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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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2
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Gao P, Huang X, Fang XY, Zheng H, Cai SL, Sun AJ, Zhao L, Zhang Y. Application of metabolomics in clinical and laboratory gastrointestinal oncology. World J Gastrointest Oncol 2021; 13:536-549. [PMID: 34163571 PMCID: PMC8204353 DOI: 10.4251/wjgo.v13.i6.536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Metabolites are versatile bioactive molecules. They are not only the substrates and/or the products of enzymatic reactions but also act as the regulators in the systemic metabolism. Metabolomics is a high-throughput analytical strategy to qualify or quantify as many metabolites as possible in the metabolomes. It is an indispensable part of systems biology. The leading techniques in this field are mainly based on mass spectrometry and nuclear magnetic resonance spectroscopy. The metabolomic analysis has gained wide use in bioscience fields. In the tumor research arena, metabolomics can be employed to identify biomarkers for prediction, diagnosis, and prognosis. Chemotherapeutic effect evaluation and personalized medicine decision-making can also benefit from metabolomic analysis of patient biofluid or biopsy samples. Many cell-level studies can help in disease exploration. In this review, the basic features and principles of varied metabolomic analysis are introduced. The value of metabolomics in clinical and laboratory gastrointestinal cancer studies is discussed, especially for mass spectrometry applications. Besides, combined use of metabolomics and other tools to solve problems in cancer practice is briefly illustrated. In summary, metabolomics paves a new way to explore cancerous diseases in the light of small molecules.
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Affiliation(s)
- Peng Gao
- Department ofClinical Laboratory, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Xin Huang
- Department of Internal Medicine, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Xue-Yan Fang
- Department of Nursing, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Hui Zheng
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Shu-Ling Cai
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Ai-Jun Sun
- Clinical Research Center, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Liang Zhao
- Department of Internal Medicine, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
| | - Yong Zhang
- Department of Surgery, Dalian Sixth People's Hospital, Dalian 116031, Liaoning Province, China
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3
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Abstract
AbstractDuring three decades, only about 20 new drugs have been developed for malaria, tuberculosis and all neglected tropical diseases (NTDs). This critical situation was reached because NTDs represent only 10% of health research investments; however, they comprise about 90% of the global disease burden. Computational simulations applied in virtual screening (VS) strategies are very efficient tools to identify pharmacologically active compounds or new indications for drugs already administered for other diseases. One of the advantages of this approach is the low time-consuming and low-budget first stage, which filters for testing experimentally a group of candidate compounds with high chances of binding to the target and present trypanocidal activity. In this work, we review the most common VS strategies that have been used for the identification of new drugs with special emphasis on those applied to trypanosomiasis and leishmaniasis. Computational simulations based on the selected protein targets or their ligands are explained, including the method selection criteria, examples of successful VS campaigns applied to NTDs, a list of validated molecular targets for drug development and repositioned drugs for trypanosomatid-caused diseases. Thereby, here we present the state-of-the-art of VS and drug repurposing to conclude pointing out the future perspectives in the field.
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4
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Liberti MV, Allen AE, Ramesh V, Dai Z, Singleton KR, Guo Z, Liu JO, Wood KC, Locasale JW. Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis. J Biol Chem 2020; 295:111-124. [PMID: 31748414 PMCID: PMC6952593 DOI: 10.1074/jbc.ra119.010903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/10/2019] [Indexed: 12/20/2022] Open
Abstract
Aerobic glycolysis or the Warburg effect (WE) is characterized by increased glucose uptake and incomplete oxidation to lactate. Although the WE is ubiquitous, its biological role remains controversial, and whether glucose metabolism is functionally different during fully oxidative glycolysis or during the WE is unknown. To investigate this question, here we evolved resistance to koningic acid (KA), a natural product that specifically inhibits glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-controlling glycolytic enzyme, during the WE. We found that KA-resistant cells lose the WE but continue to conduct glycolysis and surprisingly remain dependent on glucose as a carbon source and also on central carbon metabolism. Consequently, this altered state of glycolysis led to differential metabolic activity and requirements, including emergent activities in and dependences on fatty acid metabolism. These findings reveal that aerobic glycolysis is a process functionally distinct from conventional glucose metabolism and leads to distinct metabolic requirements and biological functions.
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Affiliation(s)
- Maria V Liberti
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.
| | - Annamarie E Allen
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Vijyendra Ramesh
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Katherine R Singleton
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Zufeng Guo
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
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5
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González-Chávez Z, Vázquez C, Moreno-Sánchez R, Saavedra E. Metabolic Control Analysis for Drug Target Prioritization in Trypanosomatids. Methods Mol Biol 2020; 2116:689-718. [PMID: 32221950 DOI: 10.1007/978-1-0716-0294-2_41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To validate therapeutic targets in metabolic pathways of trypanosomatids, the criterion of enzyme essentiality determined by gene knockout or knockdown is usually being applied. Since, it is often found that most of the enzymes/proteins analyzed are essential, additional criteria have to be implemented for drug target prioritization. Metabolic control analysis (MCA), often in conjunction with kinetic pathway modeling, offers such possibility for prioritization. MCA is a theoretical and experimental approach to analyze how metabolic pathways are controlled. It involves strategies to perform quantitative analyses to determine the degree in which an enzyme controls a pathway flux, a value called flux control coefficient ([Formula: see text]). By determining the [Formula: see text] of individual steps in a metabolic pathway, the distribution of control of the pathway is established, that is, the identification of the main flux-controlling steps. Therefore, MCA can help in ranking pathway enzymes as drug targets from a metabolic perspective. In this chapter, three approaches to determine [Formula: see text] are reviewed: (1) In vitro pathway reconstitution, (2) manipulation of enzyme activities within parasites, and (3) in silico kinetic modeling of the metabolic pathway. To perform these methods, accurate experimental data of enzyme activities, metabolite concentrations and pathway fluxes are necessary. The methodology is illustrated with the example of trypanothione metabolism of Trypanosoma cruzi and protocols to determine such experimental data for this metabolic process are also described. However, the MCA strategy can be applied to any metabolic pathway in the parasite and general directions to perform it are provided in this chapter.
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Affiliation(s)
- Zabdi González-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico.
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6
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Saavedra E, González-Chávez Z, Moreno-Sánchez R, Michels PA. Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling. Curr Med Chem 2019; 26:6652-6671. [DOI: 10.2174/0929867325666180917104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
Abstract
In the search for therapeutic targets in the intermediary metabolism of trypanosomatids
the gene essentiality criterion as determined by using knock-out and knock-down genetic
strategies is commonly applied. As most of the evaluated enzymes/transporters have
turned out to be essential for parasite survival, additional criteria and approaches are clearly
required for suitable drug target prioritization. The fundamentals of Metabolic Control
Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic
modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification
of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient)
and metabolic intermediate concentrations (concentration control coefficient). MCA
studies have demonstrated that metabolic pathways usually have two or three enzymes with
the highest control of flux; their inhibition has more negative effects on the pathway function
than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest
pathway control are the most convenient targets for therapeutic intervention. In this review,
the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients
and metabolic modeling are analyzed. MCA and kinetic modeling have been applied
to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently
validated in vivo. The results showed that three out of ten enzyme reactions analyzed
in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and
metabolic modeling allow a further step in target prioritization for drug development against
trypanosomatids and other parasites.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Zabdi González-Chávez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Paul A.M. Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
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7
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Targeting pteridine reductase 1 and dihydrofolate reductase: the old is a new trend for leishmaniasis drug discovery. Future Med Chem 2019; 11:2107-2130. [DOI: 10.4155/fmc-2018-0512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases in the world and it is considered endemic in 88 countries. This disease is transmitted by a Leishmania spp. infected sandfly and it may lead to cutaneous or systemic manifestations. The preconized treatment has low efficacy and there are cases of resistance to some drugs. Therefore, the search for new efficient molecular targets that can lead to the preparation of new drugs must be pursued. This review aims to evaluate both Leishmania enzymes PTR1 and DHFR-TS as potential drug targets, highlight their inhibitors and to discuss critically the use of chemoinformatics to elucidate interactions and propose new molecules against these enzymes.
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8
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Gamma-glutamylcysteine synthetase and tryparedoxin 1 exert high control on the antioxidant system in Trypanosoma cruzi contributing to drug resistance and infectivity. Redox Biol 2019; 26:101231. [PMID: 31203195 PMCID: PMC6581782 DOI: 10.1016/j.redox.2019.101231] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/31/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022] Open
Abstract
Trypanothione (T(SH)2) is the main antioxidant metabolite for peroxide reduction in Trypanosoma cruzi; therefore, its metabolism has attracted attention for therapeutic intervention against Chagas disease. To validate drug targets within the T(SH)2 metabolism, the strategies and methods of Metabolic Control Analysis and kinetic modeling of the metabolic pathway were used here, to identify the steps that mainly control the pathway fluxes and which could be appropriate sites for therapeutic intervention. For that purpose, gamma-glutamylcysteine synthetase (γECS), trypanothione synthetase (TryS), trypanothione reductase (TryR) and the tryparedoxin cytosolic isoform 1 (TXN1) were separately overexpressed to different levels in T. cruzi epimastigotes and their degrees of control on the pathway flux as well as their effect on drug resistance and infectivity determined. Both experimental in vivo as well as in silico analyses indicated that γECS and TryS control T(SH)2 synthesis by 60–74% and 15–31%, respectively. γECS overexpression prompted up to a 3.5-fold increase in T(SH)2 concentration, whereas TryS overexpression did not render an increase in T(SH)2 levels as a consequence of high T(SH)2 degradation. The peroxide reduction flux was controlled for 64–73% by TXN1, 17–20% by TXNPx and 11–16% by TryR. TXN1 and TryR overexpression increased H2O2 resistance, whereas TXN1 overexpression increased resistance to the benznidazole plus buthionine sulfoximine combination. γECS overexpression led to an increase in infectivity capacity whereas that of TXN increased trypomastigote bursting. The present data suggested that inhibition of high controlling enzymes such as γECS and TXN1 in the T(SH)2 antioxidant pathway may compromise the parasite's viability and infectivity. The trypanothione synthesis flux is primarily but not exclusively controlled by γECS. Tryparedoxin exerts high control on the peroxide reduction flux. Kinetic metabolic modeling may reliably predict the in vivo pathway behavior. TXN1 overexpression provides benznidazole resistance. γECS and TXN contribute to parasite infectivity.
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9
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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10
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Abstract
Glycolysis, the breakdown of glucose, is one of the most conserved and extensively studied biochemical pathways. Designing principles from chemistry and thermodynamics allow for energy production, biosynthesis and cellular communication. However, the kinetics or metabolic flux through the pathway also determines its function. Recently, there have been numerous developments that establish new allosteric interactions of glycolytic enzymes with small molecule metabolites and other mechanisms that may cooperate to allow for addition complex regulation of glycolysis. This review surveys these newfound sources of glycolysis regulation and discusses their possible roles in establishing kinetic design principles of glycolysis.
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Affiliation(s)
- Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
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11
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Saidin S, Othman N, Noordin R. In Vitro Testing of Potential Entamoeba histolytica Pyruvate Phosphate Dikinase Inhibitors. Am J Trop Med Hyg 2017; 97:1204-1213. [PMID: 28820699 DOI: 10.4269/ajtmh.17-0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Adverse effects and resistance to metronidazole have motivated the search for new antiamoebic agents against Entamoeba histolytica. Control of amoeba growth may be achieved by inhibiting the function of the glycolytic enzyme and pyruvate phosphate dikinase (PPDK). In this study, we screened 10 compounds using an in vitro PPDK enzyme assay. These compounds were selected from a virtual screening of compounds in the National Cancer Institute database. The antiamoebic activity of the selected compounds was also evaluated by determining minimal inhibitory concentrations (MICs) and IC50 values using the nitro-blue tetrazolium reduction assay. Seven of the 10 compounds showed inhibitory activities against the adenosine triphosphate (ATP)/inorganic phosphate binding site of the ATP-grasp domain. Two compounds, NSC349156 (pancratistatin) and NSC228137 (7-ethoxy-4-[4-methylphenyl] sulfonyl-3-oxido-2, 1, 3-benzoxadiazol-3-ium), exhibited inhibitory effects on the growth of E. histolytica trophozoites with MIC values of 25 and 50 μM, and IC50 values of 14 and 20.7 μM, respectively.
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Affiliation(s)
- Syazwan Saidin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Nurulhasanah Othman
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
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12
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Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. Int J Mol Sci 2017; 18:ijms18040876. [PMID: 28425930 PMCID: PMC5412457 DOI: 10.3390/ijms18040876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 11/25/2022] Open
Abstract
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5′-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.
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Affiliation(s)
- Yanfei Zhang
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
| | - Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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13
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He F, Murabito E, Westerhoff HV. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. J R Soc Interface 2016; 13:rsif.2015.1046. [PMID: 27075000 DOI: 10.1098/rsif.2015.1046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/21/2016] [Indexed: 12/25/2022] Open
Abstract
Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.
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Affiliation(s)
- Fei He
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Ettore Murabito
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK
| | - Hans V Westerhoff
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK Department of Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands Department of Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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14
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Prati F, Bergamini C, Molina MT, Falchi F, Cavalli A, Kaiser M, Brun R, Fato R, Bolognesi ML. 2-Phenoxy-1,4-naphthoquinones: From a Multitarget Antitrypanosomal to a Potential Antitumor Profile. J Med Chem 2015; 58:6422-34. [DOI: 10.1021/acs.jmedchem.5b00748] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Federica Prati
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Christian Bergamini
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Teresa Molina
- Instituto de Química Médica (IQM-CSIC), c/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Federico Falchi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Andrea Cavalli
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Marcel Kaiser
- Swiss Tropical & Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz
1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical & Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz
1, 4003 Basel, Switzerland
| | - Romana Fato
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
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15
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Hassan IA, Wang S, Xu L, Yan R, Song X, XiangRui L. Immunological response and protection of mice immunized with plasmid encodingToxoplasma gondiiglycolytic enzyme malate dehydrogenase. Parasite Immunol 2014; 36:674-83. [DOI: 10.1111/pim.12146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/16/2014] [Indexed: 12/31/2022]
Affiliation(s)
- I. A. Hassan
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
| | - S. Wang
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
| | - L. Xu
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
| | - R. Yan
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
| | - X. Song
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
| | - L. XiangRui
- Key Laboratory of Animal Diseases Diagnosis and Immunology; Ministry of Agriculture; College of Veterinary Medicine; Nanjing Agricultural University; Nanjing Jiangsu China
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16
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Parasite aquaporins: Current developments in drug facilitation and resistance. Biochim Biophys Acta Gen Subj 2014; 1840:1566-73. [DOI: 10.1016/j.bbagen.2013.10.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 10/02/2013] [Accepted: 10/06/2013] [Indexed: 01/15/2023]
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17
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Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W. Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One 2013; 8:e79195. [PMID: 24324546 PMCID: PMC3852239 DOI: 10.1371/journal.pone.0079195] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 09/19/2013] [Indexed: 12/24/2022] Open
Abstract
The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments.
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Affiliation(s)
- Natalie J. Stanford
- School of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
- * E-mail:
| | - Timo Lubitz
- Institut für Biologie, Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kieran Smallbone
- School of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
| | - Edda Klipp
- Institut für Biologie, Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pedro Mendes
- School of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
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18
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Reis M, Alves CN, Lameira J, Tuñón I, Martí S, Moliner V. The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach. Phys Chem Chem Phys 2013; 15:3772-85. [PMID: 23389436 DOI: 10.1039/c3cp43968b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular mechanical (QM/MM) potentials to obtain the Potential of Mean Force of the catalytic oxidative phosphorylation mechanism of the G3P substrate used by GAPDH. According to our results, the first stage of the reaction (oxidoreduction) takes place in the Pi site (energetically more favourable), with the formation of oxyanion thiohemiacetal and thioacylenzyme intermediates without acid-base assistance of His194. Analysis of the interaction energy by residues shows that Arg249 has an important role in the ability of the enzyme to bind the G3P substrate, which interacts with NAD+ and other important residues, such as Cys166, Glu109, Thr167, Ser247 and Thr226, in the GAPDH active site. Finally, the inhibition mechanism of the GAPDH enzyme by the 3-(p-nitrophenoxycarboxyl)-3-ethylene propyl dihydroxyphosphonate inhibitor was investigated in order to contribute to the design of new inhibitors of GAPDH from Trypanosoma cruzi.
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Affiliation(s)
- Mauro Reis
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110, Belém, PA, Brazil
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19
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Tymoshenko S, Oppenheim RD, Soldati-Favre D, Hatzimanikatis V. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics 2013; 12:316-27. [PMID: 23793264 PMCID: PMC3743259 DOI: 10.1093/bfgp/elt017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project in 2002 provided a comprehensive foundation for functional genomic studies on this pathogen in the following decade. Over this period, a large spectrum of experimental approaches has been deployed to improve and expand the scope of functionally annotated genes. Meanwhile, rapidly evolving methods of systems biology have also begun to contribute to a more global understanding of various aspects of the biology and pathogenesis of malaria. Herein we provide an overview on metabolic modelling, which has the capability to integrate information from functional genomics studies in P. falciparum and guide future malaria research efforts towards the identification of novel candidate drug targets.
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Affiliation(s)
- Stepan Tymoshenko
- Institute of Chemical Engineering, Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, CH-1015, Switzerland.
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20
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Sanchez MA. Molecular identification and characterization of an essential pyruvate transporter from Trypanosoma brucei. J Biol Chem 2013; 288:14428-14437. [PMID: 23569205 DOI: 10.1074/jbc.m113.473157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyruvate export is an essential physiological process for the bloodstream form of Trypanosoma brucei as the parasite would otherwise accumulate this end product of glucose metabolism to toxic levels. In the studies reported here, genetic complementation in Saccharomyces cerevisiae has been employed to identify a gene (TbPT0) that encodes this vital pyruvate transporter from T. brucei. Expression of TbPT0 in S. cerevisiae reveals that TbPT0 is a high affinity pyruvate transporter. TbPT0 belongs to a clustered multigene family consisting of five members, whose expression is up-regulated in the bloodstream form. Interestingly, TbPT family permeases are related to polytopic proteins from plants but not to characterized monocarboxylate transporters from mammals. Remarkably, inhibition of the TbPT gene family expression in bloodstream parasites by RNAi is lethal, confirming the physiological relevance of these transporters. The discovery of TbPT0 reveals for the first time the identity of the essential pyruvate transporter and provides a potential drug target against the mammalian life cycle stage of T. brucei.
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Affiliation(s)
- Marco A Sanchez
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239.
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21
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Beitz E. Aquaporins from pathogenic protozoan parasites: structure, function and potential for chemotherapy. Biol Cell 2012; 97:373-83. [PMID: 15901246 DOI: 10.1042/bc20040095] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Infectious diseases, caused by protozoa, such as malaria, sleeping sickness, Chagas' disease or leishmaniasis, are a global threat. The increase in the number of affected individuals and the rapid spread of drug-resistant strains call for specific novel strategies to combat human pathogenic parasites. In the search for novel drug targets, transport proteins for nutrients and metabolites of the parasite-host interface are getting into focus. The present review summarizes and discusses the currently available results on protozoan aquaporins. Various genes coding for aquaporin water and solute channels have been identified in the protozoan genomes and they are probable elements of the parasite's cell membrane. Phylogenetic analysis reveals that individual aquaporin genes are of bacterial or plant origin. So far, six protozoan aquaporins have been cloned and functionally characterized. Typically, these are bifunctional channels and pass water at intermediate to high rates as well as uncharged solutes. In the present review, amino acid compositions of the individual pore entries are compared and permeability properties are attributed to specific protein features. Furthermore, possible physiological roles in osmotic protection and metabolism are discussed. Finally, the potential of protozoan aquaporins for use as a target or entry pathway for chemotherapeutic compounds is reviewed.
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Affiliation(s)
- Eric Beitz
- Department of Pharmaceutical Chemistry, University of Tübingen, Morgenstelle 8, D-72076 Tübingen, Germany.
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22
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Murabito E, Smallbone K, Swinton J, Westerhoff HV, Steuer R. A probabilistic approach to identify putative drug targets in biochemical networks. J R Soc Interface 2011; 8:880-95. [PMID: 21123256 PMCID: PMC3104352 DOI: 10.1098/rsif.2010.0540] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/09/2010] [Indexed: 01/18/2023] Open
Abstract
Network-based drug design holds great promise in clinical research as a way to overcome the limitations of traditional approaches in the development of drugs with high efficacy and low toxicity. This novel strategy aims to study how a biochemical network as a whole, rather than its individual components, responds to specific perturbations in different physiological conditions. Proteins exerting little control over normal cells and larger control over altered cells may be considered as good candidates for drug targets. The application of network-based drug design would greatly benefit from using an explicit computational model describing the dynamics of the system under investigation. However, creating a fully characterized kinetic model is not an easy task, even for relatively small networks, as it is still significantly hampered by the lack of data about kinetic mechanisms and parameters values. Here, we propose a Monte Carlo approach to identify the differences between flux control profiles of a metabolic network in different physiological states, when information about the kinetics of the system is partially or totally missing. Based on experimentally accessible information on metabolic phenotypes, we develop a novel method to determine probabilistic differences in the flux control coefficients between the two observable phenotypes. Knowledge of how differences in flux control are distributed among the different enzymatic steps is exploited to identify points of fragility in one of the phenotypes. Using a prototypical cancerous phenotype as an example, we demonstrate how our approach can assist researchers in developing compounds with high efficacy and low toxicity.
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Affiliation(s)
- Ettore Murabito
- Doctoral Training Centre Integrative Systems Biology from Molecules to Life, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M60 1QD, UK
| | - Kieran Smallbone
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- School of Mathematics, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jonathan Swinton
- Computational Biology/Advanced Science and Technology Laboratory, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - Hans V. Westerhoff
- School of Mathematics, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Netherlands Institute for Systems Biology, FALW, VU University Amsterdam, De Boelelaan 1085, 1081, HV Amsterdam, The Netherlands
| | - Ralf Steuer
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M60 1QD, UK
- Institute for Theoretical Biology, Humboldt University of Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
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23
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Nutrient transport and pathogenesis in selected parasitic protozoa. EUKARYOTIC CELL 2011; 10:483-93. [PMID: 21216940 DOI: 10.1128/ec.00287-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Parasitic protozoa, such as malaria parasites, trypanosomes, and Leishmania, acquire a plethora of nutrients from their hosts, employing transport proteins located in the plasma membrane of the parasite. Application of molecular genetic approaches and the completion of genome projects have allowed the identification and functional characterization of a cohort of transporters and their genes in these parasites. This review focuses on a subset of these permeases that have been studied in some detail, that import critical nutrients, and that provide examples of approaches being undertaken broadly with these and other parasite transporters. Permeases reviewed include those for hexoses, purines, iron, polyamines, carboxylates, and amino acids. Topics of special emphasis include structure-function approaches, critical roles for transporters in parasite viability and physiology, regulation of transporter expression, and subcellular targeting. Investigations of parasite transporters impact a broad spectrum of basic biological problems in these protozoa.
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24
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Mathematical modeling: bridging the gap between concept and realization in synthetic biology. J Biomed Biotechnol 2010; 2010:541609. [PMID: 20589069 PMCID: PMC2878679 DOI: 10.1155/2010/541609] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 03/07/2010] [Indexed: 11/17/2022] Open
Abstract
Mathematical modeling plays an important and often indispensable role in synthetic biology because it serves as a crucial link between the concept and realization of a biological circuit. We review mathematical modeling concepts and methodologies as relevant to synthetic biology, including assumptions that underlie a model, types of modeling frameworks (deterministic and stochastic), and the importance of parameter estimation and optimization in modeling. Additionally we expound mathematical techniques used to analyze a model such as sensitivity analysis and bifurcation analysis, which enable the identification of the conditions that cause a synthetic circuit to behave in a desired manner. We also discuss the role of modeling in phenotype analysis such as metabolic and transcription network analysis and point out some available modeling standards and software. Following this, we present three case studies—a metabolic oscillator, a synthetic counter, and a bottom-up gene regulatory network—which have incorporated mathematical modeling as a central component of synthetic circuit design.
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25
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Abstract
Glucose and related hexoses play central roles in the biochemistry and metabolism of single-cell parasites such as Leishmania, Trypanosoma, and Plasmodium that are the causative agents of leishmaniasis, African sleeping sickness, and malaria. Glucose transporters and the genes that encode them have been identified in each of these parasites and their functional properties have been scrutinized. These transporters are related in sequence and structure to mammalian facilitative glucose transporters of the SLC2 family, but they are nonetheless quite divergent in sequence. Hexose transporters have been shown to be essential for the viability of the infectious stage of each of these parasites and thus may represent targets for development of novel anti-parasitic drugs. The study of these transporters also illuminates many aspects of the basic biology of Leishmania, trypanosomes, and malaria parasites.
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26
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Aguirre-Alvarado C, Zaragoza-Martínez F, Rodríguez-Páez L, Téllez-Rendón JL, Nogueda B, Baeza I, Wong C. Trypanocidal activity of the ethyl esters of N-propyl and N-isopropyl oxamates on intracellular amastigotes of Trypanosoma cruzi acute infected mice. J Enzyme Inhib Med Chem 2009; 25:111-5. [DOI: 10.3109/14756360903027741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Charmina Aguirre-Alvarado
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Fabiola Zaragoza-Martínez
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Lorena Rodríguez-Páez
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Juan Luis Téllez-Rendón
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Benjamín Nogueda
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Isabel Baeza
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
| | - Carlos Wong
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas–Instituto Politécnico Nacional, Mexico City, Mexico
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27
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Frayne J, Taylor A, Cameron G, Hadfield AT. Structure of insoluble rat sperm glyceraldehyde-3-phosphate dehydrogenase (GAPDH) via heterotetramer formation with Escherichia coli GAPDH reveals target for contraceptive design. J Biol Chem 2009; 284:22703-12. [PMID: 19542219 PMCID: PMC2755679 DOI: 10.1074/jbc.m109.004648] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/21/2009] [Indexed: 11/06/2022] Open
Abstract
Sperm glyceraldehyde-3-phosphate dehydrogenase has been shown to be a successful target for a non-hormonal contraceptive approach, but the agents tested to date have had unacceptable side effects. Obtaining the structure of the sperm-specific isoform to allow rational inhibitor design has therefore been a goal for a number of years but has proved intractable because of the insoluble nature of both native and recombinant protein. We have obtained soluble recombinant sperm glyceraldehyde-3-phosphate dehydrogenase as a heterotetramer with the Escherichia coli glyceraldehyde-3-phosphate dehydrogenase in a ratio of 1:3 and have solved the structure of the heterotetramer which we believe represents a novel strategy for structure determination of an insoluble protein. A structure was also obtained where glyceraldehyde 3-phosphate binds in the P(s) pocket in the active site of the sperm enzyme subunit in the presence of NAD. Modeling and comparison of the structures of human somatic and sperm-specific glyceraldehyde-3-phosphate dehydrogenase revealed few differences at the active site and hence rebut the long presumed structural specificity of 3-chlorolactaldehyde for the sperm isoform. The contraceptive activity of alpha-chlorohydrin and its apparent specificity for the sperm isoform in vivo are likely to be due to differences in metabolism to 3-chlorolactaldehyde in spermatozoa and somatic cells. However, further detailed analysis of the sperm glyceraldehyde-3-phosphate dehydrogenase structure revealed sites in the enzyme that do show significant difference compared with published somatic glyceraldehyde-3-phosphate dehydrogenase structures that could be exploited by structure-based drug design to identify leads for novel male contraceptives.
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Affiliation(s)
- Jan Frayne
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Abby Taylor
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Gus Cameron
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Andrea T. Hadfield
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
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28
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Penha LL, Sant'Anna CB, Mendonça-Previato L, Cunha-e-Silva NL, Previato JO, Lima APCA. Sorting of phosphoglucomutase to glycosomes in Trypanosoma cruzi is mediated by an internal domain. Glycobiology 2009; 19:1462-72. [PMID: 19696235 DOI: 10.1093/glycob/cwp121] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trypanosoma cruzi relies on highly galactosylated molecules as virulence factors and the enzymes involved in sugar biosynthesis are potential therapeutic targets. The synthesis of UDP-galactose in T. cruzi requires the activity of phosphoglucomutase (PGM), the enzyme that catalyzes the interconversion of glucose-6-phosphate and glucose-1-phosphate. Several enzymes that participate in carbohydrate metabolism in trypanosomes are confined to specialized peroxisome-like organelles called glycosomes. The majority of glycosomal proteins contain peroxisome-targeting signals (PTS) at the COOH- or at the amino-terminus, which drive their transport to glycosomes. We had previously identified the T. cruzi PGM gene (TcPGM) and demonstrated that it encodes a functional enzyme. Here, we show that, in contrast to yeast and mammalian cells, TcPGM resides in glycosomes of the parasite. However, no classical PTS1 or PTS2 motif is present in its sequence. We investigated glycosomal targeting by generating T. cruzi cell lines expressing different domains of TcPGM fused to the green fluorescent protein (GFP). The analysis of the subcellular localization of fusion proteins revealed that an internal targeting signal of TcPGM, residing between amino acid residues 260 and 380, is capable of targeting GFP to glycosomes. These results demonstrate that, in T. cruzi, PGM import into glycosomes is mediated by a novel non-PTS domain that is located internally in the protein.
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Affiliation(s)
- Luciana L Penha
- Instituto de Biofísica Carlos Chagas Filho, Centro de Ciências da Saúde, Bloco G, Universidade Federal do Rio de Janeiro, 21 944 970, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
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29
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Glucose uptake in the mammalian stages of Trypanosoma cruzi. Mol Biochem Parasitol 2009; 168:102-8. [PMID: 19631694 DOI: 10.1016/j.molbiopara.2009.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 07/14/2009] [Accepted: 07/15/2009] [Indexed: 02/06/2023]
Abstract
Trypanosoma cruzi, the agent of Chagas' disease, alternates between different morphogenetic stages that face distinct physiological conditions in their invertebrate and vertebrate hosts, likely in the availability of glucose. While the glucose transport is well characterized in epimastigotes of T. cruzi, nothing is known about how the mammalian stages acquire this molecule. Herein glucose transport activity and expression were analyzed in the three developmental stages present in the vertebrate cycle of T. cruzi. The infective trypomastigotes showed the highest transport activity (V(max)=5.34+/-0.54 nmol/min per mg of protein; K(m)=0.38+/-0.01 mM) when compared to intracellular epimastigotes (V(max)=2.18+/-0.20 nmol/min per mg of protein; K(m)=0.39+/-0.01 mM). Under the conditions employed no transport activity could be detected in amastigotes. The gene of the glucose transporter is expressed at the mRNA level in trypomastigotes and in intracellular epimastigotes but not in amastigotes, as revealed by real-time PCR. In both trypomastigotes and intracellular epimastigotes protein expression could be detected by Western blot with an antibody raised against the glucose transporter correlating well with the transport activity measured experimentally. Interestingly, anti-glucose transporter antibodies showed a strong reactivity with glycosome and reservosome organelles. A comparison between proline and glucose transport among the intracellular differentiation forms is presented. The data suggest that the regulation of glucose transporter reflects different energy and carbon requirements along the intracellular life cycle of T. cruzi.
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30
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Navid A, Ghim CM, Fenley AT, Yoon S, Lee S, Almaas E. Systems biology of microbial communities. Methods Mol Biol 2009; 500:469-94. [PMID: 19399434 DOI: 10.1007/978-1-59745-525-1_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.
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Affiliation(s)
- Ali Navid
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, CA, USA
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31
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Comparative molecular docking of antitrypanosomal natural products into multiple Trypanosoma brucei drug targets. Molecules 2009; 14:1513-36. [PMID: 19384282 PMCID: PMC6254181 DOI: 10.3390/molecules14041513] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 01/28/2023] Open
Abstract
Antitrypanosomal natural products with different structural motifs previously shown to have growth inhibitory activity against Trypanosoma brucei were docked into validated drug targets of the parasite, which include trypanothione reductase, rhodesain, farnesyl diphosphate synthase, and triosephosphate isomerase. The in-silico calculations predicted that lowest energy docked poses of a number of the compounds can interact with catalysis-dependent residues, thus making them possible catalytic inhibitors and of course physiologically active. Compounds that possess a number of hydrogen-bond-accepting and/or -donating groups like phenolics and quinones show extensive interactions with the targets. Compounds like cissampeloflavone, 3-geranylemodin and ningpogenin thus offer profound promise.
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32
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Arsenieva D, Appavu BL, Mazock GH, Jeffery CJ. Crystal structure of phosphoglucose isomerase fromTrypanosoma bruceicomplexed with glucose-6-phosphate at 1.6 Å resolution. Proteins 2009; 74:72-80. [DOI: 10.1002/prot.22133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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33
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Abstract
Probably one of the most characteristic features of a living system is its continual propensity to change as it juggles the demands of survival with the need to replicate. Internally these adjustments are manifest as changes in metabolite, protein, and gene activities. Such changes have become increasingly obvious to experimentalists, with the advent of high-throughput technologies. In this chapter we highlight some of the quantitative approaches used to rationalize the study of cellular dynamics. The chapter focuses attention on the analysis of quantitative models based on differential equations using biochemical control theory. Basic pathway motifs are discussed, including straight chain, branched, and cyclic systems. In addition, some of the properties conferred by positive and negative feedback loops are discussed, particularly in relation to bistability and oscillatory dynamics.
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Affiliation(s)
- Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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Metabolic control analysis: a tool for designing strategies to manipulate metabolic pathways. J Biomed Biotechnol 2008; 2008:597913. [PMID: 18629230 PMCID: PMC2447884 DOI: 10.1155/2008/597913] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 01/16/2008] [Accepted: 03/26/2008] [Indexed: 02/06/2023] Open
Abstract
The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when is working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.
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da Silva R, Saraiva J, de Albuquerque S, Curti C, Donate PM, Bianco TNC, Bastos JK, Silva MLA. Trypanocidal structure-activity relationship for cis- and trans-methylpluviatolide. PHYTOCHEMISTRY 2008; 69:1890-1894. [PMID: 18479721 DOI: 10.1016/j.phytochem.2008.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 02/08/2008] [Accepted: 04/02/2008] [Indexed: 05/26/2023]
Abstract
The trypanocidal activity of racemic mixtures of cis- and trans-methylpluviatolides was evaluated in vitro against trypomastigote forms of two strains of Trypanosoma cruzi, and in the enzymatic assay of T. cruzi gGAPDH. The cytotoxicity of the compounds was assessed by the MTT method using LLC-MK2 cells. The effect of the compounds on peroxide and NO production were also investigated. The mixture of the trans stereoisomers displayed trypanocidal activity (IC50 approximately 89.3 microM). Therefore, it was separated by chiral HPLC, furnishing the (+) and (-)-enantiomers. Only the (-)-enantiomer was active against the parasite (IC50 approximately 18.7 microM). Despite being inactive, the (+)-enantiomer acted as an antagonistic competitor. Trans-methylpluviatolide displayed low toxicity for LLC-MK2 cells, with an IC50 of 6.53 mM. Furthermore, methylpluviatolide neither inhibited gGAPDH activity nor hindered peroxide and NO production at the evaluated concentrations.
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Affiliation(s)
- R da Silva
- Núcleo de Ciências Exatas e Tecnológicas, Universidade de Franca, Avenida Dr. Armando Salles de Oliveira, 2001, 14404-600 Franca, SP, Brazil
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Cardoso CL, de Moraes MC, Carvalho Guido RV, Oliva G, Andricopulo AD, Wainer IW, Cass QB. The development of an immobilized enzyme reactor containing glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi: the effect of species' specific differences on the immobilization. Analyst 2008; 133:93-9. [DOI: 10.1039/b711145b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Saavedra E, Marín-Hernández A, Encalada R, Olivos A, Mendoza-Hernández G, Moreno-Sánchez R. Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica. FEBS J 2007; 274:4922-40. [PMID: 17824961 DOI: 10.1111/j.1742-4658.2007.06012.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Glycolysis in the human parasite Entamoeba histolytica is characterized by the absence of cooperative modulation and the prevalence of pyrophosphate-dependent (over ATP-dependent) enzymes. To determine the flux-control distribution of glycolysis and understand its underlying control mechanisms, a kinetic model of the pathway was constructed by using the software gepasi. The model was based on the kinetic parameters determined in the purified recombinant enzymes, and the enzyme activities, and steady-state fluxes and metabolite concentrations determined in amoebal trophozoites. The model predicted, with a high degree of accuracy, the flux and metabolite concentrations found in trophozoites, but only when the pyrophosphate concentration was held constant; at variable pyrophosphate, the model was not able to completely account for the ATP production/consumption balance, indicating the importance of the pyrophosphate homeostasis for amoebal glycolysis. Control analysis by the model revealed that hexokinase exerted the highest flux control (73%), as a result of its low cellular activity and strong AMP inhibition. 3-Phosphoglycerate mutase also exhibited significant flux control (65%) whereas the other pathway enzymes showed little or no control. The control of the ATP concentration was also mainly exerted by ATP consuming processes and 3-phosphoglycerate mutase and hexokinase (in the producing block). The model also indicated that, in order to diminish the amoebal glycolytic flux by 50%, it was required to decrease hexokinase or 3-phosphoglycerate mutase by 24% and 55%, respectively, or by 18% for both enzymes. By contrast, to attain the same reduction in flux by inhibiting the pyrophosphate-dependent enzymes pyrophosphate-phosphofructokinase and pyruvate phosphate dikinase, they should be decreased > 70%. On the basis of metabolic control analysis, steps whose inhibition would have stronger negative effects on the energy metabolism of this parasite were identified, thus becoming alternative targets for drug design.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México DF, México.
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Pinney JW, Papp B, Hyland C, Wambua L, Westhead DR, McConkey GA. Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol 2007; 23:548-54. [PMID: 17950669 DOI: 10.1016/j.pt.2007.08.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 08/20/2007] [Accepted: 08/20/2007] [Indexed: 01/29/2023]
Abstract
With the completion of sequencing projects for several parasite genomes, efforts are ongoing to make sense of this mass of information in terms of the gene products encoded and their interactions in the growth, development and survival of parasites. The emerging science of systems biology aims to explain the complex relationship between genotype and phenotype by using network models. One area in which this approach has been particularly successful is in the modeling of metabolism. With an accurate picture of the set of metabolic reactions encoded in a genome, it is now possible to identify enzymes or transporters that might be viable targets for new drugs. Because these predictions greatly depend on the quality and completeness of the genome annotation, there are substantial efforts in the scientific community to increase the numbers of metabolic enzymes identified. In this review, we discuss the opportunities for using metabolic reconstruction and analysis tools in parasitology research, and their applications to protozoan parasites.
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Affiliation(s)
- John W Pinney
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK
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39
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Hornberg JJ, Bruggeman FJ, Bakker BM, Westerhoff HV. Metabolic control analysis to identify optimal drug targets. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:171, 173-89. [PMID: 17195475 DOI: 10.1007/978-3-7643-7567-6_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This chapter describes the basic principles of Metabolic Control Analysis (MCA) which is a quantitative methodology to evaluate the importance and relative contribution of individual metabolic steps in the overall functioning of a particular system. The control on the flux through a metabolic pathway or subsystem can be quantified by the control coefficients of the individual enzymes or components which reflects the extent to which the component is rate-limiting. The perturbation of an individual step is measured by its elasticity coefficient. The effect of perturbation of a single step on the entire pathway or subsystem is, in turn, measured by the response coefficient. Differential control analysis can be used to compare flux through a single metabolic pathway in a pathogen with the same pathway in its host to identify uniquely vulnerable steps with the greatest potential for specifically inhibiting flux through the pathogen metabolic pathway. The utility of this methodology is illustrated with the glycolysis in Trypanosomes and with oncogenic signaling.
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Affiliation(s)
- Jorrit J Hornberg
- Department of Molecular Cell Physiology, Institute for Molecular Cell Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
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40
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Barrett MP, Gilbert IH. Targeting of toxic compounds to the trypanosome's interior. ADVANCES IN PARASITOLOGY 2006; 63:125-83. [PMID: 17134653 DOI: 10.1016/s0065-308x(06)63002-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Drugs can be targeted into African trypanosomes by exploiting carrier proteins at the surface of these parasites. This has been clearly demonstrated in the case of the melamine-based arsenical and the diamidine classes of drug that are already in use in the treatment of human African trypanosomiasis. These drugs can enter via an aminopurine transporter, termed P2, encoded by the TbAT1 gene. Other toxic compounds have also been designed to enter via this transporter. Some of these compounds enter almost exclusively through the P2 transporter, and hence loss of the P2 transporter leads to significant resistance to these particular compounds. It now appears, however, that some diamidines and melaminophenylarsenicals may also be taken up by other routes (of yet unknown function). These too may be exploited to target new drugs into trypanosomes. Additional purine nucleoside and nucleobase transporters have also been subverted to deliver toxic agents to trypanosomes. Glucose and amino acid transporters too have been investigated with a view to manipulating them to carry toxins into Trypanosoma brucei, and recent work has demonstrated that aquaglyceroporins may also have considerable potential for drug-targeting. Transporters, including those that carry lipids and vitamins such as folate and other pterins also deserve more attention in this regard. Some drugs, for example suramin, appear to enter via routes other than plasma-membrane-mediated transport. Receptor-mediated endocytosis has been proposed as a possible way in for suramin. Endocytosis also appears to be crucial in targeting natural trypanocides, such as trypanosome lytic factor (TLF) (apolipoprotein L1), into trypanosomes and this offers an alternative means of selectively targeting toxins to the trypanosome's interior. Other compounds may be induced to enter by increasing their capacity to diffuse over cell membranes; in this case depending exclusively on selective activity within the cell rather than selective uptake to impart selective toxicity. This review outlines studies that have aimed to exploit trypanosome nutrient uptake routes to selectively carry toxins into these parasites.
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Affiliation(s)
- Michael P Barrett
- Division of Infection & Immunity, Institute of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8QQ, UK
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41
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Galkin A, Kulakova L, Melamud E, Li L, Wu C, Mariano P, Dunaway-Mariano D, Nash TE, Herzberg O. Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia. J Biol Chem 2006; 282:4859-4867. [PMID: 17166851 DOI: 10.1074/jbc.m609534200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Class I and class II fructose-1,6-bisphosphate aldolases (FBPA), glycolytic pathway enzymes, exhibit no amino acid sequence homology and utilize two different catalytic mechanisms. The mammalian class I FBPA employs a Schiff base mechanism, whereas the human parasitic protozoan Giardia lamblia class II FBPA is a zinc-dependent enzyme. In this study, we have explored the potential exploitation of the Giardia FBPA as a drug target. First, synthesis of FBPA was demonstrated in Giardia trophozoites by using an antibody-based fluorescence assay. Second, inhibition of FBPA gene transcription in Giardia trophozoites suggested that the enzyme is necessary for the survival of the organism under optimal laboratory growth conditions. Third, two crystal structures of FBPA in complex with the transition state analog phosphoglycolohydroxamate (PGH) show that the enzyme is homodimeric and that its active site contains a zinc ion. In one crystal form, each subunit contains PGH, which is coordinated to the zinc ion through the hydroxamic acid hydroxyl and carbonyl oxygen atoms. The second crystal form contains PGH only in one subunit and the active site of the second subunit is unoccupied. Inspection of the two states of the enzyme revealed that it undergoes a conformational transition upon ligand binding. The enzyme cleaves d-fructose-1,6-bisphosphate but not d-tagatose-1,6-bisphosphate, which is a tight binding competitive inhibitor. The essential role of the active site residue Asp-83 in catalysis was demonstrated by amino acid replacement. Determinants of catalysis and substrate recognition, derived from comparison of the G. lamblia FBPA structure with Escherichia coli FBPA and with a closely related enzyme, E. coli tagatose-1,6-bisphosphate aldolase (TBPA), are described.
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Affiliation(s)
- Andrey Galkin
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850
| | - Liudmila Kulakova
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850
| | - Eugene Melamud
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850
| | - Ling Li
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Chun Wu
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Patrick Mariano
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Debra Dunaway-Mariano
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Theodore E Nash
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Osnat Herzberg
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850.
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Boshoff HIM, Manjunatha UH. The impact of genomics on discovering drugs against infectious diseases. Microbes Infect 2006; 8:1654-61. [PMID: 16690340 DOI: 10.1016/j.micinf.2005.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 11/30/2005] [Indexed: 01/30/2023]
Abstract
Genomics is accelerating the progress in data generation and interpretation in the global analyses of components of cells, including the spectrum of lipids, RNA, metabolites, proteins, mutational phenotypes or DNA methylation sites. Integration of the knowledge generated by these diverse strategies is predicted to have a tremendous impact on approaches to rational drug discovery against infectious diseases.
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Affiliation(s)
- Helena I M Boshoff
- National Institutes of Health, Tuberculosis Research Section, LIG/NIAID/NIH, Twinbrook II, Room 239, 12441 Parklawn Drive, Rockville, MD 20852, USA.
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43
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Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J. Cancer: a Systems Biology disease. Biosystems 2006; 83:81-90. [PMID: 16426740 DOI: 10.1016/j.biosystems.2005.05.014] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 04/15/2005] [Accepted: 05/26/2005] [Indexed: 12/01/2022]
Abstract
Cancer research has focused on the identification of molecular differences between cancerous and healthy cells. The emerging picture is overwhelmingly complex. Molecules out of many parallel signal transduction pathways are involved. Their activities appear to be controlled by multiple factors. The action of regulatory circuits, cross-talk between pathways and the non-linear reaction kinetics of biochemical processes complicate the understanding and prediction of the outcome of intracellular signaling. In addition, interactions between tumor and other cell types give rise to a complex supra-cellular communication network. If cancer is such a complex system, how can one ever predict the effect of a mutation in a particular gene on a functionality of the entire system? And, how should one go about identifying drug targets? Here, we argue that one aspect is to recognize, where the essence resides, i.e. recognize cancer as a Systems Biology disease. Then, more cancer biologists could become systems biologists aiming to provide answers to some of the above systemic questions. To this aim, they should integrate the available knowledge stemming from quantitative experimental results through mathematical models. Models that have contributed to the understanding of complex biological systems are discussed. We show that the architecture of a signaling network is important for determining the site at which an oncologist should intervene. Finally, we discuss the possibility of applying network-based drug design to cancer treatment and how rationalized therapies, such as the application of kinase inhibitors, may benefit from Systems Biology.
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Affiliation(s)
- Jorrit J Hornberg
- Department of Molecular Cell Physiology, Institute for Molecular Cell Biology, BioCentrum Amsterdam, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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44
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Cardoso CL, Lima VV, Zottis A, Oliva G, Andricopulo AD, Wainer IW, Moaddel R, Cass QB. Development and characterization of an immobilized enzyme reactor (IMER) based on human glyceraldehyde-3-phosphate dehydrogenase for on-line enzymatic studies. J Chromatogr A 2005; 1120:151-7. [PMID: 16297925 DOI: 10.1016/j.chroma.2005.10.063] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 10/25/2005] [Accepted: 10/31/2005] [Indexed: 11/17/2022]
Abstract
Immobilized enzyme reactors (IMERs) for on-line enzymatic studies are useful tool to select specific inhibitors and may be used for direct determination of drug-receptor binding interactions and for the rapid on-line screening to identify specific inhibitors. This technique has been shown to increase the stability of enzymes. The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in the life cycle of the Trypanosoma cruzi and it has become a key target in the drug discovery program for Chagas' disease. Crystallographic studies have indicated that there are significant inter-species differences in GAPDH activity and sensitivity. For example the active sites of GAPDH in T. cruzi and humans differ by a substitution of ASP(210) (T. cruzi) by Leu(194) in human. Based on this information we initiated the study to develop optimal conditions for the covalent immobilization of the human GAPDH enzyme on a modified capillary support (400 mm x 0.10 mm). The chromatographic separation of NAD from NADH was achieved using a RP-Spherex-diol-OH (10 cm x 0.46 cm, 10 microm, 100 A) column. By using multidimensional HPLC chromatography system it was possible to investigate the activity and kinetic parameters of the GAPDH-IMER. The values obtained for D-GA3P and NAD were K(m)=3.5+/-0.2 mM and 0.75+/-0.04 mM, respectively, and were compared with values obtained with the free enzyme. The activity of the immobilized GAPDH has been preserved for over 120 days.
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Affiliation(s)
- Carmem L Cardoso
- Departamento de Química, Universidade Federal de São Carlos Cx. Postal 676, São Carlos 13565-905 SP, Brazil
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45
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Albert MA, Haanstra JR, Hannaert V, Van Roy J, Opperdoes FR, Bakker BM, Michels PAM. Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei. J Biol Chem 2005; 280:28306-15. [PMID: 15955817 DOI: 10.1074/jbc.m502403200] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mathematical model of glycolysis in bloodstream form Trypanosoma brucei was developed previously on the basis of all available enzyme kinetic data (Bakker, B. M., Michels, P. A. M., Opperdoes, F. R., and Westerhoff, H. V. (1997) J. Biol. Chem. 272, 3207-3215). The model predicted correctly the fluxes and cellular metabolite concentrations as measured in non-growing trypanosomes and the major contribution to the flux control exerted by the plasma membrane glucose transporter. Surprisingly, a large overcapacity was predicted for hexokinase (HXK), phosphofructokinase (PFK), and pyruvate kinase (PYK). Here, we present our further analysis of the control of glycolytic flux in bloodstream form T. brucei. First, the model was optimized and extended with recent information about the kinetics of enzymes and their activities as measured in lysates of in vitro cultured growing trypanosomes. Second, the concentrations of five glycolytic enzymes (HXK, PFK, phosphoglycerate mutase, enolase, and PYK) in trypanosomes were changed by RNA interference. The effects of the knockdown of these enzymes on the growth, activities, and levels of various enzymes and glycolytic flux were studied and compared with model predictions. Data thus obtained support the conclusion from the in silico analysis that HXK, PFK, and PYK are in excess, albeit less than predicted. Interestingly, depletion of PFK and enolase had an effect on the activity (but not, or to a lesser extent, expression) of some other glycolytic enzymes. Enzymes located both in the glycosomes (the peroxisome-like organelles harboring the first seven enzymes of the glycolytic pathway of trypanosomes) and in the cytosol were affected. These data suggest the existence of novel regulatory mechanisms operating in trypanosome glycolysis.
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Affiliation(s)
- Marie-Astrid Albert
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
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Saavedra E, Encalada R, Pineda E, Jasso-Chávez R, Moreno-Sánchez R. Glycolysis in Entamoeba histolytica. Biochemical characterization of recombinant glycolytic enzymes and flux control analysis. FEBS J 2005; 272:1767-83. [PMID: 15794763 DOI: 10.1111/j.1742-4658.2005.04610.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The synthesis of ATP in the human parasite Entamoeba histolytica is carried out solely by the glycolytic pathway. Little kinetic and structural information is available for most of the pathway enzymes. We report here the gene cloning, overexpression and purification of hexokinase, hexose-6-phosphate isomerase, inorganic pyrophosphate-dependent phosphofructokinase, fructose-1,6 bisphosphate aldolase (ALDO), triosephosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase, phosphoglycerate mutase (PGAM), enolase, and pyruvate phosphate dikinase (PPDK) enzymes from E. histolytica. Kinetic characterization of these 10 recombinant enzymes was made, establishing the kinetic constants at optimal and physiological pH values, analyzing the effect of activators and inhibitors, and investigating the storage stability and oligomeric state. Determination of the catalytic efficiencies at the pH optimum and at pH values that resemble those of the amoebal trophozoites was performed for each enzyme to identify possible controlling steps. This analysis suggested that PGAM, ALDO, GAPDH, and PPDK might be flux control steps, as they showed the lowest catalytic efficiencies. An in vitro reconstruction of the final stages of glycolysis was made to determine their flux control coefficients. Our results indicate that PGAM and PPDK exhibit high control coefficient values at physiological pH.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Tlalpan, México DF, México.
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47
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Joët T, Morin C, Fischbarg J, Louw AI, Eckstein-Ludwig U, Woodrow C, Krishna S. Why is the Plasmodium falciparum hexose transporter a promising new drug target? Expert Opin Ther Targets 2005; 7:593-602. [PMID: 14498822 DOI: 10.1517/14728222.7.5.593] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chemotherapy of malaria parasites is limited by established drug resistance and lack of novel treatment options. Intraerythrocytic stages of Plasmodium falciparum, the causative agent of severe malaria, are wholly dependent upon host glucose for energy. A facilitative hexose transporter (PfHT), encoded by a single-copy gene, mediates glucose uptake and is therefore an attractive potential target. The authors first established heterologous expression in Xenopus laevis to allow functional characterisation of PfHT. They then used this expression system to compare the interaction of substrates with PfHT and mammalian Gluts (hexose transporters) and identified important differences between host and parasite transporters. Certain Omethyl derivatives of glucose proved to be particularly useful discriminators between mammalian transporters and PfHT. The authors exploited this selectivity and synthesised an O-3 hexose derivative that potently inhibits PfHT expressed in oocytes. This O-3 derivative (compound 3361) also kills cultured P. falciparum with comparable potency. Compound 3361 acts with reasonable specificity against PfHT orthologues encoded by other parasites such as Plasmodium vivax, Plasmodium yoelii and Plasmodium knowlesi. Multiplication of Plasmodium berghei in a mouse model is also significantly impeded by this compound. These findings validate PfHT as a novel target.
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Affiliation(s)
- T Joët
- Department of Cellular and Molecular Medicine, Infectious Diseases, St George's Hospital Medical School, Cranmer Terrace, London, SW17 ORE, UK
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48
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Abstract
A 96-well plate assay has been devised for estimation of sublethal metabolic activity for compounds administered to in vitro cell cultures during 6- and 24-h exposures. This screen combines a resazurin reduction assay with lactate production and glucose consumption rate assays to assess effects of compounds on both culture viability and metabolic inhibition. In this article, the assay is demonstrated by determining the extent to which five glycolysis inhibitors, namely, phloretin, 2-deoxyglucose, iodoacetate, fluoride, and oxamate, induce metabolic inhibition without cell death for in vitro fibroblast cell cultures. During 6-h exposures, iodoacetate was found to be the most potent inhibitor of glycolysis, whereas iodoacetate and phloretin were most cytolethal. 2-Deoxyglucose had the largest sublethal metabolic range, spanning just over two orders of magnitude in concentrations between its IC(50) values for cytolethality and metabolic inhibition. This method provides a simple and inexpensive way to determine global metabolic and cytolethal effects of compounds for in vitro cell culture systems. It should be of use directly for large-scale screening and ranking of compounds during drug discovery and development, in conjunction with or following some more direct measure of therapeutic efficacy of a prospective drug candidate. Moreover, firsthand determination of the concentrations over which a compound has lethal, sublethal metabolic, or no such effects should serve as a cost-effective and time-saving first step in a given research study, preceding more expensive, lengthy, and/or detailed in vitro methods.
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Affiliation(s)
- Yuansheng Yang
- Department of Chemical Engineering, Vanderbilt University, Nashville, TN, USA
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49
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Moyersoen J, Choe J, Fan E, Hol WGJ, Michels PAM. Biogenesis of peroxisomes and glycosomes: trypanosomatid glycosome assembly is a promising new drug target. FEMS Microbiol Rev 2005; 28:603-43. [PMID: 15539076 DOI: 10.1016/j.femsre.2004.06.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 06/14/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022] Open
Abstract
In trypanosomatids (Trypanosoma and Leishmania), protozoa responsible for serious diseases of mankind in tropical and subtropical countries, core carbohydrate metabolism including glycolysis is compartmentalized in peculiar peroxisomes called glycosomes. Proper biogenesis of these organelles and the correct sequestering of glycolytic enzymes are essential to these parasites. Biogenesis of glycosomes in trypanosomatids and that of peroxisomes in other eukaryotes, including the human host, occur via homologous processes involving proteins called peroxins, which exert their function through multiple, transient interactions with each other. Decreased expression of peroxins leads to death of trypanosomes. Peroxins show only a low level of sequence conservation. Therefore, it seems feasible to design compounds that will prevent interactions of proteins involved in biogenesis of trypanosomatid glycosomes without interfering with peroxisome formation in the human host cells. Such compounds would be suitable as lead drugs against trypanosomatid-borne diseases.
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Affiliation(s)
- Juliette Moyersoen
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, ICP-TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium
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Naula C, Burchmore R. A plethora of targets, a paucity of drugs: progress towards the development of novel chemotherapies for human African trypanosomiasis. Expert Rev Anti Infect Ther 2004; 1:157-65. [PMID: 15482108 DOI: 10.1586/14787210.1.1.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human African trypanosomiasis is a major health problem in large regions of Africa. Current chemotherapeutic options are limited and far from ideal. A diverse range of drug targets has been identified and validated in trypanosomes. These include several organelles (glycosomes, acidocalcisomes, kinetoplast) that are not represented in the mammalian host and biochemical pathways that differ significantly from host counterparts (carbohydrate metabolism, protein and lipid modification, response to oxidative stress, cell cycle). However, there has been little progress in developing novel drugs. Pharmaceutical companies are unwilling to invest in the development of drugs for a market that comprises some of the worlds poorest people. This review highlights some of the most attractive drug targets in trypanosomes.
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Affiliation(s)
- Christina Naula
- Wellcome Centre for Molecular Parasitology, The Anderson College, University of Glasgow, Glasgow, UK
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