Comprehensive Analysis of Parasite Biology E-Book
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- Herausgeber: Wiley-VCH
- Kategorie: Wissenschaft und neue Technologien
- Serie: Drug Discovery in Infectious Diseases
- Sprache: Englisch
Written and edited by experts in the field, this book brings together the current state of the art in phenotypic and rational, target-based approaches to drug discovery against pathogenic protozoa. The chapters focus particularly on virtual compounds and high throughput screening, natural products, computer-assisted drug design, structure-based drug design, mechanism of action identification, and pathway modelling. Furthermore, state-of the art "omics" technologies are described and currently studied enzymatic drug targets are discussed. Mathematical, systems biology-based approaches are introduced as new methodologies for dissecting complex aspects of pathogen survival mechanisms and for target identification. In addition, recently developed anti-parasitic agents targeting particular pathways, which serve as lead compounds for further drug development, are presented.
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Veröffentlichungsjahr: 2016
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Table of Contents
Cover
Title Page
Copyright
List of Contributors
Foreword
Preface
Part One: Identification and Validation of New Drugs and Targets
Chapter 1: Discovery of the Mechanism of Action of Novel Compounds That Target Unicellular Eukaryotic Parasites
Introduction
Principles
Initial Investigations
Biochemical Methods and Candidate Genes
Classical Genetics and Genomics
Changes in mRNA Levels
Reverse Genetic Screens
Proteins and Proteomes
Metabolomics
Validation
Conclusions
References
Chapter 2: Antiparasitics from Algae
Introduction
Plasmodium falciparum
Kinetoplastida –
Trypanosoma brucei sp.
,
Trypanosoma cruzi
, and
Leishmania
sp
Anaerobic Protozoan Parasites –
Entamoeba histolytica, Giardia lamblia, and Trichomonas vaginalis
Helminths
Microalgae
Conclusion
References
Chapter 3: Contribution of Natural Products to Drug Discovery in Tropical Diseases
Introduction
Antiparasitic Natural Product Compound Classes
Discussion
Conclusion and Future Perspectives
References
Chapter 4: Isoxazolines: A Novel Chemotype Highly Effective on Ectoparasites
Arthropod Ectoparasites: Burden to the Agricultural and Veterinary Sectors
Ligand-Gated Chloride Channels as Suitable Targets for Ectoparasiticides
Mode of Action
Isoxazolines: Novel Ectoparasiticides Acting on GABACls and GluCls
Structure and Active Sites of Chloride Channels
Isoxazoline Mode of Action and Binding Site
Selectivity and Safety Profile
Isoxazoline Derivatives: Continuous Exploration of the Novel Chemotype
Conclusions
Acknowledgments
References
Chapter 5: Trypanosomal Cysteine Peptidases: Target Validation and Drug Design Strategies
Cysteine Peptidases from
Trypanosoma cruzi
Cysteine Peptidases from
Trypanosoma brucei
Development of Antitrypanosomal Cysteine Peptidase Inhibitors
Peptidic Derivatives
Nonpeptidic Derivatives
Conclusion
Acknowledgments
References
Chapter 6: Potential of Pyrimidine Metabolism for Antitrypanosomal Drug Discovery
Introduction
De novo
Biosynthesis of Pyrimidines
Pyrimidine Salvage
UMP Downstream Enzymes
Final Remarks
References
Chapter 7: Phosphatidylcholine and Phosphatidylethanolamine Biosynthesis Pathways in Plasmodium
Introduction
Kinases
Cytidylyltransferases
Phosphotransferase
Transversal Pathways
Conclusion
Acknowledgments
References
Chapter 8: Immunophilins as Possible Drug Targets in Apicomplexan Parasites
Immunophilins
Immunophilins in Apicomplexa
Immunophilins as Drug Targets
Conclusions
References
Chapter 9: Targeting the Atg8 Conjugation Pathway for Novel Anti-Apicomplexan Drug Discovery
Autophagy: An Overview
Phylum, Apicomplexa
Conservation of Autophagy in Apicomplexa
Functions of Apicomplexan Autophagy Proteins
Targeting the Plasmodial (and Apicomplexan) Atg8-Conjugation Pathway
Concluding Remarks
References
Chapter 10: Turnover of Glycosomes in Trypanosomes – Perspectives for Drug Discovery
Glycosomes of Trypanosomatid Parasites Are Unique, Peroxisome-Related Organelles
Glycosomes are Essential Organelles
Glycosomal Metabolism Changes during the Life Cycle of the Parasites
Biogenesis of Glycosomes
Autophagy and Pexophagy of Glycosomes
Proteins Involved in Glycosome Biogenesis and Degradation are Potential Drug Targets
Discussion and Conclusions
Acknowledgments
References
Chapter 11: Glideosome of Apicomplexans as a Drug Target
Economic and Public Health Burden of Apicomplexans
Phylogenetic Relation of Human and Livestock Apicomplexan Pathogens
Burden of Malaria
Life Cycle of the Parasite
Invasion Machinery (Glideosome)
Conservation of the Glideosome in Apicomplexans
Components of the Glideosome: Function and Potential as Drug Targets
Exploring the Essentiality of the Adhesins and Glideosome Components
Concluding Remarks
References
Chapter 12: N-Myristoyltransferase as a Target for Drug Discovery in Malaria
Introduction: Malaria and the Need for New Drugs
Phenotypic Screening and Inhibitors Directed toward PI4K and eEF2
Protein
N-
Myristoylation in
Plasmodium
Structure, Specificity, and Mechanism of NMT
NMT as a Drug Target
Discovery of Inhibitors of
Plasmodium
NMT – “Piggyback” Approaches
Discovery of Inhibitors of
Plasmodium
NMT – High-Throughput Approaches
Using NMT Inhibitors to Validate NMT as a Drug Target in Malaria
Essential Function of NMT in Plasmodium Parasites
Conclusion
Acknowledgments
References
Part Two: Metabolomics in Drug and Target Discovery
Chapter 13: Methods to Investigate Metabolic Systems in Trypanosoma
Trypanosomes, Unconventional Organisms
Metabolomics
Application of Metabolomics to
T. brucei
– Selected Illustrations
Concluding Remarks
References
Chapter 14: The Role of Metabolomics in Antiparasitic Drug Discovery
Introduction
Principles of Metabolomics
Metabolomics in Drug Discovery
Metabolomics Methodology
Metabolomics for Drug Discovery in Kinetoplastid Parasites
Metabolomics for Drug Discovery in Apicomplexan Parasites
Summary
References
Chapter 15: The Importance of Targeting Lipid Metabolism in Parasites for Drug Discovery
Introduction
Parasites Nutrient Requirements from the Host for Lipid Metabolism
Drugs Affecting Phospholipid Metabolism in Protozoan Parasites
Drugs Affecting Sterol Metabolism in Protozoan Parasites
Drug Resistances and Its Association with Altered Lipid Composition
Modern Technological Methods to Phenotype Changes in Lipid Content
Perspectives
Acknowledgments
References
Chapter 16: Carbon Metabolism of Plasmodium falciparum
Introduction
Cytosolic Glucose Metabolism
Mitochondrial Metabolism
Apicoplast Metabolism
Conclusions
Acknowledgments
References
Part Three: Gene Expression and Its Regulation – A Promising Research Area for Drug Discovery
Chapter 17: Epigenetic Gene Regulation: Key to Development and Survival of Malaria Parasites
Introduction
Epigenetics – An Overview
The Unique Genome and Chromatin Landscape of
Plasmodium falciparum
Epigenetic Regulation of Gene Expression in
P. falciparum
Concluding Remarks and Perspective
References
Chapter 18: Mechanisms Regulating Transcription in Plasmodium falciparum as Targets for Novel Antimalarial Drugs
Transcription in
Plasmodium falciparum
Nucleosome Landscape
Chromatin Remodeling Enzymes
Histone Posttranslational Modifications
Histone-Modifying Enzymes
Nuclear Architecture
Proteins Involved in Nuclear Organization
Long Noncoding RNAs
Posttranscriptional Control of Gene Expression
Conclusions
References
Chapter 19: Aminoacyl t-RNA Synthetases as Antimalarial Drug Targets
Introduction
Alanyl-tRNA Synthetase (AlaRS)
Isoleucyl-tRNA Synthetase (IleRS)
Threonyl-tRNA Synthetase (ThrRS)
Methionyl-tRNA Synthetase (MetRS)
Lysyl-tRNA Synthetase (LysRS)
Prolyl-tRNA Synthetase (ProRS)
Conclusions
References
Part Four: Mathematical Approaches to Drug and Target Discovery
Chapter 20: Mathematical Modeling and Omic Data Integration to Understand Dynamic Adaptation of Apicomplexan Parasites and Identify Pharmaceutical Targets
Introduction
Omics-Based Approaches
Mathematical Modeling
Role of Kinetic Models to Elucidate Mechanism of Effectors and Identify Putative Drug Target
Conclusion and Future Perspectives
References
Chapter 21: Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-Based Modeling
Introduction
Genome-Scale Reconstruction
Metabolic Model Simulation
Applications of Flux Balance Analysis in Identifying Potential Drug Targets
Conclusion
References
Chapter 22: Attacking Blood-Borne Parasites with Mathematics
The Importance of Flexible Metabolism for the Parasites
Trypanosoma brucei
and
Plasmodium falciparum
Metabolism as a Drug Target
Computer Models Can Aid Our Understanding of Metabolism
Construction and Validation of Detailed Kinetic Models of Glycolysis of BSF
T. brucei
and of the Trophozoite Stage of
P. falciparum
Metabolic Control Analysis Ranks Enzymes for Drug Target Potential
Work in Progress: Future Extensions and Use of the Kinetic Models of
T. brucei
and
P. falciparum
Do It Yourself: Databases and Tools to Do Your Own Simulations with the Detailed Kinetic Models
Concluding Remarks
Acknowledgments
References
Index
End User License Agreement
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Guide
Cover
Table of Contents
Foreword
Preface
Part One: Identification and Validation of New Drugs and Targets
Begin Reading
List of Illustrations
Chapter 1: Discovery of the Mechanism of Action of Novel Compounds That Target Unicellular Eukaryotic Parasites
Figure 1.1 Schematic representation of the different possible approaches for target deconvolution described in the text.
Chapter 2: Antiparasitics from Algae
Figure 2.1 Marine natural products with antiplasmodial activity. IC
50
values are given next to the chemical formula.
Figure 2.2 Marine natural products with antileishmanial, trypanocidal, trichomonacidal, and anthelmintic activities. IC
50
values are given below the chemical formula.
Chapter 3: Contribution of Natural Products to Drug Discovery in Tropical Diseases
Figure 3.1 Most potent natural product compounds against
Plasmodium
(IC
50
≤ 0.2 μM or ≤0.5 µg/ml).
Figure 3.2 Most potent natural product compounds against the kinetoplastids (IC
50
≤ 1 μM or ≤1 µg/ml). (a) Compounds active against
T. cruzi.
(b) Compounds active against
T. brucei
. (c) Compounds active against
Leishmania
parasites.
Chapter 4: Isoxazolines: A Novel Chemotype Highly Effective on Ectoparasites
Figure 4.1 Schematic representation of the transmembrane domain of a ligand-gated chloride channel. (a) Four transmembrane helices (M1–M4) that make up one subunit are depicted with their connecting loops. (b) Arrangement of the transmembrane subunits to form a pentameric ion channel with M2 helices (orange) lining the pore, M1 and M3 linking the adjacent subunits, and M4 facing the outside of the pore. Helices M3′ and M4′ of the foremost subunit have been omitted for clarity. Only three of the five subunits reveal their composition of helices.
Figure 4.2 Homology model of GABACl in a proposed closed form. Sequences of
Erwinia chrysanthemi
GABACl and dlr-GABACl of
Ctenocephalides felis
were aligned using the BLAST algorithm, and final modeling was performed with the MOE software package [41]. The five individual subunits are shaded in different colors. The Cys loop of one subunit is highlighted in light green (light-green arrows), the resistance-inducing mutation in dark green (dark-green arrow). (a) Protein shown parallel to membrane; horizontal gray bars indicate membrane boundaries. (b) View along the channel pore axis from the extracellular side, with M2 helices visible as the inner pore lining. (c) View along the channel pore axis from the intracellular side, with resistance-inducing residue (red dot) highlighted with a red arrow.
Figure 4.3 GluCl crystal structure of
C. elegans
represented in an activated, open-channel state. These images are based on an original X-ray crystallographic structure (PDB ID: 3RHW) [49] and were produced with the MOE software package [41]. Fab molecules are omitted for clarity. The five individual subunits are shaded in different colors. The surface of one ivermectin-binding pocket is highlighted in yellow. The Cys loop of one subunit is highlighted in light green (light-green arrows). (a) Protein parallel to membrane, horizontal gray bars indicate membrane boundaries. (b) View along the channel pore axis from the extracellular side, with M2 helices visible as the inner pore lining. (c) View along channel pore axis from the intracellular side.
Figure 4.4 Schematic representation of CysLGCCs in a sectional view with only three units of the pentameric transmembrane region depicted for clarity. Positioning of isoxazolines is putative.
Chapter 5: Trypanosomal Cysteine Peptidases: Target Validation and Drug Design Strategies
Figure 5.1 Cruzain promotes cell invasion through a kinin-mediated pathway. Cruzain generates bradykinin from kininogen, a cysteine peptidase activity inhibited by E-64 and K777 () and enhanced by heparan sulfate (). Bradykinin acts on bradykinin receptors type 1 and 2 (B
1
R and B
2
R), leading to Ca
2+
release and increasing vascular permeability, edema, and plasma leakage. Captopril, an angiotensin-converting enzyme (ACE) inhibitor, reduces bradykinin degradation and potentiates
T. cruzi
invasion.
Figure 5.2 Different classes of potent cysteine peptidase inhibitors. Regions shaded in gray represent exploited portions in SAR studies.
Chapter 6: Potential of Pyrimidine Metabolism for Antitrypanosomal Drug Discovery
Figure 6.1 UMP synthesis routes in humans and kinetoplastida. In humans, the first three activities of
de novo
synthesis of pyrimidines are expressed as a single polypeptide (CAD protein) while kinetoplastids express CPSII, ACT, and DHO as individual proteins but with the capacity to establish intermolecular interactions and to form a CAD-like enzyme complex [1]. The subcellular distribution of the enzymes involved in
de novo
biosynthesis also differs between humans and parasites. In humans, CAD is cytosolic but DHODH is localized in the inner membrane of mitochondria. In contrast, protozoan CPSII, ACT, DHO, and DHODH are all cytosolic enzymes [2]. Human DHODH is directly linked to the mitochondrial respiratory chain using ubiquinone as electron acceptor while parasite DHODHs catalyze the electron transfer from dihydroorotate to fumarate to generate succinate [3–5]. The final reaction steps that lead to UMP biosynthesis are catalyzed by a single bifunctional protein referred to as
UMP synthase
. In kinetoplastids, the functional domains are reversed with respect to mammals, with the N-terminal domain corresponding to OMPDC and the C-terminal to OPRT [6]. These final two enzymatic reactions take place in kinetoplastid-specific organelles called glycosomes [2]. Human UMPs are localized in the cytosol around and outside the mitochondria [7]. Enzyme abbreviations: carbamoyl phosphate synthetase (CPSII), aspartate carbamoyltransferase (ACT), dihydroorotase (DHO), dihydroorotate dehydrogenase (DHODH), orotidine 5′-monophosphate decarboxylase (OMPDC), and orotate phosphoribosyltransferase (OPRT).
Figure 6.2 Integrated view of the pathways that lead to the synthesis of pyrimidine nucleotides. Kinetoplastids salvage preformed pyrimidine nucleobases or nucleosides from the host's fluids to obtain pyrimidine nucleotides. After the entrance into the parasite through specific transporters, all pyrimidines, except thymidine, are converted into uracil, which is then phosphorylated to UMP by UPRT. Thymidine is phosphorylated via TK to produce dTMP, which is subsequently phosphorylated to dTTP. UMP is a common intermediate of
de novo
and salvage pathways and all the reactions downstream UMP synthesis are catalyzed by enzymes performing nonredundant functions. Kinetoplastid CTPS, RNR, DHFR-TS, and dUTPase are included in this group. Enzyme abbreviations: uracil phosphoribosyltransferase (UPRT), thymidine kinase (TK), cytidine triphosphate synthetase (CTPS), ribonucleotide reductase (RNR), dihydrofolate reductase–thymidylate synthase (DHFR-TS), and deoxyuridine triphosphate nucleotidohydrolase (dUTPase).
Chapter 7: Phosphatidylcholine and Phosphatidylethanolamine Biosynthesis Pathways in Plasmodium
Figure 7.1 Enzymes of the
de novo
phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthesis pathways in
P. falciparum
blood stage parasites. (a) PC and PE
de novo
biosynthesis pathways. Choline (Cho) and ethanolamine (Etn) are scavenged from the host. Shown in black are the two parallel
de novo
Kennedy pathways of PC and PE synthesis, in green the transversal PMT pathway, and in orange the transversal PE methylation pathway. Enzymes are boxed and the question mark corresponds to enzyme activity for which the corresponding gene has not been identified yet. RBCM: red blood cell membrane, PPM: parasite plasma membrane, PVM: parasitophorous vacuole membrane, NPP: new permeation pathways, and DAG: diacylglycerol. Details concerning enzymes, substrates, and products are given in the text. (b) Schematic representation of the
P. falciparum
enzymes of the PC and PE biosynthesis pathways
.
For
Pf
CK,
Pf
EK,
Pf
CCT, and
Pf
ECT, catalytic domains are represented by gray boxes and membrane-binding domains of
Pf
CCT by pink boxes. Conserved motifs and family signatures are indicated by colored rectangles and described in the text. Cylinders in the
Pf
CEPT representation correspond to predicted transmembrane domains. CT: cytidylyltransferase domain (catalytic domain) and M: membrane binding domain.
Figure 7.2 Structures of the enzymes of the
de novo
PC and PE biosynthesis pathways in
Plasmodium.
(a) X-ray crystal structures of
P. vivax
EK (left) and
P. knowlesi
CK (right) with Cho bound in the binding site (inset). Cho (gray) and residues participating in its binding (composite aromatic box) are in pink sticks. (b) 3D comparative models of the domains CT of
P. falciparum
ECT (left) and CCT (right) with CDP–choline in the binding site (inset). CDP-Cho (gray) and residues participating in the coordination of CDP-Cho are represented as sticks. Yellow: HxGH motif, purple: RTEGVSTT motif, pink: composite aromatic box. (c) X-ray crystal structure of
P. falciparum
PMT with P-Etn and SAH bound in the active site (inset). Important residues binding to the ligands are indicated as sticks. Orange: residues involved in catalysis, light pink: tyrosine residues participating in the coordination of the phosphate moiety of P-Etn. All Figure have been generated using PyMol [35].
Chapter 8: Immunophilins as Possible Drug Targets in Apicomplexan Parasites
Figure 8.1 Chemical structures of ligands mentioned.
Figure 8.2
Pf
FKBP35 ligands. (a) FK506 (in blue 2VN1 crystal structure [57]) and rapamycin (in purple 4QT2 crystal structure [94]) on
Pf
FKBD active site. The binding site map (blue) and residue Cys106 (yellow) are highlighted. (b) D44 (in green 4J4N crystal structure [56]) and SRA (in orange 4MGV crystal structure [93]). The binding site map (green) and residue Cys106 (yellow) are highlighted.
Chapter 9: Targeting the Atg8 Conjugation Pathway for Novel Anti-Apicomplexan Drug Discovery
Figure 9.1 An overview of canonical macroautophagy in yeast and
Plasmodium
. (a) Step 1: induction and phagophore assembly. The Atg1 complex forms at the PAS, leading to recruitment and activation of the PI3K class III complex. The PI3K complex converts PI to PI3P in the phagophore membrane resulting in Atg2, Atg18, and Atg9 binding. Step 2: phagophore elongation and closure to form the autophagosome. This step relies on Atg8 being conjugated to PE. Atg8-PE is the product of the Atg8 conjugation pathway, the last step of which is facilitated by Atg12-Atg5-Atg16. Atg12-Atg5 is the product of the Atg12 conjugation pathway. Step 3: autophagosome fuses with the lysosome to form an autolysosome. Step 4: digestion of autolysosomal contents and release of recycled amino acids. Atg15 and Atg22 facilitate breakdown of the membrane-bound vesicle within the autolysosome to expose the contents for digestion. The products of digestion, amino acids, are then released into the cell. (b) Conservation of canonical macroautophagy proteins within
Plasmodium
[12, 13]. Bold text on a green background indicates a conserved homolog exists; regular text on a yellow background, potential homologs identified; italics on a red background, no detectable homolog. * – Atg7 is involved in both Atg8 and Atg12 conjugation pathways.
Figure 9.2
Plasmodium
and apicomplexan Atg8 proteins. (a) Multiple sequence alignment of various apicomplexan, human, and yeast Atg8 homologs generated by ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). Visualized with ESPript 3.0, with global score set to 0.4 (espript.ibcp.fr). Ovals indicate side-chain contacts in the three pockets on
Pf
Atg8; triangles indicated backbone contacts in these pockets. Magenta corresponds to the W-site pocket; cyan, the L-site pocket; and yellow, the A-loop pocket. The A-loop itself is outlined in yellow, revealing conservation of the A-loop within apicomplexan, but not in human or yeast homologs. The C-terminal glycine is indicated by a black asterisk, illustrating that this glycine is exposed in most apicomplexan Atg8 homologs, but not in
C
.
parvum
, human, or yeast Atg8. (b) Conservation of pockets on
Pf
Atg8 (PDB ID 4EOY) generated using ConSurf with the default values (consurf.tau.ac.il). The W- and L-sites are highly conserved, while the A-loop pocket is not. (c) Structure of
Pf
Atg8 color-coded as in (a): magenta, W-site; cyan, L-site; yellow, A-loop pocket. The pink region between the W- and L-sites indicates residues involved in both sites. (d) Electrostatic surface representation of PfAtg8 rendered using OpenEye Vida and POV-Ray (povray.org). Predicted binding modes of one of the PTA ligands, bound in the W- and L-sites, and ALC25, bound in the A-loop pocket. From these poses, it appears there is the potential to link the two sites.
Chapter 10: Turnover of Glycosomes in Trypanosomes – Perspectives for Drug Discovery
Figure 10.1 Major glycosomal processes and enzymes in bloodstream-form (a) and procyclic-form
T. brucei
(b). Metabolic end products are boxed. Thickness of arrows indicates relative importance of fluxes. The yellow circles represent solute translocation systems (channels or transporters [10, 11]) in the glycosomal membrane. In bloodstream-form cells, glucose catabolism by aerobic glycolysis results predominantly in pyruvate production and may yield smaller, variable amounts of succinate and alanine. Electrons from NADH formed in the GAPDH reaction are transferred to O
2
via a shuttle involving a mitochondrial GPO complex (shown in blue), which is not coupled to oxidative phosphorylation. Under anaerobic conditions, approximately equimolar amounts of pyruvate and glycerol are produced, the latter with concomitant ATP production by reversal of the GK reaction (shown in green). Other processes and enzymes found in the glycosomes but quantitatively minor compared to the glycolytic enzymes and flux are listed; several of these processes and enzymes may have (variable) dual localization in glycosomes and cytosol. In procyclic trypanosomes, levels of glycolytic enzymes and the glycolytic flux are reduced compared to the situation in bloodstream-form parasites; production of succinate and alanine from glucose is increased. Under glucose-depleted conditions, gluconeogenesis may occur to produce G6P. Note that one of the enzymes in the succinate-production pathway, Fum, is found predominantly in the cytosol. Abbreviations: PPP, pentose-phosphate pathway; enzymes: ALAT, alanine amino transferase; ALD, aldolase; ENO, enolase; FRD, fumarate dehydrogenase; FUM, fumarase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GK, glycerol kinase; G3PDH, glycerol-3-phosphate dehydrogenase; GPO, glycerol-3-phosphate oxidase system; HK, hexokinase; MDH, malate dehydrogenase; PEPCK, phosphoenolpyruvate carboxykinase; PFK, phosphofructokinase; PGAM, phosphoglycerate mutase; PGI, phosphoglucose isomerase; PGK, phosphoglycerate kinase; PPdK, pyruvate phosphate dikinase; PYK, pyruvate kinase; and TPI, triosephosphate isomerase; metabolites: 1,3BPGA, 1,3-bisphosphoglycerate; DHAP, dihydroxyacetone phosphate; FBP, fructose 1,6-bisphosphate; F6P, fructose 6-phosphate; GAP, glyceraldehyde 3-phosphate; G3P, glycerol 3-phosphate; G6P, glucose 6-phosphate; PEP, phosphoenolpyruvate; 2PGA, 2-phosphoglycerate; 3PGA, 3-phosphoglycerate; Pi, inorganic phosphate; and PPi, inorganic pyrophosphate. For a more detailed description of glycosomal processes and enzymes, see reviews in [12, 13].
Figure 10.2 Turnover of glycosomes in trypanosomatid parasites. (a) Glycosome biogenesis can involve both
de novo
formation starting from the endoplasmic reticulum and growth and fission. (b) The different steps of glycosome biogenesis and the PEX proteins involved therein as identified in
T. brucei
. The numbers given in asterisks correspond to those of the five consecutive stages of peroxisomal matrix protein import as mentioned in the text mPTS corresponds to peroxisomal membrane-targeting signal. (c) Glycosome degradation may occur by selective autophagy (“pexophagy”) or nonselective autophagy; either via the sequestering of the organelles by formation of autophagosomes, which are subsequently directed to the lysosome where their contents are released for degradation, a process called
macroautophagy/-pexophagy
, or by their direct engulfment at the lysosomal membrane, called
microautophagy/-pexophagy
. Autophagy-related proteins (ATGs) functionally identified in trypanosomatid parasites as being involved in steps of glycosome degradation are indicated. For more details, see text and reviews in [11, 37–40] for glycosome biogenesis and degradation, respectively.
Figure 10.3 Comparison of corresponding PEX proteins involved in the biogenesis of peroxisomes in humans and glycosomes in
T. brucei
and
Leishmania
spp. and their interaction maps. Characteristic regions and motifs – many involved in specific interactions as shown in the Figure – are as follows.
PTS1
and
PTS2
(
P
eroxisomal
T
argeting
S
ignals) are two different motifs, present at the C-terminus and close to the N-terminus, respectively, of proteins to be imported into the peroxisomal matrix.
PEX5
s contain pentapeptide motifs (defined as WXXX(F/Y)) in their N-terminal half and seven TPR motifs, organized in two clusters (TPR1-3 and TPR5-7) with the fourth motif as a hinge connecting them in their C-terminal domain. The major part of the
PEX7
polypeptide is made up of six WD repeats; trypanosomatid PEX7 contains a long C-terminal extension enriched in proline residues.
PEX13
has an N-terminal region enriched in Tyr- and Gly-residues. Moreover, in most groups (but not trypanosomatids), a short Pro-rich region is found near the N-terminus. However, these Tyr/Gly- and Pro-rich regions do not form specific conserved motifs. The central part of PEX13 contains predicted transmembrane regions and is followed by a C-terminal SH3 region. Only trypanosomatids have been reported to contain two PEX13 isoforms, which are very divergent. The first isoform (13.1) possesses uniquely a PTS1 motif adjacent to the SH3 domain, while the other isoform (13.2) lacks the SH3 domain and has no PTS1. The N-terminal half of
PEX14
contains a typical hydrophobic region; more downstream is a PXXP motif and a hydrophobic membrane-interaction region. Question marks indicate that regions involved in specific interactions have not yet been identified. For more details, see the text and the reviews in [37, 38].
Chapter 11: Glideosome of Apicomplexans as a Drug Target
Figure 11.1 Phylogenetic tree of apicomplexan pathogens based on the amino acid sequences of aldolase, actin, and myosin A. Distances between phylogram leaves are indicated with a scale bar.
Figure 11.2 Migration, traversal, and invasion in the skin and liver stages. When the mosquito takes a blood meal, sporozoites (red) are injected into the dermis. These “migratory” sporozoites are capable of traversing and migrating the dermis, comprised of cells with under-sulfated HSPGs on their surface (gray stars), in a random motion. When they encounter the endothelium of a blood vessel, they can enter the bloodstream. The sporozoite then travels to the liver where it exits the sinusoid and can traverse several hepatocytes. Here, the sporozoite encounters highly sulfated HSPGs (orange stars) on the surface of the hepatocytes, which triggers signaling inside the parasite and cleavage of the circumsporozoite protein (CSP), activating the sporozoite for invasion (green).
Figure 11.3 Schematic of apicomplexan glideosome. Protein structures solved from both
T. gondii
and
Plasmodium
spp. and homologous protein structures were combined with the results of biochemical and genetic data to depict the glideosome model. The actin–myosin motor (gray/black and magenta/light pink) is bridged by tetrameric aldolase (multicolor) to extracellular adhesins such as TRAP (
Plasmodium
spp.) or MIC2 (
T. gondii
) (cyan), which connect to unknown cellular receptors on the host cell membrane (gray). The motor is anchored to the inner membrane complex (IMC) via its interaction with MTIP (
Plasmodium
spp.) or MLC1/ELC1 (
T. gondii
) (purple). The conserved GAP45, acylated at the N- and C-terminus, spans the supra-alveolar space between the IMC and parasite plasma membranes and interacts with the MyoA-MTIP complex. The motor complex also interacts with the polytopic integral membrane protein, GAP40 (orange), and GAP50 (red) located in the lumen of the IMC and attached via a C-terminal membrane helix. The integral membrane protein GAPMs (blue) are located on the cytosolic side of the IMC membrane and interact with the alveolins (white/gray).
Figure 11.4 Conservation of key glideosome proteins. Conservation is depicted on a gradient colorimetric scale from cyan to magenta indicating low to high conservation, respectively. Actin is the most conserved protein within the glideosome assembly while the catalytic site of aldolase is completely conserved.
Chapter 12: N-Myristoyltransferase as a Target for Drug Discovery in Malaria
Figure 12.1 Structures of clinically important antimalarial drugs and molecules identified through screening programs discussed in the text.
Figure 12.2
N
-Myristoyltransferase catalytic mechanism and structure. (a) Scheme showing the ordered binding of myristoyl-CoA (MyrCoA) and the substrate protein followed by the ordered release of coenzyme A (CoA-SH) and the myristoylated substrate protein. (b) The crystal structure of the ternary complex of NMT from
P. vivax
(
Pv
NMT
,
PDB code 4C68) with NHM (a myristoyl-CoA analog;
S
-(2-oxo)pentadecyl-CoA); and a peptidomimetic (
N
-(10-aminodecanoyl)-l-seryl-
N
-(2-cyclohexylethyl)-l-lysinamide) inhibitor bound in the active site. Ribbon representation of protein with the chain color-ramped from the N-terminus (blue) to the C-terminus (red). NHM is represented in cylinder format and the peptidomimetic is shown as spheres. The atoms are colored by type: carbon, gray; nitrogen, blue; oxygen, red; sulfur, yellow; phosphorus, magenta. (c) Top: Chemical structure of the peptidomimetic inhibitor. Bottom: Electrostatic surface rendering of the protein molecule revealing the substrate binding groove. The ligands are represented as before except that carbon atoms are colored in green. (d) Schematic of a step in the reaction mechanism showing the active site following binding of substrates and deprotonation of the peptide's α-amino group by the carboxylate of Leu410. (e) The binding of the inhibitor DDD85646 (thick cylinders with gray carbons) to
Pv
NMT (PDB code 2YND) with selected enzyme residues shown including Leu410 and Ser319, which form important polar contacts (dashed lines).
Figure 12.3 NMT inhibitor optimization. (a) The evolution of the benzofuran
1
to the potent inhibitor
7
by structure-guided medicinal chemistry. Arrows are labeled with associated references. The
K
i
and the EC
50
values refer to inhibition of
Pf
NMT and the
in vitro
potency against
P. falciparum
respectively. (b) Hybridization of the binding modes of
8
and
9
to give
10
with a 40-fold increase in potency toward
Leishmania donovani
NMT (
Ld
NMT). In the center,
8
,
9
, and
10
from their complexes with
Ld
NMT and myristoyl-CoA are shown overlaid following superposition of the protein chains. The carbon atoms are colored according to the inhibitor: ice blue,
8
; gray,
9
; and light green,
10
. The PDB codes are 4CGL, 4CGN, and 4CYO, respectively [55].
Chapter 13: Methods to Investigate Metabolic Systems in Trypanosoma
Figure 13.1 Scheme of workflow in metabolomics. Abbreviations: LC, liquid chromatography; GC, gas chromatography; IEC, ion-exchange chromatography; HILIC, hydrophilic interaction liquid chromatography; NP, normal phase; RP, reversed phase; MS, mass spectrometry; and NMR, nuclear magnetic resonance.
Figure 13.2 Schematic representation of central carbon metabolism in procyclic
T. brucei.
Each node represents a metabolite; direction of reactions in glycolytic or gluconeogenetic flux is not indicated. Abbreviations of enzymes (indicated in bold italic): HXK, hexokinase; PGI, glucose-6-phosphate isomerase; PFK, phosphofructokinase; TIM, triose-phosphate isomerase; GAPD, glyceraldehyde-3-phosphate dehydrogenase; PGKB, phospho-glycerol kinase (isoform B); PYK, pyruvate kinase; PPDK, pyruvate phosphate dikinase; PEPCK, phosphoenolpyruvate carboxykinase; MDHg, malate dehydrogenase; FHg/FHc, fumarate hydratase glycosomal/fumarate hydratase cytosolic; FRDg/FRDm, fumarate reductase glycosomal/fumarate reductase mitochondrial; SDH, succinate dehydrogenase; MEc/MEm, malic enzyme cytosolic/malic enzyme mitochondrial; PDH, pyruvate dehydrogenase complex; ACH, acetyl-CoA thioesterase; ASCT, acetyl:succinyl-CoA transferase; CS, citrate synthase; ACO, aconitase; IDH, isocitrate dehydrogenase, 2KGDH, 2-ketoglutarate dehydrogenase; SCS, succinyl-CoA synthetase; PRODH, proline dehydrogenase; TDH, threonine 3-dehydrogenase; AKCL, 2-amino-3-ketobutyrate-coenzyme A ligase. Abbreviation of pathway: PPP, pentose phosphate pathway. Abbreviations of compounds: d-Glu, d-glucose; l-Pro, l-proline; l-Thr, l-threonine; l-Gln, l-glutamine; Glu-6-P, glucose-6-phosphate; Rib-5-P, ribose-5-phosphate; Fru-6P, fructose-6-phosphate; Fru-1,6-BP, fructose-1,6-bisphosphate; DHAP, dihydroxyacetone phosphate; GA-3-P, glyceraldehyde-3-phosphate; 1,3-BPG, 1,3-bisphosphoglycerate; 3-PG, 3-phosphoglycerate; PEP, phosphoenolpyruvate; OAA, oxaloacetate; MAL, malate; FUM, fumarate; SUC, succinate; AC, acetate; CIT, citrate; isoCIT, isocitrate; 2-KG, 2-ketoglutarate; GLU, glutamate; SAG, glutamate semialdehyde; and AOB, amino-oxobutyrate; GPDH, glycerol-3-phosphate dehydrogenase.
Chapter 14: The Role of Metabolomics in Antiparasitic Drug Discovery
Figure 14.1 General metabolomics workflow for
in vitro
drug mechanism of action studies using protozoan parasites. Parasites are grown in culture and incubated with the test compound for the desired duration. Metabolism is then quenched by rapid cooling, and the parasitic cells may be isolated before metabolite extraction using organic solvent. Metabolite extracts are then analyzed using an appropriate detection method such as mass spectrometry (MS) or nuclear magnetic resonance (NMR) after chromatographic separation with either gas chromatography (GC). liquid chromatography (LC) or capillary electrophoresis (CE) after chromatographic separation. The raw metabolite data must then be processed to determine specific drug-induced metabolic perturbations responsible for parasite death.
Figure 14.2 Schematic of metabolic mechanisms of action of three anti-apicomplexan compounds. (a) Atovaquone inhibits the cyctochrome bc1 complex in the mitochondria. This inhibits oxidation of the ubiquinone cofactor resulting in dysfunction of dihydroorotate dehydrogenase (DHODH) such that dihydroorotate accumulates and pyrimidine synthesis is disrupted [96]. (b) Fosmidomycin inhibits deoxyxylulose phosphate reductoisomerase (DXR) causing accumulation of 1-d-deoxyxylulose 5-phosphate (DOXP). It also inhibits methylerythritol phosphate cytidylyltransferase (IspD) causing the accumulation of 2-
C
-methylerythrose and methylerythritol phosphate (MEP) and the depletion of cytidine diphosphate methylerythritol (CDP-ME). This disrupts isoprenoid biosynthesis [42]. (c) Together, eflornithine and MDL73811 inhibit the bifunctional enzyme,
S
-adenosylmethionine decarboxylase/ornithine decarboxylase (AdoMetDC/ODC), which leads to the depletion of polyamines and is ultimately fatal to the parasite. The substrate of AdoMetDC, AdoMet, does not accumulate as expected upon AdoMetDC inhibition. This is due to the decreased expression of AdoMet synthetase, as revealed by transcriptomics and proteomics, such that less AdoMet is synthesized. Similarly, the substrate of ODC, ornithine, does not accumulate as expected upon ODC inhibition. This is due to the increase in ornithine aminotransferase (OAT) expression, which degrades ornithine [41].
Chapter 15: The Importance of Targeting Lipid Metabolism in Parasites for Drug Discovery
Figure 15.1 Structures of compounds with antiparasitic activity. (a) Ajoene; (b) albitiazolium; (c) TC95; (d) amphotericin B; (e) miltefosine; (f) fosmidomycin; and (g) pamidronate.
Figure 15.2 Mass spectrometer scanning modes: (a) survey scan, (b) parent ion scanning, (c) daughter product scanning, (d) neutral loss, and (e) single/multiple reaction monitoring.
Figure 15.3 NMR spectra of (a) a mixture of lipid standards and (b) lipid extract from
Crithidia fasciculata
(density 1 × 10
8
cells/ml). Fos-Cho 8 is used as an internal standard.
Chapter 16: Carbon Metabolism of Plasmodium falciparum
Figure 16.1 Glucose metabolism in the cytosol of
Plasmodium
. Glucose transport is increased approximately 75-fold upon the infection of RBC with
Plasmodium.
Transport is mediated through the hexose transporter (HT) in the plasma membrane of the parasites [14]. Glucose is catabolized via glycolysis with lactate being the major metabolic end product [15] that is excreted from the parasite cell via the formate–nitrite transporter (FNT, PF3D7_0316600) [16, 17]. Several metabolic pathways branch off glycolysis such as the pentose phosphate pathway (PPP) [18], the carboxylation of phosphoenolpyruvate (PEP) via PEPC to generate aspartate and malate [19]. Aspartate (Asp) is an important precursor for the salvage of purines or the biosynthesis of pyrimidines [20], while malate is imported into the mitochondrion through an α-ketoglutarate (α-KG)-malate carrier (PF3D7_0823900) [21] or excreted from the parasites potentially via FNT [16, 17, 19]. Pyruvate enters the mitochondrion by a mitochondrial pyruvate carrier (MPC 2, PF3D7_1470400) where it feeds into TCA metabolism and is involved in maintenance of intramitochondrial redox balance. PEP and triose phosphates (triose-P) are transported into the apicoplast by a triose phosphate/PEP–inorganic phosphate translocator (PF3D7_0530200) [22], which provides metabolic intermediates required for downstream synthetic pathways such as type II fatty acid biosynthesis (FAS II), phospholipid biosynthesis (P-lipids), and the synthesis of isoprenoid precursors via the nonmevalonate pathway (not shown) operating in the organelle.
Figure 16.2 Mitochondrial TCA cycle and its links to intermediary metabolism. There are three major entry points into
Plasmodium
TCA metabolism: acetyl-CoA (AcCoA) generated from pyruvate via BCKDH, member of the α-ketoacid dehydrogenase complexes [28], malate [19], and α-ketoglutarate (α-KG) derived from glutamine [19, 23]. It is not clear whether it is oxaloacetate (OAA) or citrate (Cit) that leaves the mitochondrion to maintain the malate shuttle and to feed pyrimidine biosynthesis. In addition, it is possible that Cit contributes to the transfer of AcCoA from the mitochondrion to the cytosol; however, no experimental evidence has so far been provided to support this proposal [25, 28]. Bulusu and colleagues showed that fumarate (Fum), either derived from purine salvage or provided by the host cell, enters the mitochondrion via an unidentified transporter [20]. All TCA cycle enzymes are dispensable during blood-stage development of
P. falciparum
apart from fumarate hydratase (FH) and malate:quinone oxidoreductase (MQO) [78] emphasizing the importance of maintaining a functional malate shuttle. Abbreviations: AcCoA, acetyl coenzyme A; Aco, aconitase (Pf3D7_1342100) or aconitate; Asp, aspartate; α-KG, α-ketoglutarate; BCKDH, branched-chain α-ketoacid dehydrogenase (PF3D7_1311800; PF3D7_1312600; PF3D7_0504600; PF3D7_0303700); CS, citrate synthase (Pf3D7_1022500); FH, fumarate hydratase (Pf3D7_0927400); Cit, citrate; Fum, fumarate; Isocit, isocitrate; ICDH, isocitrate dehydrogenase (Pf3D7_1345700); Mal, malate; MQO, malate:quinone oxidoreductase (PF3D7_0616800); OAA, oxaloacetate; Pyr, pyruvate; SCS, succinyl CoA synthetase (PF3D7_1108500; PF3D7_1431600); SDH, succinate dehydrogenase (PF3D7_1033800; PF3D7_1034400; PF3D7_1212800; PF3D7_1010300); Succ, succinate; and Succ CoA, succinyl coenzyme A.
Figure 16.3 Carbon metabolism in
Plasmodium
apicoplast. Triose phosphates are the principal carbon sources in the apicoplast, transported into the organelle by plant-derived pPT [110, 112]. PEP and DHAP play an important role in FASII and isoprenoid biosynthesis pathways, respectively [97]. Synthesis of [Fe–S] clusters is necessary to sustain numerous of the metabolic pathways in the organelle [115]; therefore, Cys and Fe
2+
are required and are possibly transported into the apicoplast by putative, chloroplast-like transporters; these have been identified in the parasite genome but still need to be characterized. Enzymes involved in phosphatidic acid synthesis are essential for liver-stage development of rodent malaria parasites [116]; whether the lysophosphatidic acid (LPA) synthesized is transported into the cytosol or used in the apicoplast is still unclear [116]. FASII is not essential for the intraerythrocytic stages of the parasite [117, 118]; fatty acids synthesized at different life-cycle stages can be used as substrates for phosphatidic acid synthesis, phospholipid biosynthesis, or octanoic acid is used by enzymes of the lipoylation system (LipA, LipB, and LplA2) essential for the function of apicoplast PDC [119–121]. How the apicoplast maintains its ADP/ATP and NAD(P)
+
/NAD(P)H + H
+
balance is not fully understood, and this Figure provides some information about cofactor requirements of different pathways. GDH2 is shown as a possible source for NADPH in the apicoplast [122, 123]. Abbreviations: AA-T, amino acid transporter (PF3D7_1231400); ACCase, acetyl-coenzyme A carboxylase (PF3D7_1026900; PF3D7_1469600); AcCoA, acetyl-coenzyme A; ACP, acyl carrier protein (PF3D7_0208500); Cat-T, cation transporter (PF3D7_0516100; PF3D7_0727800); DHAP, dihydroxyacetone phosphate; DMAP, dimethylallyl-pyrophosphate; DOXP, 1-deoxy-d-xylulose 5-phosphate; DXS, 1-deoxy-d-xylulose 5-phosphate synthase (PF3D7_1337200); E2, dihydrolipoamide acyltransferase (PF3D7_1020800); Fab B/F, 3-oxoacyl-acyl-carrier protein synthase I/II (PF3D7_0626300); FabD, malonyl coenzyme A-ACP transacylase precursor (PF3D7_1312000); FabG, beta-ketoacyl-ACP reductase (PF3D7_0922900); FabH, beta-ketoacyl-ACP synthase III (PF3D7_0211400); FabI, enoyl-ACP reductase (PF3D7_0615100); FabZ, beta-hydroxyacyl-ACP dehydratase (PF3D7_1323000); FNR, ferredoxin–NADP reductase (PF3D7_0623200); FASII, fatty acid synthesis II; G3P, glycerol 3-phosphate; G3PAT, glycerol-3-phosphate 1-
O
-acyltransferase (PF3D7_1318200); G3PDH, glycerol 3-phosphate dehydrogenase (PF3D7_1216200); GA3P, glyceraldehyde 3-phosphate; GDH2, NADP-specific glutamate dehydrogenase (PF3D7_1430700); GluSy, NAD(P)H-dependent glutamate synthase (PF3D7_1435300); IPP, isopentenyl-pyrophosphate; IspC, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (PF3D7_1467300); IspD, 2-
C
-methyl-d-erythritol 4-phosphate cytidylyltransferase (PF3D7_0106900); IspE, 4-diphosphocytidyl-2-
C
-methyl-d-erythritol kinase (PF3D7_0503100); IspF, 2-
C
-methyl-d-erythritol 2,4-cyclodiphosphate synthase (PF3D7_0209300); IspG, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (PF3D7_1022800); IspH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (PF3D7_0104400); LipA, lipoyl synthase (PF3D7_1344600); LipB, lipoate–protein ligase B (PF3D7_0823600); LPA, lysophosphatidic acid; LplA2, lipoate–protein ligase 2 (PF3D7_0923600); MalCoA, malonyl-coenzyme A; PDC, pyruvate dehydrogenase complex (PF3D7_1124500; PF3D7_1446400; PF3D7_1020800; PF3D7_1232200); PEP, phosphoenolpyruvate; pPT, plastid phosphate transporter (PF3D7_0530200; PF3D7_0508300); PYK, pyruvate kinase; and Pyr, pyruvate.
Chapter 17: Epigenetic Gene Regulation: Key to Development and Survival of Malaria Parasites
Figure 17.1 Schematic representation of
P. falciparum
's chromatin landscape and stage-specific or transcription-coupled chromatin changes. Euchromatin (white parts of the schematic chromosome): Euchromatic intergenic regions are demarcated by PfH2A.Z/PfH2B.Z double-variant nucleosomes, H3K4me3 and H3K9ac. H3K4me3 marks euchromatic intergenic regions in a stage-specific manner: low in early blood stages, high in late blood stages. H3K9ac is placed in a transcription-coupled manner: high in 5′ upstream regions of active genes, low in 5′ upstream regions of inactive genes. Centromere (silver ellipse): The centromere is a 4–4.5 kb region demarked by PfH2A.Z/PfH2B.Z/PfCenH3 triple-variant nucleosomes; its 2–2.5 kb AT-rich core is flanked by bidirectional promoters that give rise to small ncRNAs. Heterochromatin (black blocks): Subtelomeres and intrachromosomal islands are marked by H3K9me3, PfHP1, and H3K36me3. lncRNAs are transcribed in sense and antisense orientation from bidirectional intronic
var
gene promoters. 5′ upstream and bidirectional intronic
var
gene promoter of an active
var
gene are marked with H2A.Z/H2B.Z double-variant nucleosomes, H3K9ac and H3K4me3. In the subtelomeric non-coding region TAREs 1–6 express lncRNAs.
Chapter 18: Mechanisms Regulating Transcription in Plasmodium falciparum as Targets for Novel Antimalarial Drugs
Figure 18.1 Schematic overview of the mechanisms that regulate transcription. (a) The preinitiation complex consisting of RNA polymerase II and the general transcription factors. (b) The nucleosome landscape around
P. falciparum
genes, with strongly positioned nucleosomes at the start and end of the gene, a fuzzy array of nucleosomes inside the gene, and nucleosomes containing histone variants H2A.Z and H2B.Z in the intergenic regions. The preinitiation complex (PIC) binds to the nucleosome-depleted region (NDR) upstream of the transcription start site (TSS). (c) ATP-dependent nucleosome remodelers change the nucleosome landscape by sliding nucleosomes along the DNA, partially unwrap DNA from the nucleosome, evict nucleosomes, or exchange histone variants. (d) Posttranslational modifications of histones by histone acetyltransferases (HATs), histone deacetylases (HDACs), histone lysine methyltransferases (HKMTs), and histone lysine demethylases (HKDMs). (e) Architecture of the
P. falciparum
nucleus, with colocalization of centromeres (purple balls) and telomeres. The silent
var
genes (white) cluster in repressive heterochromatin, while the single active
var
gene (green) is located in transcriptionally permissive euchromatin. Note the additional looping of the blue chromosome that brings internal and subtelomeric
var
genes in close spatial proximity, while this is not observed in the red chromosome that does not harbor any internal
var
genes. (f) Overview of the complex network of regulatory mechanisms involved in telomere biology and control of
var
gene expression, including histone posttranslational modifications, proteins interacting with DNA motifs or histone-PTMs, and lncRNAs. See the main text for more details.
Chapter 19: Aminoacyl t-RNA Synthetases as Antimalarial Drug Targets
Figure 19.1 Two-step aminoacylation reaction catalyzed by aaRS family of enzymes.
Figure 19.2 Spatial distribution of
P. falciparum
aaRSs.
Figure 19.3 (a) Structural positioning of cladosporin in Lys-RS (PDB ID: 4PG3). View of
P. falciparum
Lys-RS bound to cladosporin (red) and to l-lysine (blue). The protein is dimeric (light blue and yellow) where each monomer binds one drug and one lysine. (b) Structural positioning of Halofuginone in Pro-RS (PDB ID: 4YDQ). View of
P. falciparum
Pro-RS bound to halofuginone (red) and to nonhydrolyzable ATP (AMPPNP – magenta). The protein is dimeric (blue and yellow) where each monomer binds one molecule of HF, proline, and AMPPNP.
Chapter 20: Mathematical Modeling and Omic Data Integration to Understand Dynamic Adaptation of Apicomplexan Parasites and Identify Pharmaceutical Targets
Figure 20.1 Omics data integration is needed to understand fully the regulation of biological processes during the life cycle of Apicomplexan parasites.
Figure 20.2 Schematic overview of plasmodium reactions in structural phospholipid biosynthesis as demonstrated by experimental work. R1 to R17 denote the reaction rates/fluxes. List of species: SerE = exogenous serine, Ser = intracellular serine, PS = phosphatidylserine, EtnE = exogenous ethanolamine, Etn = intracellular ethanolamine, PEtn = phosphoethanolamine, PE = phosphatidylethanolamine, ChoE = exogenous choline, Cho = intracellular choline, PCho = phosphocholine, PC = phosphatidylcholine, DAG = diacylglycerol, SD = serine decarboxylase, PSSbe = phosphatidylserine synthase I, PMT = phosphoethanolamine-
N
-methyltransferase, PEMT = phosphatidylethanolamine-
N
-methyltransferase, CCT = choline phosphate cytidylyltransferase, ECT = ethanolaminephosphate cytidylyltransferase, CEPT = choline/ethanolamine phosphotransferase, CK = choline kinase, EK = ethanolamine kinase, NPP = new permeation pathway, OCT = organic cationic transporter, and ? = putative genes found. The full mathematical model can be found (ID BIOMD0000000495) in BioModels database (www.ebi.ac.uk/biomodels, [112]).
Chapter 21: Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-Based Modeling
Figure 21.1 Steps in genome-scale metabolic model reconstruction and prediction.
Figure 21.2 Constraint-based modeling.
Chapter 22: Attacking Blood-Borne Parasites with Mathematics
Figure 22.1 Schema of the kinetic model of
Trypanosoma brucei
glycolysis with the pentose phosphate pathway. Schema of model version C from Kerkhoven
et al.
[65]. It is shown here as it is available on JWS Online (http://jjj.bio.vu.nl/models/kerkhovenC/simulate/). At JWS Online, the SBML file can also be downloaded. Green squares indicate reactions, blue circles indicate metabolites. Circles that are blue and black denote metabolites involved in more than one reaction (e.g., members of a moiety conserved cycle). Nomenclature is the same as in [65] and can be found there.
Figure 22.2 Schema of the kinetic model of glycolysis of
Plasmodium falciparum
trophozoites. Schema of model by Penkler
et al.
[59]. It is shown here as it is available on JWS Online (http://jjj.bio.vu.nl/models/penkler1/simulate/). At JWS online, the SBML file can also be downloaded. Green squares indicate reactions, blue circles indicate metabolites. Circles that are blue and black denote metabolites involved in more than one reaction (e.g., members of a moiety conserved cycle). Nomenclature is the same as in [59] and can be found there.
Figure 22.3 Do it yourself on JWS Online. Some features of the JWS Online website (http://jjj.bio.vu.nl) here demonstrated on the model of Penkler
et al.
[59] (full scheme is shown in Figure 22.2). Left panels show the items in the drop–down menu after a right-click on a metabolite. It includes information on the structure of the metabolite and direct links to the SABIO-RK database (http://sabiork.h-its.org/), which provides (kinetic) information on the reactions that the metabolite can be involved in. Right panels show the items in the drop–down menu after a right-click on an enzyme, such as a display of the rate equation. The lower right panel shows the result of a “Reaction plot” where the rate of the reaction can be plotted for custom parameter ranges and metabolite concentrations. If experimental data points are available, these will be shown in the plot.
List of Tables
Chapter 1: Discovery of the Mechanism of Action of Novel Compounds That Target Unicellular Eukaryotic Parasites
Table 1.1 Overview of drugs often cited in the text
Chapter 2: Antiparasitics from Algae
Table 2.1 Algae-derived products evaluated for antiparasitic activity
Chapter 3: Contribution of Natural Products to Drug Discovery in Tropical Diseases
Table 3.1 Natural products with antiprotozoan parasitic activity
Chapter 4: Isoxazolines: A Novel Chemotype Highly Effective on Ectoparasites
Table 4.1 Ectoparasiticides acting on ligand-gated chloride channels
Table 4.2 Isoxazoline-derived parasiticides
Table 4.3 Ectoparasiticide activity (IC
50
(nm)) in binding assays on
M. domestica
head membrane.
a
Chapter 5: Trypanosomal Cysteine Peptidases: Target Validation and Drug Design Strategies
Table 5.1 Reported properties for several classes of trypanosomal cysteine peptidase inhibitors
Chapter 7: Phosphatidylcholine and Phosphatidylethanolamine Biosynthesis Pathways in Plasmodium
Table 7.1 Kinetic parameters of the endogenous enzymes of the PC and PE biosynthesis pathways
Chapter 8: Immunophilins as Possible Drug Targets in Apicomplexan Parasites
Table 8.1 Major immunophilins of
Plasmodium
and
Toxoplasma
Chapter 13: Methods to Investigate Metabolic Systems in Trypanosoma
Table 13.1 Applications of isotopic profiling to
T. brucei
procyclic forms
Chapter 14: The Role of Metabolomics in Antiparasitic Drug Discovery
Table 14.1 Metabolomic quenching and extraction techniques for
Plasmodium
and
Trypanosomatid
parasites
Chapter 15: The Importance of Targeting Lipid Metabolism in Parasites for Drug Discovery
Table 15.1 Comparison of lipid composition of parasites
Chapter 16: Carbon Metabolism of Plasmodium falciparum
Table 16.1 Sources of energy in different
Plasmodium
species
Chapter 17: Epigenetic Gene Regulation: Key to Development and Survival of Malaria Parasites
Table 17.1 The “writers,” “erasers,” and “readers” of
P. falciparum
's epigenetic machinery [11]
Chapter 18: Mechanisms Regulating Transcription in Plasmodium falciparum as Targets for Novel Antimalarial Drugs
Table 18.1 Proteins known to be involved in mechanisms of transcriptional regulation and potential targets of novel antimalarial drugs
Chapter 20: Mathematical Modeling and Omic Data Integration to Understand Dynamic Adaptation of Apicomplexan Parasites and Identify Pharmaceutical Targets
Table 20.1 Summary of omic techniques used in the studies of Apicomplexa
Table 20.2 Summary of main mathematical modeling approaches used to unravel mechanisms of regulation of Apicomplexan life cycle
Chapter 21: Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-Based Modeling
Table 21.1 Summary of databases useful in model reconstruction
Table 21.2 Features of COBRA toolbox (version 2.0) [65]
Table 21.3 Tools for metabolic model simulations
Titles of the Series “Drug Discovery in Infectious Diseases”
Selzer, P.M. (ed.)
Antiparasitic and Antibacterial Drug Discovery
From Molecular Targets to Drug Candidates
2009
Print ISBN: 978-3-527-32327-2, also available in digital formats
Becker, K. (ed.)
Apicomplexan Parasites
Molecular Approaches toward Targeted Drug Development
2011
Print ISBN: 978-3-527-32731-7, also available in digital formats
Caffrey, C.R. (ed.)
Parasitic Helminths
Targets, Screens, Drugs and Vaccines
2012
Print ISBN: 978-3-527-33059-1, also available in digital formats
Jäger, T., Koch, O., Flohé, L. (eds.)
Trypanosomatid Diseases
Molecular Routes to Drug Discovery
2013
Print ISBN: 978-3-527-33255-7, also available in digital formats
Doerig, C., Späth, G., Wiese, M.
Protein Phosphorylation in Parasites
Novel Targets for Antiparasitic Intervention
2013
Print-ISBN: 978-3-527-33235-9, also available in digital formats
Unden, G., Thines, E., Schüffler, A. (eds)
Host - Pathogen Interaction
Microbial Metabolism, Pathogenicity and Antiinfectives
2016
Print-ISBN: 978-3-527-33745-3, also available in digital formats
Forthcoming Topics of the Series
Charles Q. Meng, Ann E. Sluder (eds.) Ectoparasites: Drug Discovery Against Moving Targets.
Edited bySylke Müller, Rachel Cerdan, and Ovidiu Radulescu
Comprehensive Analysis of Parasite Biology
From Metabolism to Drug Discovery
Editors
Prof. Sylke Müller
University of Glasgow
Medical, Veterinary & Life Sciences
120 University Place
G12 8TA Glasgow
United Kingdom
Prof. Rachel Cerdan
University Montpellier
DIMNP, UMR5235 CNRS
Place Eugène Bataillon
34095 Montpellier Cedex 5
France
Prof. Ovidiu Radulescu
University Montpellier
DIMNP, UMR5235 CNRS
Place Eugène Bataillon
34095 Montpellier Cedex 5
France
Series Editor
Prof. Dr. Paul M. Selzer
Head of Antiparasitics R&D
Boehringer Ingelheim Animal Health GmbH
Binger Strasse 173
55216 Ingelheim am Rhein
Germany
Cover
Three-dimensional model of the catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase - the rate-limiting enzyme of the phosphatidylcholine biosynthesis pathway - with the bound product CDP-choline. The protein is shown in ribbon representation. CDP-choline is depicted in stick representation. The inset shows a close-up view of the active site with residues coordinating CDP-choline depicted in stick representation. The structure visualization was prepared on the basis of a structural model provided by E. Guca et al., Chapter 7.
The positioning of nucleosomes along eukaryotic genomes is organized by ATP-dependent chromatin remodeling complexes that can promote various changes to the nucleosome landscape, including nucleosome sliding, unwrapping, eviction, and histone exchange. These changes result in altered DNA accessibility and can affect transcriptional activity, E.M. Bunnik & G. LeRoch, chapter 18.
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The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.
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Print ISBN: 978-3-527-33904-4
ePDF ISBN: 978-3-527-69409-9
ePub ISBN: 978-3-527-69411-2
Mobi ISBN: 978-3-527-69410-5
oBook ISBN: 978-3-527-69408-2
Cover Design Adam Design, Weinheim, Germany
List of Contributors
Frederick Annang
Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía
Fundación MEDINA
Screening and Target Validation
Parque Tecnológico de Ciencias de la Salud
Avenida del Conocimiento 34
E-18016 Granada
Spain
Barbara M. Bakker
Vrije Universiteit Amsterdam
Department of Molecular Cell Physiology
De Boelelaan 1085
1081 HV Amsterdam
The Netherlands
and
University of Groningen
University Medical Center Groningen
Center for Liver Digestive and
Metabolic Diseases Systems Biology
Centre for Energy Metabolism and Ageing
Department of Pediatrics
Antonius Deusinglaan 1
9713AV Groningen
The Netherlands
Richáard Bártfai
*
Radboud University
Department of Molecular Biology
Radboud Institute for Molecular Life Sciences
Geert Grooteplein 28
6525GA Nijmegen
The Netherlands
Daniela Begolo
*
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)
DKFZ-ZMBH Alliance
Im Neuenheimer Feld 282
69120 Heidelberg
Germany
Angus Bell
Moyne Institute
Trinity College Dublin
School of Genetics and Microbiology
Department of Microbiology
Dublin 2
Ireland
*
Corresponding author.
Florian Bellvert
Université de Toulouse
Institut National des Sciences
Appliquées
Laboratoire d'Ingénierie des
Systémes Biologiques et des
Procédés
135 Avenue de Rangueil
31077 Toulouse
France
and
Université de Toulouse
Centre national de la recherche
scientifique, UMR5504
Institut national de la recherche
agronomique, UMR792é
Laboratoire d'Ingénierie des
Systémes Biologiques et des Procédés
135 Avenue de Rangueil
31077 Toulouse
France
Alessandra Bianchin
*
University College Dublin
Conway Institute of Biomolecular and Biomedical Science
Belfield, Dublin 4
Ireland
Marco Biddau
University of Glasgow
Institute of Infection, Immunity and Inflammation
College of Medical, Veterinary and Life Sciences
120 University Place
G12 8TA Glasgow
UK
Jürgen Bosch
*
Johns Hopkins University
Johns Hopkins Malaria Research Institute
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry and Molecular Biology
615 North Wolfe Street
W8708 Baltimore, MD 21205
USA
Lauren E. Boucher
Johns Hopkins University
Johns Hopkins Malaria Research Institute
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry and Molecular Biology
615 North Wolfe Street
W8708 Baltimore, MD 21205
USA
James A. Brannigan
University of York
Department of Chemistry
Structural Biology Laboratory
Wentworth Way
Heslington
YO10 5DD York
UK
Ana Brennand
Rayne Institute
King's College London
Faculty of Life Sciences and Medicine
Division of Diabetes and Nutritional Sciences
Denmark Hill Campus
123 Coldharbour Lane
SE5 9NU London
UK
Frédéric Bringaud
Université de Bordeaux
Microbiologie Fondamentale et Pathogénicité
Centre national de la recherche scientifique, UMR 5234
146, rue Léo Saignat
33076 Bordeaux
France
Evelien M. Bunnik
University of California Riverside
Center for Disease Vector Research
Department of Cell Biology and Neuroscience
Institute for Integrative Genome Biology,
900 University Avenue
Riverside, CA 92521
USA
Edern Cahoreau
Université de Toulouse
Institut National des Sciences
Appliquées
Laboratoire d'Ingénierie des
Systémes Biologiques et des Procédés
135 Avenue de Rangueil
31077 Toulouse
France
and
Université de Toulouse
Centre national de la recherche
scientifique, UMR5504
Institut national de la recherche
agronomique, UMR792
Laboratoire d'Ingénierie des
Systémes Biologiques et des
Procédés
135 Avenue de Rangueil
31077 Toulouse
France
Rachel Cerdan
*
University Montpellier
Laboratory of Dynamique des Interactions Membranaires Normales et Pathologiques
UMR 5235 CNRS, UM
Place Eugéne Bataillon
34095 Montpellier Cedex 5
France
Anmol Chandele
*
International Center for Genetic Engineering and Biotechnology
Aruna Asaf Ali Marg
New Delhi 110 067
India
and
ICGEB-Emory Vaccine Center
Molecular Medicine Group
ICGEB
Aruna Asaf Ali Marg
New Delhi 110 067
India
Anthony J. Chubb
Royal College of Surgeons in Ireland
Department of Molecular and Cellular Therapeutics
123 St Stephen's Green
Dublin 2
Ireland
Christine Clayton
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)
