Metabolism and Pharmacokinetics Division, Ranbaxy Research Laboratories, Plot-18, Sector-20,
Udyog Vihar, Industrial Area, Gurgaon, Haryana 122015, India Received 11 December 2006; accepted 9 January 2007 Abstract The emergence and spread of drug-resistant malaria parasites is a serious public health problem in the tropical world. Malaria control has relied upon the traditional quinoline, antifolate and artemisinin compounds. Very few new antimalarials were developed in the last quarter of the 20th century. An alarming increase in drug-resistant strains of the malaria parasite poses a signicant problem for effective control. Recent advances in our knowledge of parasite biology as well as the availability of the genome sequence provide a wide range of novel targets for drug design. Gene products involved in controlling vital aspects of parasite metabolism and organelle function could be attractive targets. It is expected that the application of functional genomic tools in combination with modern approaches such as structure-based drug design and combinatorial chemistry will lead to the development of effective new drugs against drug-resistant malaria strains. This review discusses novel molecular targets of the malaria parasite available to the drug discovery scientist. 2007 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved. Keywords: Drug targets; Parasite transporters; Parasite proteases; Apicoplast; Cyclin-dependent kinases 1. Introduction Malaria is a devastating infectious disease and a major cause of morbidity and mortality throughout the world. The World Health Organization estimates that malaria kills an African child every 30 s [1]. Approximately 40% of the worlds population live in malaria-endemic areas and ca. 90% of cases and most deaths occur in tropical Africa. There are up to 500 million clinical cases and 3 million deaths annu- ally [2]. The majority of severe disease is due to Plasmodium falciparum. The two most widely used antimalarial drugs, chloroquine and sulfadoxine/pyrimethamine, are failing at an accelerating rate in most malaria-endemic regions owing to the development of resistance to these agents. Other anti- malarial drugs such as meoquine, halofantrine, atovaquone, proguanil, artemether and lumefantrine retain efcacy but have limitations, one of which is their high cost. The drugs currently used for malaria come from three families: the quinolines (quinine, chloroquine, meoquine,
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E-mail address: jyoti.paliwal@ranbaxy.com (J. Paliwal). primaquine), the antifolates (sulfadoxine, pyrimethamine) and the artemisinin derivatives [3]. The increasingly serious problemof malaria parasite resis- tance to currently used antimalarials has led to an urgent need to develop new and effective antimalarial molecules. This goal can be achieved in two ways: either by focusing on vali- dated targets in order to generate new drug candidates; or by identifying new potential targets for malaria chemotherapy. The advent of functional genomics and structure-based drug design should help in the search for newtargets. In this report, we examine putative novel molecular targets for the rational design of new antimalarials. 2. Potential targets for new antimalarials Drug-resistant strains of malaria parasites pose signicant challenges to drug discovery efforts. This increasing resis- tance to multiple drugs may be the result of defective DNA repair or other pathways responsible for genomic stability [4]. Sequencing of the P. falciparum genome, the emergence of drug resistance and advances in molecular techniques have refocused antimalarial drug discovery efforts. Several critical 0924-8579/$ see front matter 2007 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved. doi:10.1016/j.ijantimicag.2007.01.002 S. Jana, J. Paliwal / International Journal of Antimicrobial Agents 30 (2007) 410 5 Fig. 1. Schematic representation of novel molecular targets in plasmodia. RBCM, red blood cell membrane; PVM, parasitophorous vacuole mem- brane; PPM, parasite plasma membrane. and unrelated biochemical pathways have been exploited for drug target identication (Fig. 1; Table 1). 2.1. Targeting parasite membrane biosynthesis Intraerythrocytic parasites possess different membranes such as the food vacuolar membrane, the parasite plasma membrane (PPM) and the parasitophorous vacuole mem- brane. The amount of lipid in infected erythrocytes is therefore signicantly higher than that of normal erythro- cytes. Growing and dividing malaria parasites require large amounts of phospholipids, which are synthesised from plasma fatty acids. Phosphatidylcholine (PC) is the major parasite phospholipid. Most of the PC (7080%) is synthe- sised by de novo synthesis from choline. In infected red blood cells (RBCs), choline mobility increases signicantly via a constitutive choline carrier. This occurs from parasite- induced overactivity of a constitutive host cell transporter or parasite-driven synthesis of a new carrier. Molecules are being designed to target the parasites supply of PC. Quater- nary ammonium and bis-ammonium quaternary salts with one long lipophilic alkyl chain and bis-ammonium salts linked by a long alkyl chain showed high in vitro parasite inhibition at the nanomolar range [5]. Members of this group of compounds proved effective in vivo in experimental ani- mals. A new class of potent antimalarial drugs was identied that inhibits de novo PCbiosynthesis in the parasite [6]. G25, a lead compound, potently inhibited in vitro growth of P. fal- ciparum and Plasmodium vivax. It was also 1000-fold less toxic to mammalian cell lines and IC 50 values (inhibitory concentration of 50%) were in the low nanomolar range. A very low dose of G25 can cure monkeys infected with P. falciparum and Plasmodium cynomolgi, demonstrating the therapeutic potential of this class of compounds [7]. 2.2. Targeting parasite transporters There is a profound increase in the permeability of the host membrane to a wide range of solutes in malaria-infected erythrocytes. Molecular trafc across the host erythrocyte membrane undergoes dramatic changes with respect to inten- sity and the nature of permeating solutes. The induced permeability pathways are known as new permeability path- ways (NPPs), which are polyspecic, anion selective and confer increased permeability to a wide range of charged and low-molecular-weight solutes. These NPPs are thought to provide the major entry of some essential nutrients (pan- tothenate) required by the parasites. They also mediate the efux of various metabolic waste substances such as lactic acid from the infected cell [8]. The properties of the parasite- induced transport systems are signicantly different from those in normal human cells. Therefore, these transport sys- Table 1 Novel targets in Plasmodium falciparum Target Enzyme/process Inhibitor Membrane biosynthesis Phospholipid biosynthesis G25 Parasite transporters Unique channels Quinolines Hexose transporter O-3-hexose derivatives Parasite proteases Plasmepsins, falcipains Leupeptin, pepstatin Shikimate pathway 5-enolpyruvyl shikimate 3-phosphate synthase Glyphosate Isoprenoid biosynthesis DOXP reductoisomerase Fosmidomycin Redox system Thioredoxin reductase 5,8-Dihydroxy-1,4-naphthoquinone Gamma-GCS Buthionine sulfoximine Mitochondrial system Cytochrome c oxidoreductase Atovaquone Purine metabolism HGPRT Immucillin-H Pyrimidine metabolism Thymidylate synthase 5-Fluoroorotate Apicoplast Fab H Thiolactomycin Fab I Triclosan Cyclin-dependent protein kinases Pfmrk Oxindole derivatives, thiophene sulfonamide DOXP, 1-deoxy-d-xylulose-5-phosphate; GCS, glutamylcysteine synthetase; HGPRT, hypoxanthineguaninexanthine phosphoribosyltransferase. 6 S. Jana, J. Paliwal / International Journal of Antimicrobial Agents 30 (2007) 410 tems could potentially be exploited as targets for antimalarial chemotherapy. This could be achieved by designing cytotoxic drugs that selectively enter the parasite through these induced transporter routes. Recently, some of the transporters at the PPM have been characterised. Kirk et al. [9] suggested that a PPM-located vacuolar-type proton pump (V-type H + pump) extrudes pro- tons. As a result, there is a gradient of pH across the PPM that generates inwardly negative membrane potential (). This pump regulates cellular pH by extruding protons gener- ated by the metabolic activity of the parasite. Asexual-stage parasites require a continuous supply of glucose to survive and multiply, suggesting that the hexose transporter (PfHT) of P. falciparum is a potential drug target. It is a single copy gene (pfht) with no close paralogues in the fully sequenced falciparum genome. Joet et al. [10] reported that O-3-hexose derivatives inhibit uptake of glucose and fructose by PfHT in Xenopus oocytes and in a mouse model of Plasmodium berghei. Exploiting knowledge gained about the transport processes operating in the infected cell might well enhance the success of these approaches. 2.3. Targeting parasite proteases Plasmodia are blood-eating parasites. Proteases have an important role in parasite survival by hydrolysing a signicant proportion of the host erythrocyte proteins. Approximately 80% of the host cell haemoglobin is broken down into individual amino acids, some of which are used for parasite protein synthesis [11]. Several Plasmodium pro- teases that appear to be responsible for vital cleavage of host proteins have been characterised. The spectrumof proteolytic activity in the malarial parasite can be conveniently divided into two functional groups: proteases that are involved in invasion and rupture of the erythrocyte and proteases that are involved in haemoglobin degradation [11]. The hostparasite interactions remain elusive at the molecular level during the invasion process. It is clear that many surface proteins are proteolytically modied and that these events are critical for successful merozoite invasion [12]. The merozoite sur- face protein MSP-1, the most prominent and relatively well studied, is involved in the invasion process. The malaria par- asite P. falciparum invades human RBCs. Before infecting new erythrocytes, the merozoites must exit their host cell to enter the blood plasma. It is thought that proteases are basi- cally involved in this step. Cysteine protease inhibitors are used to study the mechanism of merozoite release using u- orescence microscopy and immunoelectron microscopy. The inhibitors block rupture of the host cell membrane, leading to clustered merozoite structures. Cysteine protease inhibitors (e.g. E64, leupeptin and chymostatin) appear to be a valuable template for the development of new inhibitors specic to individual plasmodial proteases [13]. These would be use- ful tools to dissect the molecular mechanisms underlying the process of merozoite release and consequently to develop potent antimalarial drugs. Several plasmepsin and falcipain proteins (aspartic and cysteine proteases) have been evaluated as candidate drug tar- gets [14,15]. Examples include uoromethyl ketones, vinyl sulfones and chalcones, which target the cysteine proteases [16,17]. The statine, allophenylnorstatine and diphenylurea derivatives target the aspartic proteases [18]. Detailed bio- chemical characterisation, recombinant expression and X-ray crystallographic structural analysis of parasite proteases and their role in pathogenesis of malaria remain to be carried out. 2.4. Targeting the shikimate pathway The shikimate pathway in apicomplexan parasites, including P. falciparum, provides several targets for the development of new antiparasitic agents. This pathway is not present in mammals [19]. However, it occurs in the cytosol of bacteria and fungi and is localised to the chloro- plast in plants. There are seven enzymes involved in the shikimate pathway, which catalyse sequential conversion of erythrose-4-phosphate and phosphoenolpuruvate to cho- rismate. This molecule is utilised by several pathways for the synthesis of different critical molecules including tryptophan, phenylalanine, tyrosine, vitamin K, ubiquinone and p-aminobenzoic acid (PABA), which is utilised for folate generation. Glyphosate is a herbicide that inhibits 5- enolpyruvylshikimate 3-phosphate synthase in the shikimate pathway [20]. 6-S-uoroshikimate and 6-R-uoroshikimate have been shown to inhibit P. falciparum growth and have been shown to be specic to the shikimate pathway [21]. A single gene encoding the terminal enzyme in the shikimate pathway has been identied in the genome annotation [22]. The coding DNA sequence of chorismate synthase has been identied in P. falciparum and has been shown to be located in the parasite cytosol [23]. Chorismate synthase has been shown to be required for normal growth and disruption of expression by RNA interference, which decreases parasite growth [24]. P. falciparum chorismate synthase is therefore a validated target for drug discovery. 2.5. Targeting isoprenoid biosynthesis Plasmodium protein farnesyltransferase (PfPFT) inhi- bition is being considered as a potential drug target. PFT inhibitors have been developed for the treatment of human cancer. These inhibitors act by inhibiting post- translational modication pathways. A similar concept is being explored by medicinal chemistry and pharmacokinetics to develop PFT inhibitors against parasites [25]. Mam- mals and fungi both depend on mevalonate to generate the intermediate isopentyl diphosphate molecule. Plasmodium falciparum as well as bacteria utilise 1-deoxy-d-xylulose-5- phosphate (DOXP) as a precursor molecule, referred to as the mevalonate-independent pathway. The plastid-encoded mevalonate-independent pathway of isoprenoid biosynthesis has been considered as a potential target for antimalar- ial chemotherapy [26]. Fosmidomycin and its derivative S. Jana, J. Paliwal / International Journal of Antimicrobial Agents 30 (2007) 410 7 FR900098 are phosphonic acid derivatives with low toxic- ity. These compounds inhibit DOXP reductoisomerase. It is the key enzyme of the DOXP pathway, which is absent in humans. The drug fosmidomycin demonstrates signicant antiparasitic activity. This facilitates the explanation of this pathway for chemotherapeutic intervention [27]. PfPFT inhi- bition is considered to be lethal as a result of the absence of protein geranylgeranyl transferase-1 (PGGT-1), which reverses PFT-inhibited mammalian cells. 2.6. Targeting the redox system Oxidative stress is an important mechanism for destruc- tion of malaria and other intracellular parasites. In intraerythrocytic-stage malaria, parasites encounter reactive oxygen species produced either by themselves or by the ery- throcyte or host immune cells. To prevent oxidative stress, the parasite has its own battery of defence tactics and pro- duces its own antioxidant enzymes. The malaria parasite contains three antioxidant enzymes: superoxide dismutase (SOD), glutathione peroxidase (GPx) and catalase. The para- sites antioxidant defence could therefore be a potential target for antimalarial chemotherapeutics. Functional thioredoxin and glutathione systems have been shown to participate in antioxidant defence in P. falciparum and both are considered attractive targets. The key enzymes of P. falciparuminvolved in redox metabolism are glutathione reductase, glutathione peroxidase, thioredoxin reductase and thioredoxin peroxire- doxin [28]. The parasite thioredoxin reductase differs from the host enzyme, containing a pair of cysteines separated by four amino acids and lacking a selenocysteine present in the host enzyme [29]. 5,8-Dihydroxy-1,4-naphthoquinone and 5-nitro-2-furanacrolein are inhibitors of thioredoxin reduc- tase. Both these compounds have plasmodicidal effects in vitro [30]. Glutathione S-transferase (GST) catalyses the con- jugation of glutathione with a wide variety of hydrophobic compounds and as a result non-toxic products are formed, which can be readily eliminated. Plasmodium falciparum possesses only one GSTisoenzyme in contrast to other organ- isms. Plasmodial GST is a promising target for antimalarial drug development because it is highly abundant in the para- site. GST has been shown to act as a ligand for parasitotoxic hemin. The crystal structure of P. falciparum GST has been solved and shown to differ considerably from the human enzyme [31]. This feature could be exploited to search for specic inhibitors. 2.7. Targeting the mitochondrial system The mitochondrial DNA sequence of P. falciparum has been determined. There are two main functions of mitochon- dria: electron transport and protein synthesis. These appear to be essential for survival and constitute potential targets for antimalarial chemotherapy [32]. The malaria parasite mito- chondrial DNA has a 6 kb genome encoding three proteins: cytochrome b, and subunit I and III of cytochrome c oxi- dase, which is a terminal oxidase of the respiratory chain [33]. Transcripts of the 6 kb element are most abundant in the late phases of the asexual life cycle. The cytochrome b gene of the ubiquinolcytochrome c reductase (complex III) is produced primarily by asexual life stages rather than game- tocytes. The structural features of the plasmodial cytochrome b differ from mammalian cytochrome b [34], and these dif- ferences in mitochondria between malaria parasites and the host are expected to be a target for chemotherapy. Atovaquone is a ubiquinone analogue and inhibits ubiquinone binding to cytochrome b. It is effective against chloroquine-resistant strains [35]. Its primary site of action has been biochemically shown to be the ubiquinone oxidation site of the cytochrome bc1 complex (complex III). The unique properties of the respiratory chain in mitochondria have yet to be exploited and the development of a new antimalarial agent is anticipated. 2.8. Targeting nucleic acid metabolism Nucleotides are the precursors of DNA and RNA biosyn- thesis. Nucleic acid metabolism pathways differ between P. falciparum and the human host. Plasmodia synthesise purines and pyrimidines by salvage and de novo biosynthetic pathways, respectively, whilst mammalian cells synthesise purines de novo and either salvage or synthesise pyrimidine by a de novo pathway. The two pathways involve a range of essential enzymes that can be targeted for therapeutic intervention. 2.8.1. The purine pathway The malaria parasite lacks the de novo purine biosyn- thetic pathway and starvation of purines is known to cause purineless death in cultured cells. The most extensively studied enzyme of the salvage pathway is hypoxanthineguaninexanthine phosphoribosyltransferase (HGPRT). The parasite and human HGPRT share partial sequence similarity (46%) in the primary structures and differ in substrate selectivity (xanthine for plasmodia). The struc- tures give no insight into the origin of this difference. In humans and parasites, hypoxanthine production is mediated by phosphorolysis of inosine to hypoxanthine, catalysed by purine nucleotide phosphorylase (PNP). Immucillin-H is a transition state analogue that has been shown to kill the par- asite through inhibition of PNP [36]. Recently, the crystal structure of P. falciparum PNP complex with immucillin-H revealed that its active site shows structural differences from human PNP. Ting et al. [37] demonstrated that 5-methylthio- immucillin-H kills P. falciparum strain 3D7 cultures. This inhibition occurs at very low concentrations, where parasite PNP is selectively inhibited but no inhibition is reported for human PNP. These results suggest that structure-based design studies and rapid screening efforts would be helpful for dis- covering and developing new antimalarials by targeting the parasite HGPRT and PNP enzymes. 8 S. Jana, J. Paliwal / International Journal of Antimicrobial Agents 30 (2007) 410 2.8.2. The pyrimidine pathway Malaria parasites derive their pyrimidine nucleotides through a de novo pathway. They cannot utilise pre-formed pyrimidine nucleosides. Mammalian cells are capable of de novo and salvage pathways. The salvage enzymes (uridine kinase andthymidine kinase) are absent inthe parasite. The de novo enzymes are carbamoyl phosphate synthase, aspartate transcarbamylase, dihydroorotase, dihydroorotate dehydro- genase (DHODase), orotate phosphoribosyl transferase and orotidine 5
-phosphate decarboxylase [38]. Thymidylate syn-
thase (TS) is linked to dihydrofolate reductase. It is also an established target for antimalarial chemotherapy. Since TS is a highly conserved protein, selective inhibitors may be difcult to design. An alternative strategy could be the com- bination of an effective TS inhibitor and a nucleoside that can be utilised by the host. N 5 -N 10 -methylene tetrahydrofo- late analogues, which inhibit TS without being metabolised into the nucleotide pool, are considered attractive alternatives [39]. Such analogues need to be explored further. 2.9. Targeting the apicoplast By molecular and cell biological analysis it was realised that apicomplexan parasites, including P. falciparum, harbour a plastid-like organelle called the apicoplast. This organelle is derived fromthe engulfment of photosynthetic red algae in ancient times. The P. falciparum apicoplast genome contains ca. 35 kb and is much smaller than its plastid ancestor. Most of the proteins of this organelle are encoded in the nuclear genome and the proteins are subsequently transported to the apicoplast. The apicoplast contains unique metabolic path- ways such as fatty acid, isoprenoid and heme synthesis, which are not found in the human host [40]. Hence, these parasite- specic metabolic pathways make an ideal source of drug targets. Fatty acid biosynthesis is fundamental to cell growth, differentiation and homeostasis. All living organisms synthe- sise fatty acids (except mycoplasmas). Fatty acid synthesis (FAS) is a major function of the apicoplast. The enzymes involved in FAS are: acetyl-CoA carboxylase (ACC), mal- onyl transacetylase (Fab D), -ketoacyl-ACP synthase (Fab H, B/F), -ketoacyl-ACP reductase (Fab G), -hydroxyacyl- ACP dehydrase (Fab A/Z) and enoyl-ACP reductase (Fab I). There is an inherent difference between the fatty acid biosyn- thesis pathways of the parasite (type II) and the human host (type I), thus making thema promising target for the develop- ment of antimalarials. Thiolactomycin is an inhibitor of Fab H and showed inhibition of P. falciparum growth in in vitro cultures [41]. This indicates that -ketoacyl-ACP synthase III (Fab H) has a vital role for apicoplast type II fatty acid biosynthesis. Recently, enoyl-ACP reductase (Fab I) activ- ity has also been reported, and triclosan has been shown to be antiparasitic by inhibition of Fab I [42]. Further stud- ies to elucidate the functions carried out by this organelle would aid in selection of the essential enzymes for drug targeting. 2.10. Targeting the parasite cyclin-dependent protein kinases (CDKs) Several kinases from P. falciparum have been identied that are homologues to the mammalian CDKs. Based on the conservation of CDKs across species, the plasmodial CDKs are expected to play a crucial role in parasite growth [43]. The cell cycle of the parasite differs dramatically from the eukaryotic cell cycle. In eukaryotes, a single round of DNA replication per cell cycle occurs, resulting in the generation of two identical daughter cells. During schizogony, the parasite undergoes multiple rounds of DNA replication and nuclear division prior to cytokinesis. As a result, a single multinucle- ate syncytium develops. A single parasite produces between 8 and 32 merozoites. Parasitic cell division must be regulated in a manner that is different from mammals. Several P. falci- parumCDKs have been shown with a sequence and structure similar tothe mammalianhomologues [43]. Therefore, CDKs have become attractive targets for novel antimalarial thera- peutics. HumanCDK7has the highest sequence identity(46%) and similarity (64%) to Pfmrk. CDK7 has a dual function, act- ing as the cyclin-dependent kinase-activating kinase and as a transcription factor to regulate transcription and DNA repair. The parasite kinase Pfmrk shows a similar two-fold function, which would render it a highly attractive target for designing CDK inhibitors [44]. Structural studies would be helpful for rational design of potent and selective Pfmrk inhibitors as antimalarial therapeutics. 3. Future perspectives Malaria parasites have diverse metabolic systems greatly different from that of the mammalian host by which they adapt to the specic environment in the host. The key infor- mation that permits rational approaches to drug design is knowledge of the aetiology of a given disease or at least of the biochemical processes that are involved. Despite considerable advances in our understanding of parasite biol- ogy and biochemistry, it appears that these organisms often use novel modes of metabolism, signalling, protein trafck- ing pathways, cell division and extracellular communication mechanisms. The proteins involved in these processes often possess signicant sequence variation and distinct differ- ences in biochemical or catalytic properties. All proteins of P. falciparum are often referred to as good targets. Proteins available frommalaria genome sequencing projects would be potential drug targets [45]. In addition, rational drug design using structural information would be possible following structure elucidation using recombinant protein production systems. Three-dimensional structure elucidation using X- ray crystallography would allow us to design drugs based on a model of the target binding site. The best examples of these include inhibitors of parasite HGPRT and proteases. In the absence of protein structural information, quantitative S. Jana, J. Paliwal / International Journal of Antimicrobial Agents 30 (2007) 410 9 structure activity relationships can be obtained by correlat- ing the binding strength of ligands to the target molecule with their structural properties [46]. Computer-assisted molecular modelling has played an essential role in the design of poten- tial ligands that are both sterically and chemically compatible with the binding site of a target molecule. 4. Conclusions There have been considerable advances in our understand- ing of the mechanisms of action and resistance to traditional antimalarial drugs. We principally emphasise putative molec- ular targets covered based on various aspects of the malaria parasite. These putative targets could be helpful for the future development of newantimalarials. The elds of genomics and proteomics are able to play an important role in the discovery of new drugs against malaria. 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