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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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2
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Mee-udorn P, Nutho B, Chootrakool R, Maenpuen S, Leartsakulpanich U, Chitnumsub P, Rungrotmongkol T. Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferases. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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3
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Cobbold SA, V Tutor M, Frasse P, McHugh E, Karnthaler M, Creek DJ, Odom John A, Tilley L, Ralph SA, McConville MJ. Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics. Mol Syst Biol 2021; 17:e10023. [PMID: 33821563 PMCID: PMC8022201 DOI: 10.15252/msb.202010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, proliferates rapidly in human erythrocytes by actively scavenging multiple carbon sources and essential nutrients from its host cell. However, a global overview of the metabolic capacity of intraerythrocytic stages is missing. Using multiplex 13 C-labelling coupled with untargeted mass spectrometry and unsupervised isotopologue grouping, we have generated a draft metabolome of P. falciparum and its host erythrocyte consisting of 911 and 577 metabolites, respectively, corresponding to 41% of metabolites and over 70% of the metabolic reaction predicted from the parasite genome. An additional 89 metabolites and 92 reactions were identified that were not predicted from genomic reconstructions, with the largest group being associated with metabolite damage-repair systems. Validation of the draft metabolome revealed four previously uncharacterised enzymes which impact isoprenoid biosynthesis, lipid homeostasis and mitochondrial metabolism and are necessary for parasite development and proliferation. This study defines the metabolic fate of multiple carbon sources in P. falciparum, and highlights the activity of metabolite repair pathways in these rapidly growing parasite stages, opening new avenues for drug discovery.
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Affiliation(s)
- Simon A Cobbold
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Philip Frasse
- Department of MedicineWashington University School of MedicineSt. LouisMOUSA
| | - Emma McHugh
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Markus Karnthaler
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Darren J Creek
- Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleVic.Australia
| | - Audrey Odom John
- The Children’s Hospital of PhiladelphiaUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Leann Tilley
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
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4
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Dousti M, Manzano-Román R, Rashidi S, Barzegar G, Ahmadpour NB, Mohammadi A, Hatam G. A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets. Pathog Dis 2021; 79:ftaa071. [PMID: 33202000 DOI: 10.1093/femspd/ftaa071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
There is no effective vaccine against malaria; therefore, chemotherapy is to date the only choice to fight against this infectious disease. However, there is growing evidences of drug-resistance mechanisms in malaria treatments. Therefore, the identification of new drug targets is an urgent need for the clinical management of the disease. Proteomic approaches offer the chance of determining the effects of antimalarial drugs on the proteome of Plasmodium parasites. Accordingly, we reviewed the effects of antimalarial drugs on the Plasmodium falciparum proteome pointing out the relevance of several proteins as possible drug targets in malaria treatment. In addition, some of the P. falciparum stage-specific altered proteins and parasite-host interactions might play important roles in pathogenicity, survival, invasion and metabolic pathways and thus serve as potential sources of drug targets. In this review, we have identified several proteins, including thioredoxin reductase, helicases, peptidyl-prolyl cis-trans isomerase, endoplasmic reticulum-resident calcium-binding protein, choline/ethanolamine phosphotransferase, purine nucleoside phosphorylase, apical membrane antigen 1, glutamate dehydrogenase, hypoxanthine guanine phosphoribosyl transferase, heat shock protein 70x, knob-associated histidine-rich protein and erythrocyte membrane protein 1, as promising antimalarial drugs targets. Overall, proteomic approaches are able to partially facilitate finding possible drug targets. However, the integration of other 'omics' and specific pharmaceutical techniques with proteomics may increase the therapeutic properties of the critical proteins identified in the P. falciparum proteome.
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Affiliation(s)
- Majid Dousti
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Barzegar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Alireza Mohammadi
- Department of Disease Control, Komijan Treatment and Health Network, Arak University of Medical Science, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Bhosle A, Datey A, Chandrasekharan G, Singh D, Chakravortty D, Chandra N. A Strategic Target Rescues Trimethoprim Sensitivity in Escherichia coli. iScience 2020; 23:100986. [PMID: 32240953 PMCID: PMC7115098 DOI: 10.1016/j.isci.2020.100986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/09/2020] [Accepted: 03/10/2020] [Indexed: 01/03/2023] Open
Abstract
Trimethoprim, a preferred treatment for urinary tract infections, is becoming obsolete owing to the rapid dissemination of resistant E. coli. Although direct resistance mechanisms such as overexpression of a mutant FolA and dfr enzymes are well characterized, associated alterations that drive or sustain resistance are unknown. We identify the repertoire of resistance-associated perturbations by constructing and interrogating a transcriptome-integrated functional interactome. From the cross talk between perturbations in stress-response and metabolic pathways, we identify the critical dependence on serine hydroxymethyltransferase (GlyA) as an emergent vulnerability. Through its deletion, we demonstrate that GlyA is necessary to sustain high levels of resistance in both laboratory-evolved resistant E. coli and a multidrug-resistant clinical isolate. Through comparative evolution, we show that the absence of GlyA activity decelerates the acquisition of resistance in E. coli. Put together, our results identify GlyA as a promising target, providing a basis for the rational design of drug combinations. TMP-resistant E. coli show cross talk between stress response and metabolic pathways Dependence on glyA is an emergent vulnerability associated with TMP resistance Knockout of glyA partially rescues sensitivity to TMP in E. coli
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Affiliation(s)
- Amrisha Bhosle
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Akshay Datey
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Giridhar Chandrasekharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Deepshikha Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Dipshikha Chakravortty
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India.
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India; Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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6
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Linzke M, Yan SLR, Tárnok A, Ulrich H, Groves MR, Wrenger C. Live and Let Dye: Visualizing the Cellular Compartments of the Malaria Parasite Plasmodium falciparum. Cytometry A 2019; 97:694-705. [PMID: 31738009 DOI: 10.1002/cyto.a.23927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 10/03/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
Malaria remains one of the deadliest diseases worldwide and it is caused by the protozoan parasite Plasmodium spp. Parasite visualization is an important tool for the correct detection of malarial cases but also to understand its biology. Advances in visualization techniques promote new insights into the complex life cycle and biology of Plasmodium parasites. Live cell imaging by fluorescence microscopy or flow cytometry are the foundation of the visualization technique for malaria research. In this review, we present an overview of possibilities in live cell imaging of the malaria parasite. We discuss some of the state-of-the-art techniques to visualize organelles and processes of the parasite and discuss limitation and advantages of each technique. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo, São Paulo, 05508-000, Brazil
| | - Sun Liu Rei Yan
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo, São Paulo, 05508-000, Brazil
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology, Medical Faculty, University Leipzig, D-04107, Härtelstraße 16-18, Leipzig, Germany
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes 748, São Paulo, São Paulo, 05508-900, Brazil
| | - Matthew R Groves
- Structural Biology Unit, Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, 9713AV, Antonius Deusinglaan 1, AV 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, São Paulo, São Paulo, 05508-000, Brazil
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7
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Ubonprasert S, Jaroensuk J, Pornthanakasem W, Kamonsutthipaijit N, Wongpituk P, Mee-Udorn P, Rungrotmongkol T, Ketchart O, Chitnumsub P, Leartsakulpanich U, Chaiyen P, Maenpuen S. A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release. J Biol Chem 2019; 294:10490-10502. [PMID: 31118236 DOI: 10.1074/jbc.ra119.007454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (Ki of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.
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Affiliation(s)
- Sakunrat Ubonprasert
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Wichai Pornthanakasem
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | | | - Peerapong Wongpituk
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, and
| | - Pitchayathida Mee-Udorn
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and.,Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, and
| | - Onuma Ketchart
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Ubolsree Leartsakulpanich
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
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8
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Nonaka H, Nakanishi Y, Kuno S, Ota T, Mochidome K, Saito Y, Sugihara F, Takakusagi Y, Aoki I, Nagatoishi S, Tsumoto K, Sando S. Design strategy for serine hydroxymethyltransferase probes based on retro-aldol-type reaction. Nat Commun 2019; 10:876. [PMID: 30787298 PMCID: PMC6382819 DOI: 10.1038/s41467-019-08833-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/25/2019] [Indexed: 01/17/2023] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is an enzyme that catalyzes the reaction that converts serine to glycine. It plays an important role in one-carbon metabolism. Recently, SHMT has been shown to be associated with various diseases. Therefore, SHMT has attracted attention as a biomarker and drug target. However, the development of molecular probes responsive to SHMT has not yet been realized. This is because SHMT catalyzes an essential yet simple reaction; thus, the substrates that can be accepted into the active site of SHMT are limited. Here, we focus on the SHMT-catalyzed retro-aldol reaction rather than the canonical serine–glycine conversion and succeed in developing fluorescent and 19F NMR molecular probes. Taking advantage of the facile and direct detection of SHMT, the developed fluorescent probe is used in the high-throughput screening for human SHMT inhibitors, and two hit compounds are obtained. The enzyme serine hydroxymethyltransferase (SHMT) has been implicated in several diseases, however is hard to investigate. Here, the authors used a design strategy based on the retro-aldol-type reaction catalyzed by SHMT to develop SHMT-responsive fluorescence and 19F NMR molecular probes.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yuki Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoshi Kuno
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoki Ota
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kentaro Mochidome
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Yoichi Takakusagi
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa 4-9-1, Inage, Chiba-city, 263-8555, Japan.,Group of Quantum-state Controlled MRI, National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa 4-9-1, Inage, Chiba-city, 263-8555, Japan
| | - Ichio Aoki
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa 4-9-1, Inage, Chiba-city, 263-8555, Japan.,Group of Quantum-state Controlled MRI, National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa 4-9-1, Inage, Chiba-city, 263-8555, Japan
| | - Satoru Nagatoishi
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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9
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Fernandes HS, Ramos MJ, Cerqueira NMFSA. Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02321] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Henrique S. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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10
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Schwertz G, Witschel MC, Rottmann M, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Amornwatcharapong W, Ittarat W, Schäfer A, Aponte RA, Trapp N, Chaiyen P, Diederich F. Potent Inhibitors ofPlasmodialSerine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold. ChemMedChem 2018; 13:931-943. [DOI: 10.1002/cmdc.201800053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/25/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Geoffrey Schwertz
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Matthias Rottmann
- Swiss Tropical and Public Health Institute (SwissTPH); Socinstrasse 57 4051 Basel Switzerland
- Universität Basel; Petersplatz 1 4003 Basel Switzerland
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science; Mahidol University; 272 Rama VI Road Bangkok 10400 Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Anja Schäfer
- Swiss Tropical and Public Health Institute (SwissTPH); Socinstrasse 57 4051 Basel Switzerland
- Universität Basel; Petersplatz 1 4003 Basel Switzerland
| | | | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science; Mahidol University; 272 Rama VI Road Bangkok 10400 Thailand
- Department of Biomolecular Science and Engineering, School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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11
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Amornwatcharapong W, Maenpuen S, Chitnumsub P, Leartsakulpanich U, Chaiyen P. Human and Plasmodium serine hydroxymethyltransferases differ in rate-limiting steps and pH-dependent substrate inhibition behavior. Arch Biochem Biophys 2017; 630:91-100. [PMID: 28760597 DOI: 10.1016/j.abb.2017.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 01/14/2023]
Abstract
Serine hydroxymethyltransferase (SHMT), an essential enzyme for cell growth and development, catalyzes the transfer of -CH2OH from l-serine to tetrahydrofolate (THF) to form glycine and 5,10-methylenetetrahydrofolate (MTHF) which is used for nucleotide synthesis. Insights into the ligand binding and inhibition properties of human cytosolic SHMT (hcSHMT) and Plasmodium SHMT (PvSHMT) are crucial for designing specific drugs against malaria and cancer. The results presented here revealed strong and pH-dependent THF inhibition of hcSHMT. In contrast, in PvSHMT, THF inhibition and the influence of pH were not as pronounced. Ligand binding experiments performed at various pH values indicated that the hcSHMT:Gly complex binds THF more tightly at lower pH conditions, while the binding affinity of the PvSHMT:Gly complex for THF is not pH-dependent. Pre-steady state kinetic (rapid-quench) analysis of hcSHMT showed burst kinetics, indicating that glycine formation occurs fastest in the first turnover relative to the subsequent turnovers i.e. glycine release is the rate-limiting step in the hcSHMT reaction. All data suggest that excess THF likely binds E:Gly binary complex and forms the E:Gly:THF dead-end complex before glycine is released. A unique flap motif found in the structure of hcSHMT may be the key structural feature that imparts these described characteristics of hcSHMT.
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Affiliation(s)
- Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand.
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Department of Biomolecular Science and Engineering, School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.
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12
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Carey MA, Papin JA, Guler JL. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance. BMC Genomics 2017; 18:543. [PMID: 28724354 PMCID: PMC5518114 DOI: 10.1186/s12864-017-3905-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Background Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. Results Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P. falciparum parasite to expand our understanding of metabolic changes that support resistance. We identified 11 metabolic tasks to evaluate iPfal17 performance. Flux balance analysis and simulation of gene knockouts and enzyme inhibition predict candidate drug targets unique to resistant parasites. Moreover, integration of clinical parasite transcriptomes into the iPfal17 reconstruction reveals patterns associated with antimalarial resistance. These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites, including folate and polyamines. Our findings are consistent with experimental literature, while generating novel hypotheses about artemisinin resistance and parasite biology. We detect evidence that resistant parasites maintain greater metabolic flexibility, perhaps representing an incomplete transition to the metabolic state most appropriate for nutrient-rich blood. Conclusion Using this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. This perspective allows us to more productively analyze and interpret clinical expression data for the identification of candidate drug targets for the treatment of resistant parasites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3905-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA.
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, USA. .,Division of Infectious Diseases and International Health, University of Virginia, School of Medicine, Charlottesville, USA.
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13
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Schwertz G, Witschel MC, Rottmann M, Bonnert R, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Ittarat W, Schäfer A, Aponte RA, Charman SA, White KL, Kundu A, Sadhukhan S, Lloyd M, Freiberg GM, Srikumaran M, Siggel M, Zwyssig A, Chaiyen P, Diederich F. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures. J Med Chem 2017; 60:4840-4860. [DOI: 10.1021/acs.jmedchem.7b00008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Geoffrey Schwertz
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | | | - Matthias Rottmann
- Swiss Tropical and Public Health Institute (SwissTPH), Socinstrasse
57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, CH-1215 Geneva, Switzerland
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Anja Schäfer
- Swiss Tropical and Public Health Institute (SwissTPH), Socinstrasse
57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | | | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Karen L. White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Abhijit Kundu
- TCG Lifesciences Private Limited, Block BN, Plot 7, Saltlake Electronics Complex, Sector V, Kolkata 700091, West Bengal India
| | - Surajit Sadhukhan
- TCG Lifesciences Private Limited, Block BN, Plot 7, Saltlake Electronics Complex, Sector V, Kolkata 700091, West Bengal India
| | - Mel Lloyd
- Covance Laboratories Ltd., Otley Road, Harrogate HG3 1PY, United Kingdom
| | - Gail M. Freiberg
- Molecular
Characterization, Department R4AE, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Myron Srikumaran
- Molecular
Characterization, Department R4AE, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Marc Siggel
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Adrian Zwyssig
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Pimchai Chaiyen
- Department of
Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science Mahidol University, 272 Rama VI Road, Bangkok 10400, Thailand
| | - François Diederich
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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14
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Witschel MC, Rottmann M, Schwab A, Leartsakulpanich U, Chitnumsub P, Seet M, Tonazzi S, Schwertz G, Stelzer F, Mietzner T, McNamara C, Thater F, Freymond C, Jaruwat A, Pinthong C, Riangrungroj P, Oufir M, Hamburger M, Mäser P, Sanz-Alonso LM, Charman S, Wittlin S, Yuthavong Y, Chaiyen P, Diederich F. Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT): Cocrystal Structures of Pyrazolopyrans with Potent Blood- and Liver-Stage Activities. J Med Chem 2015; 58:3117-30. [DOI: 10.1021/jm501987h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Anatol Schwab
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Michael Seet
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Sandro Tonazzi
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Geoffrey Schwertz
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Frank Stelzer
- BASF SE, Carl-Bosch-Strasse
38, 67056 Ludwigshafen, Germany
| | | | - Case McNamara
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, Suite 100, La Jolla, California 92037, United States
| | - Frank Thater
- BASF SE, Carl-Bosch-Strasse
38, 67056 Ludwigshafen, Germany
| | - Céline Freymond
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chatchadaporn Pinthong
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, 272 Rama VI Road, Bangkok 10400, Thailand
| | - Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Mouhssin Oufir
- Pharmaceutical
Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Matthias Hamburger
- Pharmaceutical
Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Laura M. Sanz-Alonso
- Diseases of the
Developing World (DDW), GlaxoSmithKline, C. Severo Ochoa, 2, 28760 Tres Cantos, Spain
| | - Susan Charman
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Pimchai Chaiyen
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, 272 Rama VI Road, Bangkok 10400, Thailand
| | - François Diederich
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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15
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Maenpuen S, Amornwatcharapong W, Krasatong P, Sucharitakul J, Palfey BA, Yuthavong Y, Chitnumsub P, Leartsakulpanich U, Chaiyen P. Kinetic mechanism and the rate-limiting step of Plasmodium vivax serine hydroxymethyltransferase. J Biol Chem 2015; 290:8656-65. [PMID: 25678710 DOI: 10.1074/jbc.m114.612275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a hydroxymethyl group transfer from L-serine to tetrahydrofolate (H4folate) to yield glycine and 5,10-methylenetetrahydrofolate (CH2-H4folate). SHMT is crucial for deoxythymidylate biosynthesis and a target for antimalarial drug development. Our previous studies indicate that PvSHMT catalyzes the reaction via a ternary complex mechanism. To define the kinetic mechanism of this catalysis, we explored the PvSHMT reaction by employing various methodologies including ligand binding, transient, and steady-state kinetics as well as product analysis by rapid-quench and HPLC/MS techniques. The results indicate that PvSHMT can bind first to either L-serine or H4folate. The dissociation constants for the enzyme·L-serine and enzyme·H4folate complexes were determined as 0.18 ± 0.08 and 0.35 ± 0.06 mM, respectively. The amounts of glycine formed after single turnovers of different preformed binary complexes were similar, indicating that the reaction proceeds via a random-order binding mechanism. In addition, the rate constant of glycine formation measured by rapid-quench and HPLC/MS analysis is similar to the kcat value (1.09 ± 0.05 s(-1)) obtained from the steady-state kinetics, indicating that glycine formation is the rate-limiting step of SHMT catalysis. This information will serve as a basis for future investigation on species-specific inhibition of SHMT for antimalarial drug development.
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Affiliation(s)
- Somchart Maenpuen
- From the Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand 10400, the Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand 20131
| | - Watcharee Amornwatcharapong
- From the Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand 10400
| | - Pasupat Krasatong
- the Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand 20131
| | - Jeerus Sucharitakul
- the Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand 10300
| | - Bruce A Palfey
- the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and
| | - Yongyuth Yuthavong
- the National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand 12120
| | - Penchit Chitnumsub
- the National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand 12120
| | - Ubolsree Leartsakulpanich
- the National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand 12120
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand 10400,
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16
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Chitnumsub P, Jaruwat A, Riangrungroj P, Ittarat W, Noytanom K, Oonanant W, Vanichthanankul J, Chuankhayan P, Maenpuen S, Chen CJ, Chaiyen P, Yuthavong Y, Leartsakulpanich U. Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:3177-86. [PMID: 25478836 PMCID: PMC4257618 DOI: 10.1107/s1399004714023128] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/20/2014] [Indexed: 01/22/2023]
Abstract
Plasmodium parasites, the causative agent of malaria, rely heavily on de novo folate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) from Plasmodium spp., an enzyme involved in folate recycling and dTMP synthesis, has been shown to catalyze the conversion of L- and D-serine to glycine (Gly) in a THF-dependent reaction, the mechanism of which is not yet fully understood. Here, the crystal structures of P. vivax SHMT (PvSHMT) in a binary complex with L-serine and in a ternary complex with D-serine (D-Ser) and (6R)-5-formyltetrahydrofolate (5FTHF) provide clues to the mechanism underlying the control of enzyme activity. 5FTHF in the ternary-complex structure was found in the 6R form, thus differing from the previously reported structures of SHMT-Gly-(6S)-5FTHF from other organisms. This suggested that the presence of D-Ser in the active site can alter the folate-binding specificity. Investigation of binding in the presence of D-Ser and the (6R)- or (6S)-5FTHF enantiomers indicated that both forms of 5FTHF can bind to the enzyme but that only (6S)-5FTHF gives rise to a quinonoid intermediate. Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs. Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed. Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.
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Affiliation(s)
- Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Krittikar Noytanom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Worrapoj Oonanant
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Jarunee Vanichthanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
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17
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Lauron EJ, Oakgrove KS, Tell LA, Biskar K, Roy SW, Sehgal RNM. Transcriptome sequencing and analysis of Plasmodium gallinaceum reveals polymorphisms and selection on the apical membrane antigen-1. Malar J 2014; 13:382. [PMID: 25261185 PMCID: PMC4182871 DOI: 10.1186/1475-2875-13-382] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/17/2014] [Indexed: 11/15/2022] Open
Abstract
Background Plasmodium erythrocyte invasion genes play a key role in malaria parasite transmission, host-specificity and immuno-evasion. However, the evolution of the genes responsible remains understudied. Investigating these genes in avian malaria parasites, where diversity is particularly high, offers new insights into the processes that confer malaria pathogenesis. These parasites can pose a significant threat to birds and since birds play crucial ecological roles they serve as important models for disease dynamics. Comprehensive knowledge of the genetic factors involved in avian malaria parasite invasion is lacking and has been hampered by difficulties in obtaining nuclear data from avian malaria parasites. Thus the first Illumina-based de novo transcriptome sequencing and analysis of the chicken parasite Plasmodium gallinaceum was performed to assess the evolution of essential Plasmodium genes. Methods White leghorn chickens were inoculated intravenously with erythrocytes containing P. gallinaceum. cDNA libraries were prepared from RNA extracts collected from infected chick blood and sequencing was run on the HiSeq2000 platform. Orthologues identified by transcriptome sequencing were characterized using phylogenetic, ab initio protein modelling and comparative and population-based methods. Results Analysis of the transcriptome identified several orthologues required for intra-erythrocytic survival and erythrocyte invasion, including the rhoptry neck protein 2 (RON2) and the apical membrane antigen-1 (AMA-1). Ama-1 of avian malaria parasites exhibits high levels of genetic diversity and evolves under positive diversifying selection, ostensibly due to protective host immune responses. Conclusion Erythrocyte invasion by Plasmodium parasites require AMA-1 and RON2 interactions. AMA-1 and RON2 of P. gallinaceum are evolutionarily and structurally conserved, suggesting that these proteins may play essential roles for avian malaria parasites to invade host erythrocytes. In addition, host-driven selection presumably results in the high levels of genetic variation found in ama-1 of avian Plasmodium species. These findings have implications for investigating avian malaria epidemiology and population dynamics. Moreover, this work highlights the P. gallinaceum transcriptome as an important public resource for investigating the diversity and evolution of essential Plasmodium genes. Electronic supplementary material The online version of this article (doi:10.1186/1475-2875-13-382) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elvin J Lauron
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
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18
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Chitnumsub P, Ittarat W, Jaruwat A, Noytanom K, Amornwatcharapong W, Pornthanakasem W, Chaiyen P, Yuthavong Y, Leartsakulpanich U. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1517-27. [PMID: 24914963 PMCID: PMC4051499 DOI: 10.1107/s1399004714005598] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/11/2014] [Indexed: 11/10/2022]
Abstract
Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.
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Affiliation(s)
- Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Krittikar Noytanom
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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19
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Pinthong C, Maenpuen S, Amornwatcharapong W, Yuthavong Y, Leartsakulpanich U, Chaiyen P. Distinct biochemical properties of human serine hydroxymethyltransferase compared with thePlasmodiumenzyme: implications for selective inhibition. FEBS J 2014; 281:2570-83. [DOI: 10.1111/febs.12803] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/25/2014] [Accepted: 03/31/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chatchadaporn Pinthong
- Department of Biochemistry and Center of Excellence in Protein Structure and Function; Mahidol University; Bangkok Thailand
| | | | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center of Excellence in Protein Structure and Function; Mahidol University; Bangkok Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology; National Science and Technology Development Agency; Pathumthani Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology; National Science and Technology Development Agency; Pathumthani Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function; Mahidol University; Bangkok Thailand
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20
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Prommana P, Uthaipibull C, Wongsombat C, Kamchonwongpaisan S, Yuthavong Y, Knuepfer E, Holder AA, Shaw PJ. Inducible knockdown of Plasmodium gene expression using the glmS ribozyme. PLoS One 2013; 8:e73783. [PMID: 24023691 PMCID: PMC3758297 DOI: 10.1371/journal.pone.0073783] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/23/2013] [Indexed: 01/07/2023] Open
Abstract
Conventional reverse genetic approaches for study of Plasmodium malaria parasite gene function are limited, or not applicable. Hence, new inducible systems are needed. Here we describe a method to control P. falciparum gene expression in which target genes bearing a glmS ribozyme in the 3' untranslated region are efficiently knocked down in transgenic P. falciparum parasites in response to glucosamine inducer. Using reporter genes, we show that the glmS ribozyme cleaves reporter mRNA in vivo leading to reduction in mRNA expression following glucosamine treatment. Glucosamine-induced ribozyme activation led to efficient reduction of reporter protein, which could be rapidly reversed by removing the inducer. The glmS ribozyme was validated as a reverse-genetic tool by integration into the essential gene and antifolate drug target dihydrofolate reductase-thymidylate synthase (PfDHFR-TS). Glucosamine treatment of transgenic parasites led to rapid and efficient knockdown of PfDHFR-TS mRNA and protein. PfDHFR-TS knockdown led to a growth/arrest mutant phenotype and hypersensitivity to pyrimethamine. The glmS ribozyme may thus be a tool for study of essential genes in P. falciparum and other parasite species amenable to transfection.
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Affiliation(s)
- Parichat Prommana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Chairat Uthaipibull
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Chayaphat Wongsombat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Ellen Knuepfer
- Division of Parasitology, MRC National Institute for Medical Research, London, United Kingdom
| | - Anthony A. Holder
- Division of Parasitology, MRC National Institute for Medical Research, London, United Kingdom
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
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Folate metabolism in human malaria parasites—75 years on. Mol Biochem Parasitol 2013; 188:63-77. [DOI: 10.1016/j.molbiopara.2013.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/21/2022]
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Salcedo-Sora JE, Ward SA. The folate metabolic network of Falciparum malaria. Mol Biochem Parasitol 2013; 188:51-62. [PMID: 23454873 DOI: 10.1016/j.molbiopara.2013.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 02/04/2013] [Accepted: 02/11/2013] [Indexed: 01/07/2023]
Abstract
The targeting of key enzymes in the folate pathway continues to be an effective chemotherapeutic approach that has earned antifolate drugs a valuable position in the medical pharmacopoeia. The successful therapeutic use of antifolates as antimalarials has been a catalyst for ongoing research into the biochemistry of folate and pterin biosynthesis in malaria parasites. However, our understanding of the parasites folate metabolism remains partial and patchy, especially in relation to the shikimate pathway, the folate cycle, and folate salvage. A sizeable number of potential folate targets remain to be characterised. Recent reports on the parasite specific transport of folate precursors that would normally be present in the human host awaken previous hypotheses on the salvage of folate precursors or by-products. As the parasite progresses through its life-cycle it encounters very contrasting host cell environments that present radically different metabolic milieus and biochemical challenges. It would seem probable that as the parasite encounters differing environments it would need to modify its biochemistry. This would be reflected in the folate homeostasis in Plasmodium. Recent drug screening efforts and insights into folate membrane transport substantiate the argument that folate metabolism may still offer unexplored opportunities for therapeutic attack.
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Affiliation(s)
- J Enrique Salcedo-Sora
- Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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