 10.1016/j.ijpara.2022.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022]
Abstract
Malaria is a major global health problem which predominantly afflicts developing countries. Although many antimalarial therapies are currently available, the protozoan parasite causing this disease, Plasmodium spp., continues to evade eradication efforts. One biological phenomenon hampering eradication efforts is the parasite's ability to arrest development, transform into a drug-insensitive form, and then resume growth post-therapy. Currently, the mechanisms by which the parasite enters arrested development, or dormancy, and later recrudesces or reactivates to continue development, are unknown and the malaria field lacks techniques to study these elusive mechanisms. Since Plasmodium spp. salvage purines for DNA synthesis, we hypothesised that alkyne-containing purine nucleosides could be used to develop a DNA synthesis marker which could be used to investigate mechanisms behind dormancy. Using copper-catalysed click chemistry methods, we observe incorporation of alkyne modified adenosine, inosine, and hypoxanthine in actively replicating asexual blood stages of Plasmodium falciparum and incorporation of modified adenosine in actively replicating liver stage schizonts of Plasmodium vivax. Notably, these modified purines were not incorporated in dormant liver stage hypnozoites, suggesting this marker could be used as a tool to differentiate replicating and non-replicating liver forms and, more broadly, as a tool for advancing our understanding of Plasmodium dormancy mechanisms.
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Affiliation(s)
- Alona Botnar
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Grant Lawrence
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Steven P Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Benoît Witkowski
- Malaria Molecular Epidemiology Unit, Pasteur Institute of Cambodia, Phnom Penh, Cambodia
| | - Justine C Shiau
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Emilio F Merino
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - David De Vore
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Christian Yang
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Cameron Murray
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Maria B Cassera
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - James W Leahy
- Department of Chemistry, University of South Florida, Tampa, FL, United States; The Florida Center for Excellence for Drug Discovery and Innovation, University of South Florida, Tampa, GA, United States; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, GA, United States
| | - Dennis E Kyle
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States; Department of Cellular Biology, University of Georgia, Athens, GA, United States.
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Pang L, Zanki V, Strelkov SV, Van Aerschot A, Gruic-Sovulj I, Weeks SD. Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Commun Biol 2022; 5:883. [PMID: 36038645 PMCID: PMC9424281 DOI: 10.1038/s42003-022-03825-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022] Open
Abstract
To correctly aminoacylate tRNALeu, leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNALeu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.
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Affiliation(s)
- Luping Pang
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium ,grid.207374.50000 0001 2189 3846Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001 China
| | - Vladimir Zanki
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Sergei V. Strelkov
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium
| | - Ita Gruic-Sovulj
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Stephen D. Weeks
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,Pledge Therapeutics, Gaston Geenslaan 1, 3001 Leuven, Belgium
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Zhai B, He JJ, Xie SC, Qiu Y, Miao Z, Liu Y, Zhu XQ, Zhang J. Metabolomics study of cat small intestine during the early stage of Toxoplasma gondii oocyst formation identifies potential biomarkers. Vet Parasitol 2022; 309:109764. [PMID: 35870221 DOI: 10.1016/j.vetpar.2022.109764] [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: 04/17/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Toxoplasma gondii (T. gondii) is a zoonotic intracellular protozoan parasite that can invade, replicate and survive in almost all cells of warm-blooded animals. T. gondii infection threatens the life of the fetus or can cause morbidity in the infant. As the only definitive host of T. gondii, felids spread the pathogen mainly by forming oocysts in the small intestines and discharging the oocysts into the ambient environment, consequently polluting water, vegetables, and meat products. In this study, we used untargeted metabolomics technology to study the changes in metabolites that occurred during the early stage of oocyst formation in the cat small intestine following T. gondii infection and attempted to identify metabolic biomarkers that could potentially be used as diagnostic molecular markers in the future. Domestic cats (Felis catus) were infected with T. gondii Pru tissue cysts, and samples of their small intestinal epithelium were collected at 2 and 4 days post-infection (DPI) for metabolic analysis. LC-MS/MS and multivariate statistical analysis were employed to detect metabolomic signatures that discriminated between the infected and control groups. A total of 1673 ions and 1201 ions were obtained in the positive and negative modes, respectively. Of these ions, 175 were up-regulated and 127 were down-regulated in the positive ion mode; whereas, 123 were up-regulated and 81 were down-regulated in the negative ion mode. Three commonly altered ions (0.74_313.0414 m/z, 8.82_615.2621 m/z and 8.16_325.2362 m/z) were determined to have potential research value. Seventy common metabolic pathways were enriched at two time points, with arginine biosynthesis, pyrimidine metabolism, pantothenate and CoA biosynthesis being the three most significant pathways related to T. gondii. The area under the curve (AUC) of differential metabolites combined with relevant literature analysis showed that N-Methylpelletierine and 3,3-Difluoro-17-methyl-5alpha-androstan-17beta-ol have higher predictability and better potential application value than other metabolites. Our analysis of metabolic markers during the early stage of T. gondii oocyst formation in the small intestine of the definitive host (cat) provided novel insight for understanding oocyst development and a theoretical basis for the application of potential biomarkers.
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Affiliation(s)
- Bintao Zhai
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou, Gansu Province 730050, People's Republic of China
| | - Jun-Jun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province 650201, People's Republic of China
| | - Shi-Chen Xie
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province 030801, People's Republic of China; Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, People's Republic of China
| | - Yanhua Qiu
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou, Gansu Province 730050, People's Republic of China
| | - Zengqiang Miao
- Medical College of Qinghai University, Qinghai University, Xining, Qinghai Province 810016, People's Republic of China
| | - Yang Liu
- College of Life Science, Ningxia University, Yinchuan, Ningxia Hui Autonomous Region 750021, People's Republic of China
| | - Xing-Quan Zhu
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province 650201, People's Republic of China; College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province 030801, People's Republic of China.
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou, Gansu Province 730050, People's Republic of China.
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Identification of novel Plasmodium falciparum dihydroorotate dehydrogenase inhibitors for malaria using in silico studies. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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10
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Evaluating the Accuracy of the QCEIMS Approach for Computational Prediction of Electron Ionization Mass Spectra of Purines and Pyrimidines. Metabolites 2022; 12:metabo12010068. [PMID: 35050190 PMCID: PMC8779335 DOI: 10.3390/metabo12010068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/08/2022] [Accepted: 01/09/2022] [Indexed: 12/04/2022] Open
Abstract
Mass spectrometry is the most commonly used method for compound annotation in metabolomics. However, most mass spectra in untargeted assays cannot be annotated with specific compound structures because reference mass spectral libraries are far smaller than the complement of known molecules. Theoretically predicted mass spectra might be used as a substitute for experimental spectra especially for compounds that are not commercially available. For example, the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) method can predict 70 eV electron ionization mass spectra from any given input molecular structure. In this work, we investigated the accuracy of QCEIMS predictions of electron ionization (EI) mass spectra for 80 purine and pyrimidine derivatives in comparison to experimental data in the NIST 17 database. Similarity scores between every pair of predicted and experimental spectra revealed that 45% of the compounds were found as the correct top hit when QCEIMS predicted spectra were matched against the NIST17 library of >267,000 EI spectra, and 74% of the compounds were found within the top 10 hits. We then investigated the impact of matching, missing, and additional fragment ions in predicted EI mass spectra versus ion abundances in MS similarity scores. We further include detailed studies of fragmentation pathways such as retro Diels–Alder reactions to predict neutral losses of (iso)cyanic acid, hydrogen cyanide, or cyanamide in the mass spectra of purines and pyrimidines. We describe how trends in prediction accuracy correlate with the chemistry of the input compounds to better understand how mechanisms of QCEIMS predictions could be improved in future developments. We conclude that QCEIMS is useful for generating large-scale predicted mass spectral libraries for identification of compounds that are absent from experimental libraries and that are not commercially available.
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Zenchenko AA, Drenichev MS, Il’icheva IA, Mikhailov SN. Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action. Mol Biol 2021; 55:786-812. [PMID: 34955556 PMCID: PMC8682041 DOI: 10.1134/s0026893321040105] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/03/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022]
Abstract
The emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compounds, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial or antiprotozoal activity. Particular attention is paid to the mechanisms that determine the antiviral effect of nucleoside analogs containing hydrophobic fragments. Depending on the structure and position of the hydrophobic substituent, such nucleosides can either block the process of penetration of viruses into cells or inhibit the stage of genome replication. The mechanisms of inhibition of viral enzymes by compounds of nucleoside and non-nucleoside nature have been compared. The stages of creation of antiparasitic drugs, which are based on the peculiarities of metabolic transformations of nucleosides in humans body and parasites, have been considered. A new approach to the creation of drugs is described, based on the use of prodrugs of modified nucleosides, which, as a result of metabolic processes, are converted into an effective drug directly in the target organ or tissue. This strategy makes it possible to reduce the general toxicity of the drug to humans and to increase the effectiveness of its action on cells infected by the virus.
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Affiliation(s)
- A. A. Zenchenko
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - M. S. Drenichev
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - I. A. Il’icheva
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - S. N. Mikhailov
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
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12
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An Uninvited Seat at the Dinner Table: How Apicomplexan Parasites Scavenge Nutrients from the Host. Microorganisms 2021; 9:microorganisms9122592. [PMID: 34946193 PMCID: PMC8707601 DOI: 10.3390/microorganisms9122592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
Obligate intracellular parasites have evolved a remarkable assortment of strategies to scavenge nutrients from the host cells they parasitize. Most apicomplexans form a parasitophorous vacuole (PV) within the invaded cell, a replicative niche within which they survive and multiply. As well as providing a physical barrier against host cell defense mechanisms, the PV membrane (PVM) is also an important site of nutrient uptake that is essential for the parasites to sustain their metabolism. This means nutrients in the extracellular milieu are separated from parasite metabolic machinery by three different membranes, the host plasma membrane, the PVM, and the parasite plasma membrane (PPM). In order to facilitate nutrient transport from the extracellular environment into the parasite itself, transporters on the host cell membrane of invaded cells can be modified by secreted and exported parasite proteins to maximize uptake of key substrates to meet their metabolic demand. To overcome the second barrier, the PVM, apicomplexan parasites secrete proteins contained in the dense granules that remodel the vacuole and make the membrane permissive to important nutrients. This bulk flow of host nutrients is followed by a more selective uptake of substrates at the PPM that is operated by specific transporters of this third barrier. In this review, we recapitulate and compare the strategies developed by Apicomplexa to scavenge nutrients from their hosts, with particular emphasis on transporters at the parasite plasma membrane and vacuolar solute transporters on the parasite intracellular digestive organelle.
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13
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Owoloye A, Enejoh OA, Akanbi OM, Bankole OM. Molecular docking analysis of Plasmodium falciparum dihydroorotate dehydrogenase towards the design of effective inhibitors. Bioinformation 2021; 16:672-678. [PMID: 34621112 PMCID: PMC8457017 DOI: 10.6026/97320630016672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 11/23/2022] Open
Abstract
Malaria remains a global public health burden with significant mortality and morbidity. Despite the several approved drugs available for its management, the parasite has developed resistance to virtually all known antimalarial drugs. The development of a new drug that can combat resistant to Artemisinin based Combination Therapies (ACTs) for malaria is imperative. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a flavin-dependent mitochondrial enzyme is vital in the parasite's pyrimidine biosynthesis is a well-known drug target. Therefore, it is of interest to document the MOLECULAR DOCKING analysis (using Maestro, Schrodinger) data of DIHYDROOROTATE DEHYDROGENASE PfDHODH from P. falciparum towards the design of effective inhibitors. The molecular docking features of 10 compounds with reference to chloroquine with PfDHODH are documented in this report for further consideration.
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Affiliation(s)
- Afolabi Owoloye
- Parasitology Unit, Department of Animal and Environmental Biology, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Ojochenemi A Enejoh
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Olusegun M Akanbi
- Parasitology Unit, Department of Animal and Environmental Biology, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Owolabi M Bankole
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,Department of Chemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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14
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Identification of 3,4-Dihydro-2 H,6 H-pyrimido[1,2- c][1,3]benzothiazin-6-imine Derivatives as Novel Selective Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22137236. [PMID: 34281290 PMCID: PMC8268581 DOI: 10.3390/ijms22137236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022] Open
Abstract
Plasmodium falciparum's resistance to available antimalarial drugs highlights the need for the development of novel drugs. Pyrimidine de novo biosynthesis is a validated drug target for the prevention and treatment of malaria infection. P. falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the oxidation of dihydroorotate to orotate and utilize ubiquinone as an electron acceptor in the fourth step of pyrimidine de novo biosynthesis. PfDHODH is targeted by the inhibitor DSM265, which binds to a hydrophobic pocket located at the N-terminus where ubiquinone binds, which is known to be structurally divergent from the mammalian orthologue. In this study, we screened 40,400 compounds from the Kyoto University chemical library against recombinant PfDHODH. These studies led to the identification of 3,4-dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine and its derivatives as a new class of PfDHODH inhibitor. Moreover, the hit compounds identified in this study are selective for PfDHODH without inhibition of the human enzymes. Finally, this new scaffold of PfDHODH inhibitors showed growth inhibition activity against P. falciparum 3D7 with low toxicity to three human cell lines, providing a new starting point for antimalarial drug development.
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15
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Ojha PK, Kumar V, Roy J, Roy K. Recent advances in quantitative structure-activity relationship models of antimalarial drugs. Expert Opin Drug Discov 2021; 16:659-695. [PMID: 33356651 DOI: 10.1080/17460441.2021.1866535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Due to emerging resistance to the first-line artemisinin-based antimalarials and lack of efficient vaccines and limited chemotherapeutic alternatives, there is an urgent need to develop new antimalarial compounds. In this regard, quantitative structure-activity relationship (QSAR) modeling can provide essential information about required physicochemical properties and structural parameters of antimalarial drug candidates. AREAS COVERED The authors provide an overview of recent advances of QSAR models covering different classes of antimalarial compounds as well as molecular docking studies of compounds acting on different antimalarial targets reported in the last 5 years (2015-2019) to explore the mode of interactions between the molecules and the receptors. We have tried to cover most of the QSAR models of antimalarials (along with results from some other related computational methods) reported during 2015-2019. EXPERT OPINION Many QSAR reports for antimalarial compounds are based on small number of data points. This review infers that most of the present work deals with analog-based QSAR approach with a limited applicability domain (a very few cases with wide domain) whereas novel target-based computational approach is reported in very few cases, which leads to huge voids of computational work based on novel antimalarial targets.
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Affiliation(s)
- Probir Kumar Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Joyita Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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16
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Driving antimalarial design through understanding of target mechanism. Biochem Soc Trans 2020; 48:2067-2078. [PMID: 32869828 PMCID: PMC7609028 DOI: 10.1042/bst20200224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
Malaria continues to be a global health threat, affecting approximately 219 million people in 2018 alone. The recurrent development of resistance to existing antimalarials means that the design of new drug candidates must be carefully considered. Understanding of drug target mechanism can dramatically accelerate early-stage target-based development of novel antimalarials and allows for structural modifications even during late-stage preclinical development. Here, we have provided an overview of three promising antimalarial molecular targets, PfDHFR, PfDHODH and PfA-M1, and their associated inhibitors which demonstrate how mechanism can inform drug design and be effectively utilised to generate compounds with potent inhibitory activity.
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17
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Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase. Nat Commun 2020; 11:3228. [PMID: 32591529 PMCID: PMC7320144 DOI: 10.1038/s41467-020-17013-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/28/2020] [Indexed: 11/21/2022] Open
Abstract
Plasmodium falciparum (Pf) relies solely on the salvage pathway for its purine nucleotide requirements, making this pathway indispensable to the parasite. Purine nucleotide levels are regulated by anabolic processes and by nucleotidases that hydrolyse these metabolites into nucleosides. Certain apicomplexan parasites, including Pf, have an IMP-specific-nucleotidase 1 (ISN1). Here we show, by comprehensive substrate screening, that PfISN1 catalyzes the dephosphorylation of inosine monophosphate (IMP) and is allosterically activated by ATP. Crystal structures of tetrameric PfISN1 reveal complex rearrangements of domain organization tightly associated with catalysis. Immunofluorescence microscopy and expression of GFP-fused protein indicate cytosolic localization of PfISN1 and expression in asexual and gametocyte stages of the parasite. With earlier evidence on isn1 upregulation in female gametocytes, the structures reported in this study may contribute to initiate the design for possible transmission-blocking agents. Plasmodium falciparum IMP-specific 5′-nucleotidase 1 (PfISN1) is of interest as a potential malaria drug target. Here, the authors report that IMP is a substrate, and ATP an allosteric activator, of PfISN1 and present PfISN1 crystal structures in the ligand-free state and bound to either IMP or ATP.
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18
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Bosch SS, Lunev S, Batista FA, Linzke M, Kronenberger T, Dömling ASS, Groves MR, Wrenger C. Molecular Target Validation of Aspartate Transcarbamoylase from Plasmodium falciparum by Torin 2. ACS Infect Dis 2020; 6:986-999. [PMID: 32129597 DOI: 10.1021/acsinfecdis.9b00411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Malaria is a tropical disease that kills about half a million people around the world annually. Enzymatic reactions within pyrimidine biosynthesis have been proven to be essential for Plasmodium proliferation. Here we report on the essentiality of the second enzymatic step of the pyrimidine biosynthesis pathway, catalyzed by aspartate transcarbamoylase (ATC). Crystallization experiments using a double mutant ofPlasmodium falciparum ATC (PfATC) revealed the importance of the mutated residues for enzyme catalysis. Subsequently, this mutant was employed in protein interference assays (PIAs), which resulted in inhibition of parasite proliferation when parasites transfected with the double mutant were cultivated in medium lacking an excess of nutrients, including aspartate. Addition of 5 or 10 mg/L of aspartate to the minimal medium restored the parasites' normal growth rate. In vitro and whole-cell assays in the presence of the compound Torin 2 showed inhibition of specific activity and parasite growth, respectively. In silico analyses revealed the potential binding mode of Torin 2 to PfATC. Furthermore, a transgenic ATC-overexpressing cell line exhibited a 10-fold increased tolerance to Torin 2 compared with control cultures. Taken together, our results confirm the antimalarial activity of Torin 2, suggesting PfATC as a target of this drug and a promising target for the development of novel antimalarials.
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Affiliation(s)
- Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Fernando A. Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Alexander S. S. Dömling
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Matthew R. Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
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19
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Gwathmey KG, Grogan J. Nutritional neuropathies. Muscle Nerve 2019; 62:13-29. [PMID: 31837157 DOI: 10.1002/mus.26783] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/07/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Neuropathies associated with nutritional deficiencies are routinely encountered by the practicing neurologist. Although these neuropathies assume different patterns, most are length-dependent, sensory axonopathies. Cobalamin deficiency neuropathy is the exception, often presenting with a non-length-dependent sensory neuropathy. Patients with cobalamin and copper deficiency neuropathy characteristically have concomitant myelopathy, whereas vitamin E deficiency is uniquely associated with a spinocerebellar syndrome. In contrast to those nutrients for which deficiencies produce neuropathies, pyridoxine toxicity results in a non-length-dependent sensory neuronopathy. Deficiencies occur in the context of malnutrition, malabsorption, increased nutrient loss (such as with dialysis), autoimmune conditions such as pernicious anemia, and with certain drugs that inhibit nutrient absorption. When promptly identified, therapeutic nutrient supplementation may result in stabilization or improvement of these neuropathies.
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Affiliation(s)
| | - James Grogan
- University of Virginia, Charlottesville, Virginia
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20
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Weinberg J, Field JT, Ilgūnas M, Bukauskaitė D, Iezhova T, Valkiūnas G, Sehgal RNM. De novo transcriptome assembly and preliminary analyses of two avian malaria parasites, Plasmodium delichoni and Plasmodium homocircumflexum. Genomics 2019; 111:1815-1823. [PMID: 30553810 PMCID: PMC6565518 DOI: 10.1016/j.ygeno.2018.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/25/2018] [Accepted: 12/06/2018] [Indexed: 11/15/2022]
Abstract
Parasites of the genus Plasmodium infect a wide array of hosts, causing malaria in all major groups of terrestrial vertebrates including primates, reptiles, and birds. Molecular mechanisms explaining why some Plasmodium species are virulent, while other closely related malaria pathogens are relatively benign in the same hosts, remain unclear. Here, we present the RNA sequencing and subsequent transcriptome assembly of two avian Plasmodium parasites which can eventually be used to better understand the genetic mechanisms underlying Plasmodium species pathogenicity in an avian host. Plasmodium homocircumflexum, a cryptic, pathogenic species that often causes mortality and Plasmodium delichoni, a newly described, relatively benign malaria parasite that does not kill its hosts, were used to experimentally infect two Eurasian siskins (Carduelis spinus). RNA extractions were performed and RNA sequencing was completed using high throughput Illumina sequencing. Using established bioinformatics pipelines, the sequencing data from both species were used to generate transcriptomes using published Plasmodium species genomes as a scaffold. The finalized transcriptome of P. homocircumflexum contained 21,612 total contigs while that of P. delichoni contained 12,048 contigs. We were able to identify many genes implicated in erythrocyte invasion actively expressed in both P. homocircumflexum and P. delichoni, including the well described vaccine candidates Apical Membrane Antigen-1 (AMA-1) and Merozoite Surface Protein 1 (MSP1). This work acts as a stepping stone to increase available data on avian Plasmodium parasites, thus enabling future research into the evolution of pathogenicity in malaria.
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Affiliation(s)
- Joshua Weinberg
- Dept. of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA.
| | - Jasper Toscani Field
- Dept. of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
| | - Mikas Ilgūnas
- Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania
| | | | - Tatjana Iezhova
- Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania
| | | | - Ravinder N M Sehgal
- Dept. of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
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21
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Agoni C, Salifu EY, Munsamy G, Olotu FA, Soliman M. CF3‐Pyridinyl Substitution on Antimalarial Therapeutics: Probing Differential Ligand Binding and Dynamical Inhibitory Effects of a Novel Triazolopyrimidine‐Based Inhibitor onPlasmodium falciparumDihydroorotate Dehydrogenase. Chem Biodivers 2019; 16:e1900365. [DOI: 10.1002/cbdv.201900365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Clement Agoni
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Elliasu Y. Salifu
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Geraldene Munsamy
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Fisayo A. Olotu
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Mahmoud Soliman
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
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22
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Valente M, Vidal AE, González-Pacanowska D. Targeting Kinetoplastid and Apicomplexan Thymidylate Biosynthesis as an Antiprotozoal Strategy. Curr Med Chem 2019; 26:4262-4279. [PMID: 30259810 DOI: 10.2174/0929867325666180926154329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/23/2018] [Accepted: 09/14/2018] [Indexed: 02/04/2023]
Abstract
Kinetoplastid and apicomplexan parasites comprise a group of protozoans responsible for human diseases, with a serious impact on human health and the socioeconomic growth of developing countries. Chemotherapy is the main option to control these pathogenic organisms and nucleotide metabolism is considered a promising area for the provision of antimicrobial therapeutic targets. Impairment of thymidylate (dTMP) biosynthesis severely diminishes the viability of parasitic protozoa and the absence of enzymatic activities specifically involved in the formation of dTMP (e.g. dUTPase, thymidylate synthase, dihydrofolate reductase or thymidine kinase) results in decreased deoxythymidine triphosphate (dTTP) levels and the so-called thymineless death. In this process, the ratio of deoxyuridine triphosphate (dUTP) versus dTTP in the cellular nucleotide pool has a crucial role. A high dUTP/dTTP ratio leads to uracil misincorporation into DNA, the activation of DNA repair pathways, DNA fragmentation and eventually cell death. The essential character of dTMP synthesis has stimulated interest in the identification and development of drugs that specifically block the biochemical steps involved in thymine nucleotide formation. Here, we review the available literature in relation to drug discovery studies targeting thymidylate biosynthesis in kinetoplastid (genera Trypanosoma and Leishmania) and apicomplexan (Plasmodium spp and Toxoplasma gondii) protozoans. The most relevant findings concerning novel inhibitory molecules with antiparasitic activity against these human pathogens are presented herein.
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Affiliation(s)
- María Valente
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
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23
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Kennedy K, Crisafulli EM, Ralph SA. Delayed Death by Plastid Inhibition in Apicomplexan Parasites. Trends Parasitol 2019; 35:747-759. [PMID: 31427248 DOI: 10.1016/j.pt.2019.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
The discovery of a plastid in apicomplexan parasites was hoped to be a watershed moment in the treatment of parasitic diseases as it revealed drug targets that are implicitly divergent from host molecular processes. Indeed, this organelle, known as the apicoplast, has since been a productive therapeutic target for pharmaceutical interventions against infections by Plasmodium, Toxoplasma, Babesia, and Theileria. However, some inhibitors of the apicoplast are restricted in their treatment utility because of their slow-kill kinetics, and this characteristic is called the delayed death effect. Here we review the recent genetic and pharmacological experiments that interrogate the causes of delayed death and explore the foundation of this phenomenon in Plasmodium and Toxoplasma parasites.
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Affiliation(s)
- Kit Kennedy
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Emily M Crisafulli
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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24
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Cheviet T, Lefebvre-Tournier I, Wein S, Peyrottes S. Plasmodium Purine Metabolism and Its Inhibition by Nucleoside and Nucleotide Analogues. J Med Chem 2019; 62:8365-8391. [PMID: 30964283 DOI: 10.1021/acs.jmedchem.9b00182] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria still affects around 200 million people and is responsible for more than 400,000 deaths per year, mostly children in subequatorial areas. This disease is caused by parasites of the Plasmodium genus. Only a few WHO-recommended treatments are available to prevent or cure plasmodial infections, but genetic mutations in the causal parasites have led to onset of resistance against all commercial antimalarial drugs. New drugs and targets are being investigated to cope with this emerging problem, including enzymes belonging to the main metabolic pathways, while nucleoside and nucleotide analogues are also a promising class of potential drugs. This review highlights the main metabolic pathways targeted for the development of potential antiplasmodial therapies based on nucleos(t)ide analogues, as well as the different series of purine-containing nucleoside and nucleotide derivatives designed to inhibit Plasmodium falciparum purine metabolism.
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Affiliation(s)
- Thomas Cheviet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
| | - Isabelle Lefebvre-Tournier
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
| | - Sharon Wein
- Dynamique des Interactions Membranaires Normales et Pathologiques (DIMNP), UMR 5235 UM-CNRS , Université Montpellier , Place E. Bataillon , 34095 Montpellier , France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
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25
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Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P. Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine. Arch Biochem Biophys 2019; 667:6-13. [PMID: 31002765 DOI: 10.1016/j.abb.2019.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/14/2019] [Accepted: 04/11/2019] [Indexed: 10/27/2022]
Abstract
Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Here we report the crystal structure of a surface engineered PfADA at a resolution of 2.48 Å, together with results on kinetic studies of PfADA wild-type and active site variants. The structure reveals a novel inosine binding pocket linked to a distinctive PfADA substructure (residues 172-179) derived from a non-conserved gating helix loop (172-188) in Plasmodium spp. and other ADA enzymes. Variants of PfADA and human (h) ADA active site amino acids were generated in order to study their role in catalysis, including PfADA- Phe136, -Thr174, -Asp176, and -Leu179, and hADA-Met155, equivalent to PfADA-Asp176. PfADA-Leu179His showed no effect on kinetic parameters. However, kinetic results of PfADA-Asp176Met/Ala mutants and hADA-Met155Asp/Ala showed that the mutation reduced adenosine and 5'-methylthioadenosine substrate affinity in PfADA and kcat in hADA, thereby reducing catalytic efficiency of the enzyme. Phe136Leu mutant showed increased Km (>10-fold) for both substrates whereas Thr174Ile/Ala only affected 5'-methylthioadenosine binding affinity. Together, the structure with the novel inosine binding pocket and the kinetic data provide insights for rational design of inhibitors against PfADA.
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Affiliation(s)
- Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Sakunrat Ubonprasert
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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27
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Identification of a peptide derived from a Bothrops moojeni metalloprotease with in vitro inhibitory action on the Plasmodium falciparum purine nucleoside phosphorylase enzyme (PfPNP). Biochimie 2019; 162:97-106. [PMID: 30978375 DOI: 10.1016/j.biochi.2019.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2019] [Indexed: 11/22/2022]
Abstract
There is a growing need for research on new antimalarial agents against Plasmodium falciparum infection, especially in regards to planning molecular architecture for specific molecular targets of the parasite. Thus, a metalloprotease from Bothrops moojeni, known as BmooMPα-I, was explored in this study, through in silico assays, aiming at the development of a peptide generated from this molecule with potential inhibitory action on PfPNP, an enzyme necessary for the survival of the parasite. In order to isolate BmooMPα-I, cation exchange and reverse phase chromatographies were performed, followed by in vitro assays of antiparasitic activity against the W2 strain of P. falciparum. The interactions between BmooMPα-I and PfPNP were evaluated via docking, and the resulting peptide, described as Pep1 BM, was selected according to the BmooMPα-I region demonstrating the best interaction score with the target of interest. The values for the specific activities of the PfPNP reaction were measured using the inorganic phosphate substrate and MESG. The fraction corresponding to BmooMPα-I was identified as fraction 4 in the cation exchange chromatography step, due to proteolytic activity on casein and the presence of a major band at ≅ 23 kDa. BmooMPα-I was able to inhibit in vitro growth of W2 P. falciparum, with an IC50 value of 16.14 μg/mL. Virtual screening with Pep1 BM demonstrated two PfPNP target binding regions, with ΔG values at the interaction interface of -10.75 kcal/mol and -11.74 kcal/mol. A significant reduction in the enzymatic activity of PfPNP was observed in the presence of Pep 1 BM when compared to the assay in the absence of this possible inhibitor. BmooMPα-I showed activity in vitro against W2 P. falciparum. By means of in silico techniques, the Pep 1 BM was identified as having potential binding affinity to the catalytic site of PfPNP and of inhibiting its catalytic activity in vitro.
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Batista FA, Bosch SS, Butzloff S, Lunev S, Meissner KA, Linzke M, Romero AR, Wang C, Müller IB, Dömling ASS, Groves MR, Wrenger C. Oligomeric protein interference validates druggability of aspartate interconversion in Plasmodium falciparum. Microbiologyopen 2019; 8:e00779. [PMID: 30821109 PMCID: PMC6612543 DOI: 10.1002/mbo3.779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
The appearance of multi-drug resistant strains of malaria poses a major challenge to human health and validated drug targets are urgently required. To define a protein's function in vivo and thereby validate it as a drug target, highly specific tools are required that modify protein function with minimal cross-reactivity. While modern genetic approaches often offer the desired level of target specificity, applying these techniques is frequently challenging-particularly in the most dangerous malaria parasite, Plasmodium falciparum. Our hypothesis is that such challenges can be addressed by incorporating mutant proteins within oligomeric protein complexes of the target organism in vivo. In this manuscript, we provide data to support our hypothesis by demonstrating that recombinant expression of mutant proteins within P. falciparum leverages the native protein oligomeric state to influence protein function in vivo, thereby providing a rapid validation of potential drug targets. Our data show that interference with aspartate metabolism in vivo leads to a significant hindrance in parasite survival and strongly suggest that enzymes integral to aspartate metabolism are promising targets for the discovery of novel antimalarials.
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Affiliation(s)
- Fernando A. Batista
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Sabine Butzloff
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Sergey Lunev
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Kamila A. Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Atilio R. Romero
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Chao Wang
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Ingrid B. Müller
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Alexander S. S. Dömling
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Matthew R. Groves
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
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Rogée S, Larrous F, Jochmans D, Ben-Khalifa Y, Neyts J, Bourhy H. Pyrimethamine inhibits rabies virus replication in vitro. Antiviral Res 2019; 161:1-9. [DOI: 10.1016/j.antiviral.2018.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022]
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30
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Moon EK, Choi HS, Park SM, Kong HH, Quan FS. Comparison of Proteins Secreted into Extracellular Space of Pathogenic and Non-pathogenic Acanthamoeba castellanii. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:553-558. [PMID: 30630275 PMCID: PMC6327195 DOI: 10.3347/kjp.2018.56.6.553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/31/2018] [Indexed: 11/23/2022]
Abstract
Pathogenic Acanthamoeba spp. cause granulomatous amoebic encephalitis and keratitis. Acanthamoeba keratitis (AK) is a rare but serious ocular infection that can result in permanent visual impairment or blindness. However, pathogenic factors of AK remain unclear and treatment for AK is arduous. Expression levels of proteins secreted into extracellular space were compared between A. castellanii pathogenic (ACP) and non-pathogenic strains. Two-dimensional polyacrylamide gel electrophoresis revealed 123 differentially expressed proteins, including 34 increased proteins, 7 qualitative increased proteins, 65 decreased proteins, and 17 qualitative decreased proteins in ACP strain. Twenty protein spots with greater than 5-fold increase in ACP strain were analyzed by liquid chromatography triple quadrupole mass spectrometry. These proteins showed similarity each to inosine-uridine preferring nucleoside hydrolase, carboxylesterase, oxygen-dependent choline dehydrogenase, periplasmic-binding protein proteinases and hypothetical proteins. These proteins expressed higher in ACP may provide some information to understand pathogenicity of Acanthamoeba.
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Affiliation(s)
- Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Hyun-Seo Choi
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - So-Min Park
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan 49201, Korea
| | - Fu-Shi Quan
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul 02447, Korea.,Biomedical Science Institute, Kyung Hee University, Seoul 02447, Korea
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31
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Nurkanto A, Jeelani G, Yamamoto T, Hishiki T, Naito Y, Suematsu M, Hashimoto T, Nozaki T. Biochemical, Metabolomic, and Genetic Analyses of Dephospho Coenzyme A Kinase Involved in Coenzyme A Biosynthesis in the Human Enteric Parasite Entamoeba histolytica. Front Microbiol 2018; 9:2902. [PMID: 30555442 PMCID: PMC6284149 DOI: 10.3389/fmicb.2018.02902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/13/2018] [Indexed: 11/14/2022] Open
Abstract
Coenzyme A (CoA) is an essential cofactor for numerous cellular reactions in all living organisms. In the protozoan parasite Entamoeba histolytica, CoA is synthesized in a pathway consisting of four enzymes with dephospho-CoA kinase (DPCK) catalyzing the last step. However, the metabolic and physiological roles of E. histolytica DPCK remain elusive. In this study, we took biochemical, reverse genetic, and metabolomic approaches to elucidate role of DPCK in E. histolytica. The E. histolytica genome encodes two DPCK isotypes (EhDPCK1 and EhDPCK2). Epigenetic gene silencing of Ehdpck1 and Ehdpck2 caused significant reduction of DPCK activity, intracellular CoA concentrations, and also led to growth retardation in vitro, suggesting importance of DPCK for CoA synthesis and proliferation. Furthermore, metabolomic analysis showed that suppression of Ehdpck gene expression also caused decrease in the level of acetyl-CoA, and metabolites involved in amino acid, glycogen, hexosamine, nucleic acid metabolisms, chitin, and polyamine biosynthesis. The kinetic properties of E. histolytica and human DPCK showed remarkable differences, e.g., the Km values of E. histolytica and human DPCK were 58-114 and 5.2 μM toward dephospho-CoA and 15-20 and 192 μM for ATP, respectively. Phylogenetic analysis also supported the uniqueness of the amebic enzyme compared to the human counterpart. These biochemical, evolutionary features, and physiological importance of EhDPCKs indicate that EhDPCK represents the rational target for the development of anti-amebic agents.
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Affiliation(s)
- Arif Nurkanto
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Research Center for Biology, Indonesia Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Ghulam Jeelani
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takako Hishiki
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
- Clinical and Translational Research Center, School of Medicine, Keio University, Tokyo, Japan
| | - Yoshiko Naito
- Clinical and Translational Research Center, School of Medicine, Keio University, Tokyo, Japan
| | - Makoto Suematsu
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Abstract
Toxoplasma gondii is an obligate intracellular parasite belonging to the phylum Apicomplexa that infects all warm-blooded animals, including humans. T. gondii can replicate in every nucleated host cell by orchestrating metabolic interactions to derive crucial nutrients. In this review, we summarize the current status of known metabolic interactions of T. gondii with its host cell and discuss open questions and promising experimental approaches that will allow further dissection of the host-parasite interface and discovery of ways to efficiently target both tachyzoite and bradyzoite forms of T. gondii, which are associated with acute and chronic infection, respectively.
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Affiliation(s)
- Martin Blume
- NG2 - Metabolism of Microbial Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Frank Seeber
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
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33
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Radke JB, Burrows JN, Goldberg DE, Sibley LD. Evaluation of Current and Emerging Antimalarial Medicines for Inhibition of Toxoplasma gondii Growth in Vitro. ACS Infect Dis 2018; 4:1264-1274. [PMID: 29998728 PMCID: PMC6093624 DOI: 10.1021/acsinfecdis.8b00113] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Toxoplasma gondii is a common zoonotic infection of humans, and estimates indicate that 1-2 billion people are chronically infected. Although largely asymptomatic, chronic infection poses risk of serious disease due to reactivation should immunity decline. Current therapies for toxoplasmosis only control acute infection caused by actively proliferating tachyzoites but do not eradicate the chronic tissue cyst stages. As well, there are considerable adverse side effects of the most commonly used therapy of combined sulfadiazine and pyrimethamine. Targeting the folate pathway is also an effective treatment for malaria, caused by the related parasites Plasmodium spp., suggesting common agents might be used to treat both infections. Here, we evaluated currently approved and newly emerging medicines for malaria to determine if such compounds might also prove useful for treating toxoplasmosis. Surprisingly, the majority of antimalarial compounds being used currently or in development for treatment of malaria were only modestly effective at inhibiting in vitro growth of T. gondii tachyzoites. These findings suggest that many essential processes in P. falciparum that are targeted by antimalarial compounds are either divergent or nonessential in T. gondii, thus limiting options for repurposing of current antimalarial medicines for toxoplasmosis.
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Affiliation(s)
- Joshua B. Radke
- Department of Molecular Microbiology, Washington University Sch. Med., 600 S. Euclid Ave., St Louis, MO 63110
| | - Jeremy N. Burrows
- Medicines for Malaria Venture, ICC, Route de Pré3Bois 20, 1215 Geneva, Switzerland
| | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University Sch. Med., 660 S. Euclid Ave., St Louis, MO 63110
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University Sch. Med., 600 S. Euclid Ave., St Louis, MO 63110
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34
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Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun 2018; 9:2656. [PMID: 29985403 PMCID: PMC6037754 DOI: 10.1038/s41467-018-04966-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/31/2018] [Indexed: 01/12/2023] Open
Abstract
Genome-wide analysis of transcription in the malaria parasite Plasmodium falciparum has revealed robust variation in steady-state mRNA abundance throughout the 48-h intraerythrocytic developmental cycle (IDC), suggesting that this process is highly dynamic and tightly regulated. Here, we utilize rapid 4-thiouracil (4-TU) incorporation via pyrimidine salvage to specifically label, capture, and quantify newly-synthesized RNA transcripts at every hour throughout the IDC. This high-resolution global analysis of the transcriptome captures the timing and rate of transcription for each newly synthesized mRNA in vivo, revealing active transcription throughout all IDC stages. Using a statistical model to predict the mRNA dynamics contributing to the total mRNA abundance at each timepoint, we find varying degrees of transcription and stabilization for each mRNA corresponding to developmental transitions. Finally, our results provide new insight into co-regulation of mRNAs throughout the IDC through regulatory DNA sequence motifs, thereby expanding our understanding of P. falciparum mRNA dynamics. Transcriptomic analysis often doesn’t differentiate between newly synthesized and stabilized mRNAs. Using rapid 4-thiouracil incorporation, Painter et al. here define genome-wide active transcription throughout Plasmodium blood-stage developmental stages and identify associated regulatory DNA sequence motifs.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Neo Christopher Chung
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08544, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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35
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Pavithra GC, Ramagopal UA. Crystal structures of APRT from Francisella tularensis - an N-H···N hydrogen bond imparts adenine specificity in adenine phosporibosyltransferases. FEBS J 2018; 285:2306-2318. [PMID: 29694705 DOI: 10.1111/febs.14481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/24/2018] [Accepted: 04/18/2018] [Indexed: 11/27/2022]
Abstract
Francisella tularensisis, the causative agent of tularemia has been classified as a category A bioterrorism agent. Here, we present the crystal structure of apo and adenine bound form of the adenine phosphoribosyltransferase (APRT) from Francisella tularensis. APRT is an enzyme involved in the salvage of adenine (a 6-aminopurine), converting it to AMP. The purine salvage pathway relies on two essential and distinct enzymes to convert 6-aminopurine and 6-oxopurines into corresponding nucleotides. The mechanism by which these enzymes differentiate different purines is not clearly understood. Analysis of the structures of apo and adenine-bound APRT from F. tularensis, together with all other available structures of APRTs, suggests that (a) the base-binding loop is stabilized by a cluster of aromatic and conformation-restricting proline residues, and (b) an N-H···N hydrogen bond between the base-binding loop and the N1 atom of adenine is the key interaction that differentiates adenine from 6-oxopurines. These observations were corroborated by bioinformatics analysis of ~ 4000 sequences of APRTs (with 80% identity cutoff), which confirmed that the residues conferring rigidity to the base-binding loop are highly conserved. Furthermore, an F23A mutation on the base-binding loop severely affects the efficiency of the enzyme. We extended our analysis to the structure and sequences of APRTs from the Trypanosomatidae family with a destabilizing insertion on the base-binding loop and propose the mechanism by which these evolutionarily divergent enzymes achieve base specificity. Our results suggest that the base-binding loop not only confers appropriate affinity but also provides defined specificity for adenine. ENZYME EC 2.4.2.7 DATABASE: Structural data are available in Protein Data Bank (PDB) under the accession numbers 5YW2 and 5YW5.
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Affiliation(s)
- Gowribidanur C Pavithra
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, India.,Manipal Academy of Higher Education, Karnataka, India
| | - Udupi A Ramagopal
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, India
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36
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Narvaez-Ortiz HY, Lopez AJ, Gupta N, Zimmermann BH. A CTP Synthase Undergoing Stage-Specific Spatial Expression Is Essential for the Survival of the Intracellular Parasite Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:83. [PMID: 29623259 PMCID: PMC5874296 DOI: 10.3389/fcimb.2018.00083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/28/2018] [Indexed: 01/17/2023] Open
Abstract
Cytidine triphosphate synthase catalyzes the synthesis of cytidine 5′-triphosphate (CTP) from uridine 5′-triphosphate (UTP), the final step in the production of cytidine nucleotides. CTP synthases also form filamentous structures of different morphologies known as cytoophidia, whose functions in most organisms are unknown. Here, we identified and characterized a novel CTP synthase (TgCTPS) from Toxoplasma gondii. We show that TgCTPS is capable of substituting for its counterparts in the otherwise lethal double mutant (ura7Δ ura8Δ) of Saccharomyces cerevisiae. Equally, recombinant TgCTPS purified from Escherichia coli encodes for a functional protein in enzyme assays. The epitope-tagged TgCTPS under the control of its endogenous promoter displays a punctate cytosolic distribution, which undergoes spatial reorganization to form foci or filament-like structures when the parasite switches from a nutrient-replete (intracellular) to a nutrient-scarce (extracellular) condition. An analogous phenotype is observed upon nutrient stress or after treatment with a glutamine analog, 6-diazo-5-oxo-L-norleucine (DON). The exposure of parasites to DON disrupts the lytic cycle, and the TgCTPS is refractory to a genetic deletion, suggesting an essential requirement of this enzyme for T. gondii. Not least, this study, together with previous studies, supports that CTP synthase can serve as a potent drug target, because the parasite, unlike human host cells, cannot compensate for the lack of CTP synthase activity.
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Affiliation(s)
| | - Andrea J Lopez
- Departamento de Ciencias Biologicas, Universidad de los Andes, Bogota, Colombia
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
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37
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Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase. Biochem Biophys Res Commun 2018; 497:835-842. [PMID: 29476738 DOI: 10.1016/j.bbrc.2018.02.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 11/24/2022]
Abstract
Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis.
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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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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Zhou DH, Wang ZX, Zhou CX, He S, Elsheikha HM, Zhu XQ. Comparative proteomic analysis of virulent and avirulent strains of Toxoplasma gondii reveals strain-specific patterns. Oncotarget 2017; 8:80481-80491. [PMID: 29113319 PMCID: PMC5655214 DOI: 10.18632/oncotarget.19077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/18/2017] [Indexed: 12/31/2022] Open
Abstract
Research exploring the proteome of Toxoplasma gondii oocysts has gained momentum over the past few years. However, little is known about the oocyst's protein repertoires that contribute to differential virulence among T. gondii strains. Here, we used isobaric tag for relative and absolute quantitation-based proteomic analysis of oocysts of two T. gondii strains exhibiting the virulent PYS (ToxoDB#9) phenotype versus the less virulent PRU (Type II, ToxoDB#1) phenotype. Our aim was to determine protein expression patterns that contribute to the virulence of a particular phenotype. A total of 2,551 proteins were identified, of which 374 were differentially expressed proteins (DEPs) (|log2 fold change| ≥ 0.58 and P < 0.05). DEPs included 192 increased and 182 decreased proteins. Gene Ontology and KEGG pathway analyses revealed a large number of DEPs enriched in various metabolic processes. Protein interaction network analysis using STRING identified inosine monophosphate dehydrogenase (IMPDH), Bifunctional GMP synthase/glutamine amidotransferase protein, Glucose-6-phosphate 1-dehydrogenase, and Citrate synthase as the top four hubs. Of the 22 virulence proteins commonly expressed in the oocysts of the two strains, 13 and 2 proteins were increased in PYS strain and PRU strain, respectively. Also, 10 and 3 of the 22 identified oocyst wall proteins showed higher expression in oocysts of PRU strain and PYS strain, respectively. These findings revealed new proteomic differences in the oocysts of T. gondii strains of different genotypic backgrounds.
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Affiliation(s)
- Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
| | - Ze-Xiang Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
| | - Chun-Xue Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
- Department of Parasitology, Shandong University School of Basic Medicine, Jinan, Shandong Province, 250012, PR China
| | - Shuai He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, 230036, PR China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
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Abstract
The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.
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Affiliation(s)
| | - John Parkinson
- a Program in Molecular Structure and Function , Hospital for Sick Children , Toronto , Ontario , Canada
- b Departments of Biochemistry, Molecular Genetics and Computer Science , University of Toronto , Toronto , Ontario , Canada
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Painter HJ, Carrasquilla M, Llinás M. Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum. Genome Res 2017; 27:1074-1086. [PMID: 28416533 PMCID: PMC5453321 DOI: 10.1101/gr.217356.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
To capture the transcriptional dynamics within proliferating cells, methods to differentiate nascent transcription from preexisting mRNAs are desired. One approach is to label newly synthesized mRNA transcripts in vivo through the incorporation of modified pyrimidines. However, the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine deaminase/uracil phosphoribosyltransferase (FCU). We show that expression of FCU allows for the direct incorporation of thiol-modified pyrimidines into nascent mRNAs. Using developmental stage-specific promoters to express FCU-GFP enables the biosynthetic capture and in-depth analysis of mRNA dynamics from subpopulations of cells undergoing differentiation. We demonstrate the utility of this method by examining the transcriptional dynamics of the sexual gametocyte stage transition, a process that is essential to malaria transmission between hosts. Using the pfs16 gametocyte-specific promoter to express FCU-GFP in 3D7 parasites, we found that sexual stage commitment is governed by transcriptional reprogramming and stabilization of a subset of essential gametocyte transcripts. We also measured mRNA dynamics in F12 gametocyte-deficient parasites and demonstrate that the transcriptional program required for sexual commitment and maturation is initiated but likely aborted due to the absence of the PfAP2-G transcriptional regulator and a lack of gametocyte-specific mRNA stabilization. Biosynthetic labeling of Plasmodium mRNAs is incredibly versatile, can be used to measure transcriptional dynamics at any stage of parasite development, and will allow for future applications to comprehensively measure RNA-protein interactions in the malaria parasite.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuela Carrasquilla
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Singh A, Maqbool M, Mobashir M, Hoda N. Dihydroorotate dehydrogenase: A drug target for the development of antimalarials. Eur J Med Chem 2017; 125:640-651. [DOI: 10.1016/j.ejmech.2016.09.085] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/07/2016] [Accepted: 09/25/2016] [Indexed: 02/03/2023]
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Sinai AP, Watts EA, Dhara A, Murphy RD, Gentry MS, Patwardhan A. Reexamining Chronic Toxoplasma gondii Infection: Surprising Activity for a "Dormant" Parasite. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016; 3:175-185. [PMID: 28191447 PMCID: PMC5295825 DOI: 10.1007/s40588-016-0045-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW Despite over a third of the world's population being chronically infected with Toxoplasma gondii, little is known about this largely asymptomatic phase of infection. This stage is mediated in vivo by bradyzoites within tissue cysts. The absence of overt symptoms has been attributed to the dormancy of bradyzoites. In this review, we reexamine the conventional view of chronic toxoplasmosis in light of emerging evidence challenging both the nature of dormancy and the consequences of infection in the CNS. RECENT FINDINGS New and emerging data reveal a previously unrecognized level of physiological and replicative capacity of bradyzoites within tissue cysts. These findings have emerged in the context of a reexamination of the chronic infection in the brain that correlates with changes in neuronal architecture, neurochemistry, and behavior that suggest that the chronic infection is not without consequence. SUMMARY The emerging data driven by the development of new approaches to study the progression of chronic toxoplasma infection reveals significant physiological and replicative capacity for what has been viewed as a dormant state. The emergence of bradyzoite and tissue cyst biology from what was viewed as a physiological "black box" offers exciting new areas for investigation with direct implications on the approaches to drug development targeting this drug-refractory state. In addition, new insights from studies on the neurobiology on chronic infection reveal a complex and dynamic interplay between the parasite, brain microenvironment, and the immune response that results in the detente that promotes the life-long persistence of the parasite in the host.
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Affiliation(s)
- Anthony P Sinai
- Department of Microbiology Immunology and Molecular Genetics, Lexington, KY, USA
| | - Elizabeth A Watts
- Department of Microbiology Immunology and Molecular Genetics, Lexington, KY, USA
| | - Animesh Dhara
- Department of Microbiology Immunology and Molecular Genetics, Lexington, KY, USA
| | - Robert D Murphy
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Abhijit Patwardhan
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, Lexington, KY 40506, USA
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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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Review of Experimental Compounds Demonstrating Anti-Toxoplasma Activity. Antimicrob Agents Chemother 2016; 60:7017-7034. [PMID: 27600037 DOI: 10.1128/aac.01176-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Toxoplasma gondii is a ubiquitous apicomplexan parasite capable of infecting humans and other animals. Current treatment options for T. gondii infection are limited and most have drawbacks, including high toxicity and low tolerability. Additionally, no FDA-approved treatments are available for pregnant women, a high-risk population due to transplacental infection. Therefore, the development of novel treatment options is needed. To aid this effort, this review highlights experimental compounds that, at a minimum, demonstrate inhibition of in vitro growth of T. gondii When available, host cell toxicity and in vivo data are also discussed. The purpose of this review is to facilitate additional development of anti-Toxoplasma compounds and potentially to extend our knowledge of the parasite.
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Pyrimidine Pathway-Dependent and -Independent Functions of the Toxoplasma gondii Mitochondrial Dihydroorotate Dehydrogenase. Infect Immun 2016; 84:2974-81. [PMID: 27481247 DOI: 10.1128/iai.00187-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) mediates the fourth step of de novo pyrimidine biosynthesis and is a proven drug target for inducing immunosuppression in therapy of human disease as well as a rapidly emerging drug target for treatment of malaria. In Toxoplasma gondii, disruption of the first, fifth, or sixth step of de novo pyrimidine biosynthesis induced uracil auxotrophy. However, previous attempts to generate uracil auxotrophy by genetically deleting the mitochondrion-associated DHODH of T. gondii (TgDHODH) failed. To further address the essentiality of TgDHODH, mutant gene alleles deficient in TgDHODH activity were designed to ablate the enzyme activity. Replacement of the endogenous DHODH gene with catalytically deficient DHODH gene alleles induced uracil auxotrophy. Catalytically deficient TgDHODH localized to the mitochondria, and parasites retained mitochondrial membrane potential. These results show that TgDHODH is essential for the synthesis of pyrimidines and suggest that TgDHODH is required for a second essential function independent of its role in pyrimidine biosynthesis.
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Krungkrai SR, Krungkrai J. Insights into the pyrimidine biosynthetic pathway of human malaria parasite Plasmodium falciparum as chemotherapeutic target. ASIAN PAC J TROP MED 2016; 9:525-34. [PMID: 27262062 DOI: 10.1016/j.apjtm.2016.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 04/08/2016] [Indexed: 11/25/2022] Open
Abstract
Malaria is a major cause of morbidity and mortality in humans. Artemisinins remain as the first-line treatment for Plasmodium falciparum (P. falciparum) malaria although drug resistance has already emerged and spread in Southeast Asia. Thus, to fight this disease, there is an urgent need to develop new antimalarial drugs for malaria chemotherapy. Unlike human host cells, P. falciparum cannot salvage preformed pyrimidine bases or nucleosides from the extracellular environment and relies solely on nucleotides synthesized through the de novo biosynthetic pathway. This review presents significant progress on understanding the de novo pyrimidine pathway and the functional enzymes in the human parasite P. falciparum. Current knowledge in genomics and metabolomics are described, particularly focusing on the parasite purine and pyrimidine nucleotide metabolism. These include gene annotation, characterization and molecular mechanism of the enzymes that are different from the human host pathway. Recent elucidation of the three-dimensional crystal structures and the catalytic reactions of three enzymes: dihydroorotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine 5'-monophosphate decarboxylase, as well as their inhibitors are reviewed in the context of their therapeutic potential against malaria.
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Affiliation(s)
- Sudaratana R Krungkrai
- Unit of Biochemistry, Department of Medical Science, Faculty of Science, Rangsit University, Pathumthani 12000, Thailand
| | - Jerapan Krungkrai
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.
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50
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Ghosh AC, Shimell M, Leof ER, Haley MJ, O'Connor MB. UPRT, a suicide-gene therapy candidate in higher eukaryotes, is required for Drosophila larval growth and normal adult lifespan. Sci Rep 2015; 5:13176. [PMID: 26271729 PMCID: PMC4536494 DOI: 10.1038/srep13176] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 07/06/2015] [Indexed: 11/09/2022] Open
Abstract
Uracil phosphoribosyltransferase (UPRT) is a pyrimidine salvage pathway enzyme that catalyzes the conversion of uracil to uridine monophosphate (UMP). The enzyme is highly conserved from prokaryotes to humans and yet phylogenetic evidence suggests that UPRT homologues from higher-eukaryotes, including Drosophila, are incapable of binding uracil. Purified human UPRT also do not show any enzymatic activity in vitro, making microbial UPRT an attractive candidate for anti-microbial drug development, suicide-gene therapy, and cell-specific mRNA labeling techniques. Nevertheless, the enzymatic site of UPRT remains conserved across the animal kingdom indicating an in vivo role for the enzyme. We find that the Drosophila UPRT homologue, krishah (kri), codes for an enzyme that is required for larval growth, pre-pupal/pupal viability and long-term adult lifespan. Our findings suggest that UPRT from all higher eukaryotes is likely enzymatically active in vivo and challenges the previous notion that the enzyme is non-essential in higher eukaryotes and cautions against targeting the enzyme for therapeutic purposes. Our findings also suggest that expression of the endogenous UPRT gene will likely cause background incorporation when using microbial UPRT as a cell-specific mRNA labeling reagent in higher eukaryotes.
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Affiliation(s)
- Arpan C Ghosh
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - MaryJane Shimell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emma R Leof
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Macy J Haley
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael B O'Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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