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Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023; 2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Braelyn Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Pierce T O’Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Cody Timmons
- Chemistry Department, Southwestern Oklahoma State University, 100 Campus Dr., Weatherford, OK 73096, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Daniel J Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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de Lima Serafim V, Félix MB, Frade Silva DK, Rodrigues KADF, Andrade PN, de Almeida SMV, de Albuquerque dos Santos S, de Oliveira JF, de Lima MDCA, Mendonça-Junior FJB, Scotti MT, de Oliveira MR, de Moura RO. New thiophene-acridine compounds: Synthesis, antileishmanial activity, DNA binding, chemometric, and molecular docking studies. Chem Biol Drug Des 2018; 91:1141-1155. [DOI: 10.1111/cbdd.13176] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/24/2017] [Accepted: 01/20/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Vanessa de Lima Serafim
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | - Mayara Barbalho Félix
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | - Daiana Karla Frade Silva
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | - Klinger Antônio da Franca Rodrigues
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | - Patrícia Néris Andrade
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | | | | | - Jamerson Ferreira de Oliveira
- Laboratório de Química e Inovação Terapêutica (LQIT); Departamento de Antibióticos; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica (LQIT); Departamento de Antibióticos; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Francisco Jaime Bezerra Mendonça-Junior
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
- Laboratório de Síntese e Vetorização de Moléculas; Departamento de Ciências Biológicas; Universidade Estadual da Paraíba; João Pessoa PB Brazil
| | - Marcus Tullius Scotti
- Programa de Pós-Graduação em Produtos Naturais e Sintéticos Bioativos; Universidade Federal da Paraíba; João Pessoa Paraíba Brazil
| | - Márcia Rosa de Oliveira
- Laboratório de Leishmanioses; Departamento de Biologia Molecular; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Ricardo Olímpio de Moura
- Laboratório de Síntese e Vetorização de Moléculas; Departamento de Ciências Biológicas; Universidade Estadual da Paraíba; João Pessoa PB Brazil
- Departamento de Ciências Farmacêuticas; Centro de Ciências Biológicas e da Saúde; Universidade Estadual da Paraíba - Bodocongó; Campina Grande PB Brazil
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3
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Zhang Y, Liu B, Wu X, Li R, Ning X, Liu Y, Liu Z, Ge Z, Li R, Yin Y. New pyridin-3-ylmethyl carbamodithioic esters activate pyruvate kinase M2 and potential anticancer lead compounds. Bioorg Med Chem 2015; 23:4815-4823. [PMID: 26081759 DOI: 10.1016/j.bmc.2015.05.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 01/30/2023]
Abstract
Pyruvate kinase M2 (PKM2) is a key protein responsible for cancer's Warburg effect. Activation of PKM2 may alter aberrant metabolism in cancer cells, which suggests PKM2 as a tumor selective therapeutic target. In this paper, the lead compound 8 was first discovered as a new kind of PKM2 activator from a random screening of an in-house compound library. Then, a series of lead compound 8 analogs were designed, synthesized and evaluated for their activation of PKM2 and anticancer activities. 7-Azaindole analog 32 was identified as the most potent PKM2 activator. Compounds with potent enzyme activity also exhibited selective anti-proliferation activity on cancer cell lines HCT116, Hela and H1299 compared with non-tumor cell line BEAS-2B. The structure-activity relationships of these compounds were supported by molecular docking results. Preliminary pharmacological studies also showed that compound 32 arrests the cell cycle at the G2/M phase in HCT116 cell line.
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Affiliation(s)
- Yu Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Bin Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xingyu Wu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Ridong Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xianling Ning
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Yu Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Zemei Ge
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Runtao Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
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4
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Jamal S, Scaria V. Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana. BMC Bioinformatics 2013; 14:329. [PMID: 24252103 PMCID: PMC4225525 DOI: 10.1186/1471-2105-14-329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 10/01/2013] [Indexed: 02/04/2023] Open
Abstract
Background Leishmaniasis is a neglected tropical disease which affects approx. 12 million individuals worldwide and caused by parasite Leishmania. The current drugs used in the treatment of Leishmaniasis are highly toxic and has seen widespread emergence of drug resistant strains which necessitates the need for the development of new therapeutic options. The high throughput screen data available has made it possible to generate computational predictive models which have the ability to assess the active scaffolds in a chemical library followed by its ADME/toxicity properties in the biological trials. Results In the present study, we have used publicly available, high-throughput screen datasets of chemical moieties which have been adjudged to target the pyruvate kinase enzyme of L. mexicana (LmPK). The machine learning approach was used to create computational models capable of predicting the biological activity of novel antileishmanial compounds. Further, we evaluated the molecules using the substructure based approach to identify the common substructures contributing to their activity. Conclusion We generated computational models based on machine learning methods and evaluated the performance of these models based on various statistical figures of merit. Random forest based approach was determined to be the most sensitive, better accuracy as well as ROC. We further added a substructure based approach to analyze the molecules to identify potentially enriched substructures in the active dataset. We believe that the models developed in the present study would lead to reduction in cost and length of clinical studies and hence newer drugs would appear faster in the market providing better healthcare options to the patients.
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Affiliation(s)
- Salma Jamal
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
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Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Comput Biol 2013; 9:e1003159. [PMID: 23946717 PMCID: PMC3738050 DOI: 10.1371/journal.pcbi.1003159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may reflect adaptation to different environments with different concentrations of activating compounds. The combined computational approach employed can readily be applied to other enzymes.
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Affiliation(s)
- Nadine Veith
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Anna Feldman-Salit
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
- Center for Modelling and Simulation in the Biosciences (BIOMS), Heidelberg, Germany
| | - Vlad Cojocaru
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Stefan Henrich
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Ursula Kummer
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Heidelberg, Germany
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Morgan HP, McNae IW, Nowicki MW, Zhong W, Michels PAM, Auld DS, Fothergill-Gilmore LA, Walkinshaw MD. The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. J Biol Chem 2011; 286:31232-40. [PMID: 21733839 PMCID: PMC3173065 DOI: 10.1074/jbc.m110.212613] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 06/06/2011] [Indexed: 11/06/2022] Open
Abstract
Ehrlich's pioneering chemotherapeutic experiments published in 1904 (Ehrlich, P., and Shiga, K. (1904) Berlin Klin. Wochenschrift 20, 329-362) described the efficacy of a series of dye molecules including trypan blue and trypan red to eliminate trypanosome infections in mice. The molecular structures of the dyes provided a starting point for the synthesis of suramin, which was developed and used as a trypanocidal drug in 1916 and is still in clinical use. Despite the biological importance of these dye-like molecules, the mode of action on trypanosomes has remained elusive. Here we present crystal structures of suramin and three related dyes in complex with pyruvate kinases from Leishmania mexicana or from Trypanosoma cruzi. The phenyl sulfonate groups of all four molecules (suramin, Ponceau S, acid blue 80, and benzothiazole-2,5-disulfonic acid) bind in the position of ADP/ATP at the active sites of the pyruvate kinases (PYKs). The binding positions in the two different trypanosomatid PYKs are nearly identical. We show that suramin competitively inhibits PYKs from humans (muscle, tumor, and liver isoenzymes, K(i) = 1.1-17 μM), T. cruzi (K(i) = 108 μM), and L. mexicana (K(i) = 116 μM), all of which have similar active sites. Synergistic effects were observed when examining suramin inhibition in the presence of an allosteric effector molecule, whereby IC(50) values decreased up to 2-fold for both trypanosomatid and human PYKs. These kinetic and structural analyses provide insight into the promiscuous inhibition observed for suramin and into the mode of action of the dye-like molecules used in Ehrlich's original experiments.
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Affiliation(s)
- Hugh P. Morgan
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Iain W. McNae
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Matthew W. Nowicki
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Wenhe Zhong
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Paul A. M. Michels
- the Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium, and
| | - Douglas S. Auld
- the National Institutes of Health Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20850
| | - Linda A. Fothergill-Gilmore
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Malcolm D. Walkinshaw
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
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Identification of pyruvate kinase in methicillin-resistant Staphylococcus aureus as a novel antimicrobial drug target. Antimicrob Agents Chemother 2011; 55:2042-53. [PMID: 21357306 DOI: 10.1128/aac.01250-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel classes of antimicrobials are needed to address the challenge of multidrug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). Using the architecture of the MRSA interactome, we identified pyruvate kinase (PK) as a potential novel drug target based upon it being a highly connected, essential hub in the MRSA interactome. Structural modeling, including X-ray crystallography, revealed discrete features of PK in MRSA, which appeared suitable for the selective targeting of the bacterial enzyme. In silico library screening combined with functional enzymatic assays identified an acyl hydrazone-based compound (IS-130) as a potent MRSA PK inhibitor (50% inhibitory concentration [IC50] of 0.1 μM) with >1,000-fold selectivity over human PK isoforms. Medicinal chemistry around the IS-130 scaffold identified analogs that more potently and selectively inhibited MRSA PK enzymatic activity and S. aureus growth in vitro (MIC of 1 to 5 μg/ml). These novel anti-PK compounds were found to possess antistaphylococcal activity, including both MRSA and multidrug-resistant S. aureus (MDRSA) strains. These compounds also exhibited exceptional antibacterial activities against other Gram-positive genera, including enterococci and streptococci. PK lead compounds were found to be noncompetitive inhibitors and were bactericidal. In addition, mutants with significant increases in MICs were not isolated after 25 bacterial passages in culture, indicating that resistance may be slow to emerge. These findings validate the principles of network science as a powerful approach to identify novel antibacterial drug targets. They also provide a proof of principle, based upon PK in MRSA, for a research platform aimed at discovering and optimizing selective inhibitors of novel bacterial targets where human orthologs exist, as leads for anti-infective drug development.
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8
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Zoraghi R, See RH, Gong H, Lian T, Swayze R, Finlay BB, Brunham RC, McMaster WR, Reiner NE. Functional analysis, overexpression, and kinetic characterization of pyruvate kinase from methicillin-resistant Staphylococcus aureus. Biochemistry 2010; 49:7733-47. [PMID: 20707314 DOI: 10.1021/bi100780t] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Novel antimicrobial targets are urgently needed to overcome rising antibiotic resistance of important human pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Here we report the essentiality and kinetic properties of MRSA pyruvate kinase (PK). Targetron-mediated gene disruption demonstrated PK is essential for S. aureus growth and survival, suggesting that this protein may be a potential drug target. The presence of the pfk (6-phosphofructokinase)-pyk operon in MRSA252, and the nonessential nature of PFK shown by targetron, further emphasized the essential role of PK in cell viability. The importance of PK in bacterial growth was confirmed by showing that its enzymatic activity peaked during the logarithmic phase of S. aureus growth. PK from Staphylococcus and several other species of bacteria have an extra C-terminal domain (CT) containing a phosphoenolpyruvate (PEP) binding motif. To elucidate the possible structure and function of this sequence, the quaternary structures and kinetic properties of the full-length MRSA PK and truncated MRSA PK lacking the CT domain were characterized. Our results showed that (1) MRSA PK is an allosteric enzyme with homotetramer architecture activated by AMP or ribose 5-phosphate (R5P), but not by fructose 1,6-bisphosphate (FBP), which suggests a different mode of allosteric regulation when compared with human isozymes, (2) the CT domain is not required for the tetramerization of the enzyme; homotetramerization occurred in a truncated PK lacking the domain, (3) truncated enzyme exhibited high affinity toward both PEP and ADP and exhibited hyperbolic kinetics toward PEP in the presence of activators (AMP and R5P) consistent with kinetic properties of full-length enzyme, indicating that the CT domain is not required for substrate binding or allosteric regulation observed in the holoenzyme, (4) the kinetic efficiency (k(cat)/S(0.5)) of truncated enzyme was decreased by 24- and 16-fold, in ligand-free state, toward PEP and ADP, respectively, but was restored by 3-fold in AMP-bound state, suggesting that the sequence containing the CT domain (Gly(473)-Leu(585)) plays a substantial role in enzyme activity and comformational stability, and (5) full-length MRSA PK activity was stimulated at low concentrations of ATP (e.g., 1 mM) and inhibited by inorganic phosphate and high concentrations of FBP (10 mM) and ATP (e.g., >2.5 mM), whereas for truncated enzyme, stimulation at low concentrations of ATP was lost. These findings suggest that the CT domain is involved in maintaining the specificity of allosteric regulation of MRSA PK by AMP, R5P, and ATP. The CT extension also encodes a protein domain with homology to enzyme I of the Escherichia coli sugar-PTS system, suggesting that MRSA PK may also exert an important regulatory role in sugar transport metabolism. These findings yield new insights into MRSA PK function and mode of allosteric regulation which may aid in the development of clinically important drugs targeting this enzyme and further define the role of the extra C-terminal domain in modulating the enzyme's activity.
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Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of BritishColumbia, Vancouver,Britsih Columbia,CanadaV5Z3J5
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9
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Jiang JK, Boxer MB, Vander Heiden MG, Shen M, Skoumbourdis AP, Southall N, Veith H, Leister W, Austin CP, Park HW, Inglese J, Cantley LC, Auld DS, Thomas CJ. Evaluation of thieno[3,2-b]pyrrole[3,2-d]pyridazinones as activators of the tumor cell specific M2 isoform of pyruvate kinase. Bioorg Med Chem Lett 2010; 20:3387-93. [PMID: 20451379 PMCID: PMC2874658 DOI: 10.1016/j.bmcl.2010.04.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 04/05/2010] [Accepted: 04/07/2010] [Indexed: 11/21/2022]
Abstract
Cancer cells have distinct metabolic needs that are different from normal cells and can be exploited for development of anti-cancer therapeutics. Activation of the tumor specific M2 form of pyruvate kinase (PKM2) is a potential strategy for returning cancer cells to a metabolic state characteristic of normal cells. Here, we describe activators of PKM2 based upon a substituted thieno[3,2-b]pyrrole[3,2-d]pyridazinone scaffold. The synthesis of these agents, structure-activity relationships, analysis of activity at related targets (PKM1, PKR and PKL) and examination of aqueous solubility are investigated. These agents represent the second reported chemotype for activation of PKM2.
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Affiliation(s)
- Jian-kang Jiang
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Matthew B. Boxer
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Matthew G. Vander Heiden
- Koch Institute at MIT, Cambridge, Massachusetts 02139 USA
- Dana Farber Cancer Institute, Boston, Massachusetts 02115 USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Min Shen
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Amanda P. Skoumbourdis
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Noel Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Henrike Veith
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - William Leister
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Christopher P. Austin
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Hee Won Park
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada M5G 1L5
- Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - James Inglese
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Lewis C. Cantley
- Dana Farber Cancer Institute, Boston, Massachusetts 02115 USA
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
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10
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Boxer MB, Jiang JK, Vander Heiden MG, Shen M, Skoumbourdis AP, Southall N, Veith H, Leister W, Austin CP, Park HW, Inglese J, Cantley LC, Auld DS, Thomas CJ. Evaluation of substituted N,N'-diarylsulfonamides as activators of the tumor cell specific M2 isoform of pyruvate kinase. J Med Chem 2010; 53:1048-55. [PMID: 20017496 PMCID: PMC2818804 DOI: 10.1021/jm901577g] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metabolism of cancer cells is altered to support rapid proliferation. Pharmacological activators of a tumor cell specific pyruvate kinase isozyme (PKM2) may be an approach for altering the classic Warburg effect characteristic of aberrant metabolism in cancer cells yielding a novel antiproliferation strategy. In this manuscript, we detail the discovery of a series of substituted N,N'-diarylsulfonamides as activators of PKM2. The synthesis of numerous analogues and the evaluation of structure-activity relationships are presented as well as assessments of mechanism and selectivity. Several agents are found that have good potencies and appropriate solubility for use as chemical probes of PKM2 including 55 (AC(50) = 43 nM, maximum response = 84%; solubility = 7.3 microg/mL), 56 (AC(50) = 99 nM, maximum response = 84%; solubility = 5.7 microg/mL), and 58 (AC(50) = 38 nM, maximum response = 82%; solubility = 51.2 microg/mL). The small molecules described here represent first-in-class activators of PKM2.
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Affiliation(s)
- Matthew B. Boxer
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Jian-kang Jiang
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Matthew G. Vander Heiden
- Dana Farber Cancer Institute, Boston, Massachusetts 02115 USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Min Shen
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Amanda P. Skoumbourdis
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Noel Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Henrike Veith
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - William Leister
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Christopher P. Austin
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Hee Won Park
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada M5G 1L5
- Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - James Inglese
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Lewis C. Cantley
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 USA
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
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11
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Morgan HP, McNae IW, Nowicki MW, Hannaert V, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Allosteric mechanism of pyruvate kinase from Leishmania mexicana uses a rock and lock model. J Biol Chem 2010; 285:12892-8. [PMID: 20123988 DOI: 10.1074/jbc.m109.079905] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first complete series of allosteric structures, in all possible ligated states, for the tetrameric enzyme, pyruvate kinase, from Leishmania mexicana. The transition between inactive T-state and active R-state is accompanied by a simple symmetrical 6 degrees rigid body rocking motion of the A- and C-domain cores in each of the four subunits. However, formation of the R-state in this way is only part of the mechanism; eight essential salt bridge locks that form across the C-C interface provide tetramer rigidity with a coupled 7-fold increase in rate. The results presented here illustrate how conformational changes coupled with effector binding correlate with loss of flexibility and increase in thermal stability providing a general mechanism for allosteric control.
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Affiliation(s)
- Hugh P Morgan
- Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
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12
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Tulloch LB, Morgan HP, Hannaert V, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state. J Mol Biol 2008; 383:615-26. [PMID: 18775437 DOI: 10.1016/j.jmb.2008.08.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 08/14/2008] [Indexed: 11/17/2022]
Abstract
We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.
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Affiliation(s)
- Lindsay B Tulloch
- Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Edinburgh, UK
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13
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A biochemical and genetic study of Leishmania donovani pyruvate kinase. Gene 2008; 424:25-32. [PMID: 18725273 DOI: 10.1016/j.gene.2008.07.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 06/20/2008] [Accepted: 07/29/2008] [Indexed: 11/24/2022]
Abstract
Here we present a biochemical and molecular biology study of the enzyme pyruvate kinase (PYK) from the parasitic protozoa Leishmania donovani. The PYK gene was cloned, mutagenised and over expressed and its kinetic parameters determined. Like in other kinetoplastids, L. donovani PYK is allosterically stimulated by the effector fructose 2,6 biphosphate and not by fructose 1,6 biphosphate. When the putative effector binding site of L. donovani PYK was mutagenised, we obtained two mutants with extreme kinetic behavior: Lys453Leu, which retained a sigmoidal kinetics and was little affected by the effector; and His480Gln, which deployed a hyperbolic kinetics that was not changed by the addition of the effector. Molecular Dynamics (MD) studies revealed that the mutations not only altered the effector binding site of L. donovani PYK but also changed the folding of its domain C.
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14
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Kharalkar SS, Joshi GS, Musayev FN, Fornabaio M, Abraham DJ, Safo MK. Identification of novel allosteric regulators of human-erythrocyte pyruvate kinase. Chem Biodivers 2008; 4:2603-17. [PMID: 18027374 DOI: 10.1002/cbdv.200790213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Erythrocyte pyruvate kinase (PK) is an important glycolytic enzyme, and manipulation of its regulatory behavior by allosteric modifiers is of interest for medicinal purposes. Human-erythrocyte PK was expressed in Rosetta cells and purified on an Ni-NTA column. A search of the small-molecules database of the National Cancer Institute (NCI), using the UNITY software, led to the identification of several compounds with similar pharmacophores as fructose-1,6-bisphosphate (FBP), the natural allosteric activator of the human kinases. The compounds were subsequently docked into the FBP binding site using the programs FlexX and GOLD, and their interactions with the protein were analyzed with the energy-scoring function of HINT. Seven promising candidates, compounds 1-7, were obtained from the NCI, and subjected to kinetics analysis, which revealed both activators and inhibitors of the R-isozyme of PK (R-PK). The allosteric effectors discovered in this study could prove to be lead compounds for developing medications for the treatment of hemolytic anemia, sickle-cell anemia, hypoxia-related diseases, and other disorders arising from erythrocyte PK malfunction.
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Affiliation(s)
- Shilpa S Kharalkar
- Department of Medicinal Chemistry, School of Pharmacy, and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, USA
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15
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Chevalier N, Bertrand L, Rider MH, Opperdoes FR, Rigden DJ, Michels PAM. 6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in Trypanosomatidae. Molecular characterization, database searches, modelling studies and evolutionary analysis. FEBS J 2005; 272:3542-60. [PMID: 16008555 DOI: 10.1111/j.1742-4658.2005.04774.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fructose 2,6-bisphosphate is a potent allosteric activator of trypanosomatid pyruvate kinase and thus represents an important regulator of energy metabolism in these protozoan parasites. A 6-phosphofructo-2-kinase, responsible for the synthesis of this regulator, was highly purified from the bloodstream form of Trypanosoma brucei and kinetically characterized. By searching trypanosomatid genome databases, four genes encoding proteins homologous to the mammalian bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2/FBPase-2) were found for both T. brucei and the related parasite Leishmania major and four pairs in Trypanosoma cruzi. These genes were predicted to each encode a protein in which, at most, only a single domain would be active. Two of the T. brucei proteins showed most conservation in the PFK-2 domain, although one of them was predicted to be inactive due to substitution of residues responsible for ligating the catalytically essential divalent metal cation; the two other proteins were most conserved in the FBPase-2 domain. The two PFK-2-like proteins were expressed in Escherichia coli. Indeed, the first displayed PFK-2 activity with similar kinetic properties to that of the enzyme purified from T. brucei, whereas no activity was found for the second. Interestingly, several of the predicted trypanosomatid PFK-2/FBPase-2 proteins have long N-terminal extensions. The N-terminal domains of the two polypeptides with most similarity to mammalian PFK-2s contain a series of tandem repeat ankyrin motifs. In other proteins such motifs are known to mediate protein-protein interactions. Phylogenetic analysis suggests that the four different PFK-2/FBPase-2 isoenzymes found in Trypanosoma and Leishmania evolved from a single ancestral bifunctional enzyme within the trypanosomatid lineage. A possible explanation for the evolution of multiple monofunctional enzymes and for the presence of the ankyrin-motif repeats in the PFK-2 isoenzymes is presented.
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Affiliation(s)
- Nathalie Chevalier
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, Brussels, Belgium
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16
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Hannaert V, Bringaud F, Opperdoes FR, Michels PAM. Evolution of energy metabolism and its compartmentation in Kinetoplastida. KINETOPLASTID BIOLOGY AND DISEASE 2003; 2:11. [PMID: 14613499 PMCID: PMC317351 DOI: 10.1186/1475-9292-2-11] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Accepted: 10/28/2003] [Indexed: 04/27/2023]
Abstract
Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties.In this review, we describe the unique compartmentation of metabolism in Kinetoplastida and the metabolic properties resulting from this compartmentation. We discuss the evidence for our recently proposed hypothesis that a common ancestor of Kinetoplastida and Euglenida acquired a photosynthetic alga as an endosymbiont, contrary to the earlier notion that this event occurred at a later stage of evolution, in the Euglenida lineage alone. The endosymbiont was subsequently lost from the kinetoplastid lineage but, during that process, some of its pathways of energy and carbohydrate metabolism were sequestered in the kinetoplastid peroxisomes, which consequently became glycosomes. The evolution of the kinetoplastid glycosomes and the possible selective advantages of these organelles for Kinetoplastida are discussed. We propose that the possession of glycosomes provided metabolic flexibility that has been important for the organisms to adapt easily to changing environmental conditions. It is likely that metabolic flexibility has been an important selective advantage for many kinetoplastid species during their evolution into the highly successful parasites today found in many divergent taxonomic groups.Also addressed is the evolution of the kinetoplastid mitochondrion, from a supposedly pluripotent organelle, attributed to a single endosymbiotic event that resulted in all mitochondria and hydrogenosomes of extant eukaryotes. Furthermore, indications are presented that Kinetoplastida may have acquired other enzymes of energy and carbohydrate metabolism by various lateral gene transfer events different from those that involved the algal- and alpha-proteobacterial-like endosymbionts responsible for the respective formation of the glycosomes and mitochondria.
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Affiliation(s)
- Véronique Hannaert
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Frédéric Bringaud
- Laboratoire de Parasitologie Moléculaire, Université Victor Segalen, Bordeaux II, UMR-CNRS 5016, 146 Rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Fred R Opperdoes
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Paul AM Michels
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
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