Patent Publication Number: US-2023140413-A1

Title: Compounds and Methods for Treating, Detecting, and Identifying Compounds to Treat Apicomplexan Parasitic Diseases

Description:
CROSS REFERENCE 
     This application is a divisional application of U.S. patent application Ser. No. 16/063,877, filed Jun. 19, 2018, which is a U.S. national phase application of International Patent Application no. PCT/US2016/067795, filed on Dec. 20, 2016, which claims the benefit of U.S. Provisional Patent Application No. 62/270,264, filed Dec. 21, 2015, and U.S. Provisional Application No. 62/306,385, filed Mar. 10, 2016, each incorporated by reference herein in their entirety. 
    
    
     STATEMENT OF GOVERNMENT RIGHTS 
     This invention was made with government support under National Institutes of Health (NIH) contract number HHNS272200900007C, NIH, National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIAID) award numbers R01AI071319 (NIAID) and R01AI027530 (NIAID); NIAID contract Number HHNS272200900007C; NIAID award number U19AI110819: NIAID award numbers U01 AI077887 (NIAID) and U01AI082180 (NIAID); National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Grant #5T35DK062719-28: Defense Threat Reduction Agency award number 13-C-0055, and Department of Defense award numbers W911NF-09-D0001 and W911SR-07-C0101. The government has certain rights in the invention. 
    
    
     BACKGROUND 
     Apicomplexan parasitic infections, such as  Toxoplasma gondii  infections, can cause systemic symptoms, damage and destroy tissues, especially eye and brain and cause fatalities. Primary infections may be asymptomatic, or cause fever, headache, malaise, lymphadenopathy, and rarely meningoencephalitis, myocarditis, or pericarditis. Retinochoroiditis and retinal scars develop in up to 30% of infected persons, and epilepsy may occur. In immune-compromised and congenitally infected persons, active infection frequently is harmful. Recrudescence arises from incurable, dormant cysts throughout life. Current treatments against active  T. gondii  tachyzoites can have side effects such as hypersensitivity, kidney stones, and bone marrow suppression, limiting their use. Latent bradyzoites are not significantly affected by any medicines. Atovaquone partially, and transiently, limits cyst burden in mice, but resistance develops with clinical use. Thus,  T. gondii  infection is incurable with recrudescence from latent parasites posing a continual threat. Estimates of costs for available, suboptimal medicines to treat active, primary ocular, gestational and congenital infections, in just the U.S. and Brazil, exceed $5 billion per year. 
     Improved medicines are needed urgently. Molecular targets shared by  T. gondii  and Plasmodia make re-purposing compounds a productive strategy. 
     SUMMARY OF THE INVENTION 
     In one aspect, the invention provides compounds of the structure of Formula (I), pharmaceutical compositions thereof, and methods for their use in treating apicomplexan parasite related disorders): 
     
       
         
         
             
             
         
       
         
         
           
             or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, 
             wherein 
             ring A combines with Y 1  and Y 2  to form a C 3-7 cycloalkenyl or heteroaryl ring,
           wherein the C 3-7 cycloalkenyl or heteroaryl is optionally substituted by halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, cyano or phenyl;   
         
             Y 1  is C or N; 
             Y 2  is C or N; 
             X 1  is C(R x1 ) or N,
           wherein R x1  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
         
             X 2  is C(R x2 ) or N,
           wherein R x2  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
         
             X 3  is O, N(R), S or C 1-3 alkyl; 
             X 4  is C or N; 
             X 5  is C or N; 
             R 1  is hydrogen or C 1-3 alkyl; 
             R2 is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR; 
             n is 0, 1, 2, 3 or 4; 
             each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ; 
             or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane; and 
             each R is independently hydrogen or C 1-3 alkyl. 
           
         
       
    
     In another aspect, the invention provides cell lines infected with an apicomplexan parasite, wherein the apicomplexan parasite genome comprises a gene encoding an Apetela 2 IV-4 protein with an M=&gt;I modification at residue 570 (“AP2 IV-4 M570I”) compared to its orthologous gene on the reference  T. gondii  ME49 strain (gene ID: TGME49_318470), non-human animal models comprising cell lines of the invention, and methods for use of each in identifying compounds for treating an apicomplexan parasitic infection. 
     In another aspect, the invention provides methods for treating an apicomplexan parasite infection (such as a  T. gondii  infection), comprising administering to a subject in need thereof an amount effective to treat the infection of an inhibitor (of up-regulated genes) or an activator (of down-regulated genes) of 1 or more up-regulated genes as discussed herein. 
     In a further aspect, the invention provides methods for identifying test compounds for apicomplexan parasite therapy, comprising identifying test compounds that reduce expression (for up-regulated genes), or increase expression (for down-regulated genes) of 1 or more apicomplexan parasite genes as discussed herein. 
     In one aspect, the invention provides a plurality of isolated probes that in total selectively bind to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 100, 150, 200, 250, 500, or all of the markers as discussed herein, complements thereof, or their expression products, or functional equivalents thereof wherein at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or all of the probes in total are selective for markers that are upregulated in the EGS strain of  T. gondii  after infection of human fibroblasts, neuronal stem cells or monocytic lineage cells. 
     In another aspect, the invention provides a plurality of isolated probes that in total selectively bind to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 100, 150, 200, 250, 500, or all of the markers as discussed herein, complements thereof, or their expression products, or functional equivalents thereof, wherein at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or all of the probes in total are selective for markers that are upregulated in human fibroblasts, neuronal stem cells or monocytic lineage cells after infection with  T. gondii , including but not limited to infection with the EGS strain of  T. gondii.    
     In another aspect, the invention provides methods for monitoring  T. gondii  infection in a subject, comprising monitoring levels in a blood sample from the subject of one or more markers selected from the group consisting of clusterin, oxytocin, PGLYRP2 (N-acetylmuramoyl-L-alanine amidase), Apolipoprotein A1 (apoA1), miR-17-92, and miR-124, wherein a change in levels of the one or more circulating markers compared to control correlates with  T. gondii  infection in the subject. 
     In another aspect, the invention provides methods for treating a  T. gondii  infection, comprising administering to a subject with a  T. gondii  infection an amount effective to treat the infection of ApoA1. 
    
    
     
       DESCRIPTION OF THE FIGURES 
         FIG.  1 A- 1 D . EGS morphology and effect on host cell transcriptomes  FIG.  1   a   . EGS in human MM6 cells and NSC form cysts. Left NSC with EGS. Right MM6 with EGS. Note green dolichos cyst walls and BAG1 (red) in NSC. DAPI stained nuclei(blue).  FIG.  1 B ,  FIG.  1 C . Effects of EGS infection on MM6 and NSC transcriptomes: EGS transcripts in MM6 compared with NSC shows overlap of, as well as unique patterns of, transcripts. Differentially expressed genes in MM6 and NSC cells infected with EGS parasite were identified based on criteria of 1% FDR and absolute fold-change ≥2. Number of DEGs in each cell line are presented with bar graph ( FIG.  1 B ) and Venn diagram are used to show general comparison of DEGs identified between the two cell lines ( FIG.  1 B ). There is both communality, overlap in genes modulated and independence in others between cell types indicating cell type also influences cell type. Red and green colors were used to represent up- and down-regulated genes, cell line used is indicated on bottom ( FIG.  1 B - FIG.  1 C ). Functional enrichment analysis was performed for gene ontology (GO) biological process and KEGG pathways. P-values derived from analysis were −log 10 transformed and presented as a heat map. Pink and blue colors indicate GO terms or KEGG pathways enriched by up- and down-regulated genes, respectively. Enriched pathways or biological processes are listed on right of panels and cell lines are indicated on top.  FIG.  1 D . Host cell miR-seq analysis reveals that EGS regulates host cell miRNAs critical in pathogenesis and latency. An especially interesting down-modulated miRNA is hsa-miR-708-5p which is expressed particularly in brain and retina cells causing apoptosis 65 . When  T. gondii  downmodulates this as an encysted bradyzoite in neuronal cells, it would prevent hosts from initiating apoptosis to eliminate chronically infected neurons. f. Parasite genetics and human host cell type have a profound influence on  T. gondii  gene expression. MDS plot comparing  T. gondii  gene expression profiles from MM6 and NSC cells infected with EGS, GT1, ME49 and VEG strains for 18 hours and HFF cell cultures infected with EGS strain for 2, 18 and 48 hours. 
         FIG.  2 A- 2 B . Differential Gene Expression (DGE) analyses and effects of inhibition of cytochrome bc1.  FIG.  2 A . DGE analysis of bradyzoite- and tachyzoite-specific markers during EGS infections of HFF cultures at 2, 18 and 48 hours (top panel), MM6 cells at 18 hours (middle panel) or NSC cultures at 18 hours (bottom panel) versus infections of same host cells with canonical strains GT1, ME49 or VEG at 18 hours (averaged across the three canonical strains for HFF infections). Genes reported as being over- or under-expressed during bradyzoite differentiation is indicated with red or green arrows respectively. “*”, q-value ≤0.05; Log FC, logarithm of the fold change in gene expression. CST1, SAG-related sequence SRS44 s114 ; LDH2, lactate dehydrogenase 2 S115 ; LDH1, lactate dehydrogenase 1 S115 ; ENO2, enolase 2; ENO1, enolase 1 S116 ; SAG1, SAG-related sequence SRS29B; BAG1, bradyzoite antigen BAG1 S115 .  FIG.  2 B . Effect of known cytochrome b inhibitors on EGS. Morpholino conjugated to a Vivoporter (called PPMO) designed to knock down cytochrome b compared with off target control has a significant effect in reducing replication of YFP RH strain tachyzoites at 5 and 10 μM (p&lt;0.05) but only a very small effect on size and number of EGS cysts in HFF. As a poorly soluble inhibitor of cytochrome b, ELQ271 was reported to partially reduce cyst numbers in mice 27  and is shown herein also to reduce the EGS cysts in vitro at 10 μM in this novel model. This demonstrates the utility of this novel in vitro model by indicating that inhibition of cytochrome b Qi is associated with reduction of cysts in vivo in a mouse model, even when there are serious limitations caused by insolubility of this inhibitory compound. This poor solubility significantly limits ELQ271 as a candidate for progression to a medicine. Increasing selectivity for the parasite enzyme with our new scaffold is another critical challenge. 
         FIG.  3 A-  3 B .  FIG.  3 A . Structures of the ELQ class (1-3) and the tetrahydroquinolone scaffold (4). 27,45,49,53 . Low solubility of the ELQs has been a serious concern going into preclinical evaluation for treatment of malaria. 27    FIG.  3 B .  Saccharomyces cerevisiae  cytochrome bc 1  X-ray structure (PDB ID: 1KB9) 5  The complex contains 11 subunits and 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein). The cytochrome b subunit provides both quinone binding sites (Q o  and Q i ) highlighted as grey and pink surfaces respectively. 
         FIG.  4 A- 4 E . ELQ inhibitors provide a new scaffold and approach yielding compounds that are potent inhibitors of tachyzoites and cysts in vitro. Study of Inhibitors in vitro is summarized in Table 2 and led to selection of MJM170 as a promising novel scaffold for both tachyzoites and bradyzoites.  FIG.  4 A . MJM170 markedly reduces RH YFP tachyzoites in tissue culture robustly at low nanoM levels. (Standard curve left and effect on RH YFP, right panel).  FIG.  4 B ,  FIG.  4 C . MJM170 markedly reduces EGS bradyzoites in cysts in vitro. Inhibition of cytochrome b Qi eliminates cysts in HFF infected with EGS. Without inhibitory compound in HFF (note, oval cyst with green border staining dolichos) and adjacent panel with inhibitory MJM170 compound (note absence of cysts with small amount of amorphous residual dolichos). MJM170 eliminated tachyzoites followed to 10 days of culture and bradyzoites in cysts in vitro. Summary comparison of each of the compounds tested in vitro and their ADMET is in Table 2. Note improvement in solubility, properties amenable for compounds to cross blood brain barrier with new scaffold.  FIG.  4 D . EGS transfected with stage specific reporters for fluors, red tachyzoite SAG1, Green bradyzoite LDH2. 
         FIG.  5 A- 5 D . MJM170 is also effective against RH and Prugneaud tachyzoites and Me49 bradyzoites, in vivo with translucent zebrafish providing a novel model with potential for scalable in vivo assays in which tachyzoites with fluorescent reporters and bradyzoites in cysts can be visualized efficiently.  FIG.  5 A : 25 mg/kg daily MJM170 administered intraperitoneally eliminates active infection due to RH tachyzoites stably transfected with YFP in mice (RFU control vs rx with MJM 170, p&lt;0.004). For the standard curve in the inset, RFU increase with increasing concentrations of fluorescent tachyzoites (R 2 =0.99).  FIG.  5 B . MJM 170 25 mg/kg daily reduces Type 2 parasites.  FIG.  5 C . MJM 170 reduces cysts in mice infected 2.5 months earlier and treated for 17 days with 12.5 mg/kg daily then without compound for 3 days:cyst count of wet prep of brain homogenate.  FIG.  5 D . Zebra fish can be used to visualize fluorescent tachyzoites and cysts in more chronic infections. 
         FIG.  6 A- 6 G . MJM170 targets apicomplexan cytochrome bc 1  Qi: modelling, yeast surrogate assays, target validation, co-crystallography and nanoM inhibition of  P. falciparum  and  T. gondii    FIG.  6 A . Modeling: MJM170 (yellow) modelled within cytochrome b Q i  site (grey) highlighting residues (green) involved in binding.  FIG.  6 B . Mutations for yeast,  P. falciparum , predicted for  T. gondii  and bovine enzyme. Relevant mutations are indicated by colored dots in Q i  domains on the bottom of the image of mitochondrion membrane for  S. cerevesiae  and  P. falciparum , and where those amino acids are in  T. gondii , human and bovine enzymes. Red dot marks G33A/V in Q i  domain of  P. falciparum .  FIG.  6 C . Cytochrome b mutants and sequence accession numbers.  FIG.  6 D . MJM 170 inhibits wild-type but not mutant yeast. Compounds MJM 170 and ELQ 271 with wild type and mutant yeast validate predictions that M221 K/Q would create a steric clash and resistance.  FIG.  6 E . MJM170 is a potent low nM inhibitor of  Plasmodium falciparum . In Table 2, wild type  P. falciparum  also are tested and is inhibited at &lt;50 nM by this scaffold. D6 is a drug sensitive strain from Sierra Leone, C235 is a multi-drug resistant strain from Thailand, W2 is a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. Mutant G33V did not confirm prediction of a steric clash.  FIG.  6 F- 6 G . MJM170 binds within Q i  site of bovine cytochrome bc 1  as shown by X-ray crystallography.  FIG.  6 F . An omit Fo-Fc electron density map (green) at 5σ allows unambiguous positioning of MJM170 (magenta) within the Q i  site with the tetrahydroquinolone group near heme b H  (white) and diphenyl ether directed out of the channel.  FIG.  6 G  MJM 170 molecule is included into the structure, the 2Fo-Fc electron density map at 1σ (grey) allows placement of the planar head between heme b H  and Phe220 with the carbonyl group positioned in a polar region surrounded by Ser35 and Asp228. 
         FIG.  7 A- 7 C . MJM170 potently inhibits  P. falciparum  mitochondrial electron transport important for synthesis of pyrimidines, is modestly synergistic with atovaquone, additive with cycloguanil and antagonistic with Q i  inhibitor.  FIG.  7 A . MJM170 is highly potent (Dd2, black curve, EC 50 =29.5 nM) without cross-resistance in previously reported cytochrome b drug-resistant mutant parasite lines including ubiquinone reduction site mutants (Dd2 G33A  and Dd2 G33V , light blue and dark blue curves, respectively). Dose-response curve from representative assay. MJM170 cannot inhibit a parasite supplemented with a yeast cytosolic DHODH (scDHODH, green curve) demonstrating that its primary activity in  P. falciparum  is to inhibit electron transport necessary for pyrimidine biosynthesis. Inset Table. Dose-response phenotypes of a panel of  P. falciparum  cytochrome b mutant parasite lines. EC 50  values were calculated using whole-cell SYBR Green assay and listed as mean±standard deviation of three biological replicates, each with triplicate measurements.  FIG.  7 B .,  FIG.  7 C . Isobolograms with MJM170 plus atovaquone or cycloguanil or Q i  inhibitor BRD6323:  FIG.  7 B . Combinations were with atovaquone (ATV) or cycloguanil (CYG) at multiple fixed volumetric ratios (10:0, 8:2, 6:4, 4:6, 2:8, and 0:10) in Dd2 parasites. Slight synergy observed with combinations of MJM170 and atovaquone while MJM170 and cycloguanil dosed in combination showed additive effect. Fractional inhibitory concentrations (FIC) for each drug were calculated and plotted. Shown is a representative isobologram for each combination of compounds. Table below lists FICs for each compound and ratio tested (values are mean from three independent assays±standard deviation). Synergy was defined as a combined FIC&lt;1.0, addivity as FIC=1.0, and antagonism as FIC&gt;1.0.  FIG.  7 C . Isobologram Figure: MJM170 was tested in combination with previously reported reduction site inhibitor BRD6323 at multiple fixed volumetric ratios (10:0, 8:2, 6:4, 4:6, 2:8, and 0:10) in Dd2 parasites. Antagonism was observed with combinations of MJM170 and BRD6323, another bulky inhibitor of cytochrome bc, as opposed to synergy observed with oxidation site inhibitor atovaquone. Fractional inhibitory concentrations (FIC) for each drug were calculated and plotted. Representative isobologram of three independent assays is shown. Table below lists FICs for each compound and ratio tested (values are means from three independent assays±standard deviation). Definitions as in b. 
         FIG.  8   . Effects of compounds against RH—YFP. Graph is a representative example of an experiment testing two of the compounds against tachyzoites (RH—YFP). On the vertical axis is fluorescence in relative fluorescence units, where decrease in fluorescence compared to the DMSO control indicates parasite inhibition. On the horizontal axis are the different treatment conditions. 
         FIG.  9   . The results of a cytotoxicity assay. 10 μM solution of compound was compared to the DMSO control closest to 0.1% DMSO (0% DMSO) and the 50 μM solution was compared to the DMSO control closest to 0.5% DMSO (0.625% DMSO). The differences were not found to be statistically significant. 
         FIG.  10 A- 10 C . Effects of compounds against EGS.  FIG.  10 A - FIG.  10 C ) Graphs comparing the effects of JAG050 and JAG021 on EGS. 
         FIG.  11   . Binding assays show selectivity with binding to the bovine enzyme which is not as robust as has been seen with other cytbc inhibitors  FIG.  12 A- 12 D . JAG21 is a mature lead that protects against  Toxoplasma gondii  tachyzoites and cures  Plasmodium bergheii  sprorozoites, blood and liver stages with oral administration of single dose 2.5 mg/kg and 3 doses protect at 0.5 mg/kg. Single dose causal prophylaxis in 5 C57BL/6 albino mice at 2.5 mpk dosed on day 0, 1 hour after intravenous administration of 10,000  P. berghei  sporozoites. 3 dose causal prophylaxis treatment in 5 C57BL/6 albino mice at 0.6 mpk dosed on days −1, 0, and +1. A representative figure for higher dose (5 mg/kg) is shown, but all experiments with the amounts mentioned above had efficacy measured as cure measured as survival, luminesence and parasitemia quantitated by flow cytometry are similar to these. 
         FIG.  13   . Tafenoquine and JAG21 are both needed to contain RPS13Δ. One additional mouse in the tafenoquine and JAG21 died outside the time on this graph others remained healthy. 
         FIG.  14 A- 14 D . Serum biomarkers from boys with active brain disease due to  Toxoplasma  reflect infection and neurodegeneration.  FIG.  14 A . Tabular clinical summary: Three pairs of children, matched demographically; one in each pair had severe disease and one mild or no manifestations. One pair dizygotic, discordant twins. Each ill child had new myoclonic or hypsarrythmic seizures. Two children had T2 weighted abnormalities on brain MRIs similar to active inflammatory and parasitic disease in murine model 8    FIG.  14 B - FIG.  14 D . Protein and miR serum biomarkers: Panel of nanoproteomics and miR sequencing performed on serum obtained at time of new illness. MiRNA concentration measured and difference in concentration graphed. Abundance of peptides measured. Note: Presence of markers of neurodegeneration, inflammation, and protein misfolding include clusterin, diminished ApoJ, serum amyloid, and oxytocin in ill children compared with their healthy controls. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     All references cited are herein incorporated by reference in their entirety. Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as:  Molecular Cloning: A Laboratory Manual  (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press),  Gene Expression Technology  (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in  Methods in Enzymology  (M. P. Deutshcer, ed., (1990) Academic Press, Inc.);  PCR Protocols: A Guide to Methods and Applications  (Innis, et al. 1990. Academic Press, San Diego, Calif.),  Culture of Animal Cells: A Manual of Basic Technique,  2 nd  Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.),  Gene Transfer and Expression Protocols , pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.). 
     As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. “And” as used herein is interchangeably used with “or” unless expressly stated otherwise. 
     As used herein, the amino acid residues are abbreviated as follows: alanine (Ala; A), asparagine (Asn; N), aspartic acid (Asp; D), arginine (Arg; R), cysteine (Cys; C), glutamic acid (Glu; E), glutamine (Gln; Q), glycine (Gly; G), histidine (His; H), isoleucine (Ile; I), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V). 
     All embodiments of any aspect of the invention can be used in combination, unless the context clearly dictates otherwise. 
     In one aspect, the invention provides cell lines infected with an apicomplexan parasite, wherein the apicomplexan parasite genome comprises a gene encoding an Apetela 2 IV-4 protein with an M=&gt;I modification at residue 570 (“AP2 IV-4 M570I”) compared to its orthologous gene on the reference  T. gondii  ME49 strain (gene ID: TGME49_318470). As described in the examples that follow, Apetela 2 (AP2) IV-iv is known to be a bradyzoite gene expression repressor 56 , and the AP2 IV-4 M570I mutant results in an apicomplexan parasite that remains as a bradyzoite in tissue cultures passaged extensively, capable of producing oocysts when administered to cats definitively proving its true bradyzoite phenotype. 
     As further described in the examples that follow, critical flaws and limitations of available methods and models for developing medicines to cure apicomplexan infections, such as  T. gondii  infections, include lack of in vitro culture systems for cysts and scalable, easy to use animal models for screening compounds. The cell lines of this aspect of the invention unexpectedly possess a true, dormant parasite phenotype in tissue culture and can be used, for example, to screen for drugs that can be used to treat apicomplexan parasitic infections, as well as a research tool for studying apicomplexan parasites in the dormant phenotype. The cell lines can be used, for example, as a model of bradyzoite infection. A generalized apicomplexan life cycle comprises a rapidly growing tachyzoite and slow-growing, latent bradyzoite that forms tissue cysts (i.e.: dormant phenotype). Such dormant parasites are present in the brains of 2 billion persons worldwide across their lifetimes and are incurable. Quite remarkably, the inventors have discovered that in human cells this encysted parasite turns on host cell pathways important for altering ribosomal function, miss-splicing of transcripts, oxidative pathways, and, those pathways found to be altered in Alzheimer&#39;s and Parkinson&#39;s diseases. Extensive details on the model are described in the examples that follow. 
     In one embodiment, the apicomplexan parasite genome comprises a gene encoding AP2 IV-4 M570I that further differs from its orthologous gene on the reference  T. gondii  ME49 strain (gene ID: TGME49_318470) in encoding the amino acid sequence GGNRPHYHVAKQEWRVRYYMNGKRKMRTYSAKFYGYETAHTMAEDFAHYVDKH E (SEQ ID NO: 1) beginning at residue 821. In a further embodiment, the gene encoding AP2 IV-4 M570I encodes the following amino acid sequence, or functional equivalents thereof: 
     
       
         
           
               
            
               
                 (SEQ ID NO: 2) 
               
               
                 MAAPAPSAEARPAKRRCFPLPRETPVSSEDETRKTLQHDTLGCLPRSS 
               
               
                   
               
               
                 SGQPELAAASAASQVGHLSSAALLQLVQTQSAGGVPQAVLRNLFSSIH 
               
               
                   
               
               
                 RNPKPLPANALAATPNSSLYASLTSLSSAAALPGAGPAYSQAPSPASA 
               
               
                   
               
               
                 DLLQSEQFGSAAKNPSPNEASPILALLGEAARAATTPRTVPALSAVCP 
               
               
                   
               
               
                 AASSGVSLPSASDTLALAQSSLSSSTGCASDVKASRPEEHPAFASGTA 
               
               
                   
               
               
                 NRQSLLQALLLSTAPLAFSGPSLSSASTTLPASSGAVSSRNAGAYQFE 
               
               
                   
               
               
                 RLLQAEAAKVKALLPNATSKSMSQSSVPQRDLTRKTSLFPDPRGLSAD 
               
               
                   
               
               
                 DASRRYNTRGANSGGAGLRRGTGVHATTEQSGALDAGERTRPFGAGED 
               
               
                   
               
               
                 ESAQGKPDSRGRQRPGALDASNILGLLAAFQPSQAPAIRDLSAPSHLS 
               
               
                   
               
               
                 AAATGALPLTASFTASALASSQCLPAGTPASSSASPPFSEVLSTTEES 
               
               
                   
               
               
                 STTKETDASASTLLAFLQKYSAVSGLGGASDFLGQLQGKSSLPPLSLA 
               
               
                   
               
               
                 EPSSALPSSFLGGSDGGTIDTRNGNGEKTTPPIHLFQSAFR   I   PSPSQQ 
               
               
                   
               
               
                 NLLDALLASSCTTATSRSDGSGNLGCPVVDERNAKLAGPAHPLPCSFP 
               
               
                   
               
               
                 QISSSSGEPGRKTGGRVHRQGTSQSGGRVRSGKNGGSAAPPRQSSSEN 
               
               
                   
               
               
                 VPSTPTVSSHEAPHRAGFPSQTPYELSASPSHQLDLLRLGAFLGGAGK 
               
               
                   
               
               
                 QDASVHSDETGTLSGEPSHRSCSLSRGLTQESVLQLSDTTSTSREGEP 
               
               
                   
               
               
                 NEPSQGCVNVAASLPAFGPQPSSGAAKAREGRRGAGGAGAAPPVPLRA 
               
               
                   
               
               
                 DVTL   GGNRPHYHVAKQEWRVRYYMNGKRKMRTYSAKFYGYETAHTMAE     
               
               
                   
               
               
                     DFAHYVDKHE   ALPDSMMMTAMMLQAQANSAASSGQTVPLARGIRASSA 
               
               
                   
               
               
                 SAGAGGHVSKSATKGSVAASSEGSTSMGSDATRSQEGEAAELCPLAAG 
               
               
                   
               
               
                 LSRPLASMHSAAGNAVAQGRQESKEEAPGGQAWFGEPGKFRASSEAAL 
               
               
                   
               
               
                 CGSGSSAEGRDGHESEVLWATLGKVHDASQGKKIKPEKPLTVARGRLA 
               
               
                   
               
               
                 LGAEDKSQNLGVDLGDSGGAQGLPGVRQPRQMKNSEECSLRDSDKGMA 
               
               
                   
               
               
                 LSKRFGFLPSQTPSCDSMTLPFPGGFDALSLSSALSSCASLPVAHEGN 
               
               
                   
               
               
                 NFQKGHTGDIVALASQSGTQRPASVVLSRDANVSGSSPSHPTWQREGA 
               
               
                   
               
               
                 AVSGRADEFSSLSVTPSTVPLSSFTMEDIKGEEGDPSRRFALVGESMK 
               
               
                   
               
               
                 NVSAPEVQALFPTSSIANAELLPVDFLHSNSCSADKLESSIPRGLAGN 
               
               
                   
               
               
                 NPSMTATAVAATAVSHQIFDTITLFGEFLREFAKEKVNEFHEYGLEAS 
               
               
                   
               
               
                 PLTVEASPEVSLFGKATFGRCPVAGGSTPAGISKMSGETLSGLSASEL 
               
               
                   
               
               
                 SLVSARTNTTTGEEQFALARGLFPGDSEGDRDEKKPQLSQQELLVLSH 
               
               
                   
               
               
                 ALVNLTSSTYVLMHTLKASLSKSTEAVQLHQPLLEAASEAKATDEAKT 
               
               
                   
               
               
                 REEQESSECDHEYPPGSSLEATTGALPFRLSPALSASSKDLPSLSASA 
               
               
                   
               
               
                 SLESVTPFAGLPLEEGTLSASVGLASSDDEHDTSLLFKTEAAKKRSLF 
               
               
                   
               
               
                 STAADGDESRTYNDGLGQPMEEEIRSCVSTSCGEAVATTTLSAIGPGT 
               
               
                   
               
               
                 GASGALLDSESRESLGEKPGAALRAGAHTPAPSRAPTPSRTFSFTSSS 
               
               
                   
               
               
                 TATSAALLCDSNVVHEKLSAQGKDSEAGERKGDSEKEEEVEMWKEEDE 
               
               
                   
               
               
                 EVQRCTGSAETDSTEATRGEEAWRRGKQSEKKPSVITTALNLLETHRH 
               
               
                   
               
               
                 LALTISQLKRPVAQQLRFILPIAAPQLLPCILPPASFQGTGESGDGKA 
               
               
                   
               
               
                 EAEAKGSSSLGQVLETALGHGTRLAPSASAMVPPRKDEAASAVPEAKT 
               
               
                   
               
               
                 LTGLANAGVTREAASRTLEAEQVSRKRSREEVVDSETAGDEGDMENVP 
               
               
                   
               
               
                 ETRDGTTRPGSRQYDTSPSNDGTKPPATAKSRVIRDQAALERLLLAPF 
               
               
                   
               
               
                 QDTPTCSCTDRPCPCDRQQVADMIYLFYAVPARQQAESSKEGSTQRLQ 
               
               
                   
               
               
                 FAARDTNERKDARTGEETQGGETEAKEVIRDPEERGVCEGSSSQNAHT 
               
               
                   
               
               
                 QFDAETASSSMSSDPRADKESNAQDAHMADKTSFVSDLPQPSGEFAPS 
               
               
                   
               
               
                 LLSETSLDVAMADSRGTPSEIHGFFTRSDEQKRASFSSSSLLAAGHAV 
               
               
                   
               
               
                 ASFSSSLAGVVSGAGERRECAGPSLGDLSTIGLLSLSYPAMLAFILPL 
               
               
                   
               
               
                 QSLLHTVSGMILTLHKKLIHRFICAHLRLVLDDDMRRPAGGALKSRGA 
               
               
                   
               
               
                 HGDTEAAEAQVERRRREHEREETTNLAIGYREGNAEAANTFPLVDTVS 
               
               
                   
               
               
                 SLLSPGSLRQENSEVERRDNDEERLELITGIARESPKPSEKDSVSPFL 
               
               
                   
               
               
                 STAPCPGTEAESSDCSASSACSGTPTEGTEGGETGDIASFLSPSGEVK 
               
               
                   
               
               
                 QTIMLA 
               
            
           
         
       
     
     The mutations at residue 570 and beginning at residue 821 compared to the Apetela 2 IV-4 orthologous protein encoded by the reference  T. gondii  ME49 strain (gene ID: TGME49_318470) are presented in bold font and underlining in the above sequence. A “functional equivalent” is a gene encoding an Apetela 2 IV-4 protein that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence provided above, includes the noted mutations at residue 570 and beginning residues 821-874, and that does not represses bradyzoite gene expression in a tachyzoite in an apicomplexan parasite. 
     As used here, “apicomplexan parasites” are a phylum of the kingdom Protista (formerly a division of protozoa called  Sporozoa ); named for a complex of cell organelles (apical microtubule complex) at the apex of the sporozoite form that can penetrate host cells. It includes, but is not limited to, the medically important genera  Plasmodium, Toxoplasma, Cryptosporidium , and  Isospora . Thus, in one embodiment, the apicomplexan parasite is selected from the group consisting of  Plasmodium, Toxoplasma, Cryptosporidium , and  Isospora . In a specific embodiment, the apicomplexan is a wild type, mutant, or recombinant  Toxoplasma gondii  strain. In various further embodiments, the apicomplexan parasite is  Toxoplasma gondii  of clade B. 
     In another embodiment, the apicomplexan parasite is a GO arrested parasite, including but not limited to s  Toxoplasma gondii  strain RPS 13 delta (Hutson et al., PLoS One. Nov. 22, 2010; dx.doi.org/10.1371/joumal.pone.0014057). This cell line can be used, for example, to identify companion compounds for THQ that eliminate the GO arrested stage of  T. gondii  along with the active and the slowly growing bradyzoite stage. 
     In another embodiment, the apicomplexan parasite is  Toxoplasma gondii  strain EGS (ATCC® Number:PRA-396™). As described in the examples that follow, the EGS strain was extensively characterized in vitro to show that true cysts develop, making the EGS strain especially useful for drug development. 
     In all embodiments of this aspect of the invention, the cell line can be any suitable cell line capable of supporting apicomplexan parasitic infection, including but not limited to mammalian cells (mouse, rat, human, etc.), zebrafish cells, etc. In one specific embodiment, the cell line is a human cell line; exemplary human cell lines for use in this aspect of the invention include, but are not limited to fibroblasts, stem cells, neurons, monocytes, and ocular cells 9 including primary human cells). As described in the examples that follow, the apicomplexan parasites form cysts in the host cell lines that enlarge over time and then destroy host cell monolayers as single cell organisms. As such, the cell lines of the invention are extremely useful as in vitro models of apicomplexan parasite infection. Such models can be used, for example, to test for candidate compounds that inhibit cyst formation and/or destruction of host cell monolayers; such candidate compounds would be useful in treating apicomplexan parasite infection. 
     In another embodiment, the apicomplexan parasite genome is recombinantly engineered to express a reporter polypeptide, including but not limited to fluorescent or luminescent proteins. This embodiment permits ready visualization of the parasite and facilitates automated quantitative analysis. In one embodiment, the reporter polypeptide is operatively linked to a promoter that is activated in the bradyzoite stage or a promoter that is activated in the merozoite stage. Any suitable promoter that is activated in the bradyzoite stage or merozoite stage may be used. In one embodiment the promoter that is activated in the bradyzoite stage is the  T. gondii  BAG1 encoding gene promoter or a functional equivalent thereof. The BAG1 promoter sequence can be obtained as disclosed in Bohne et al., Molecular and Biochemical Parasitology 85 (1997) 89-98. In one embodiment, the BAG promoter comprises SEQ ID NO:3, or functional equivalent thereof, from the  T. gondii  VEG strain. 
     A “functional equivalent” of the BAG1 promoter is a promoter from any strain of  T. gondii  that promotes expression of BAG1 in the VEG strain, as well as an promoter nucleic acid sequence that is 50%, 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO:3 and drives expression of a BAG1 gene in a  T. gondii  strain. 
     As described in the examples that follow, the cell lines of the invention can be administered to/ingested by non-human animal models to provide an in vivo model of apicomplexan parasitic infection that develop the classic, gold standard bradyzoite phenotype of producing oocysts. This, in another aspect, the invention provides non-human animal models of apicomplexan parasitic infection, comprising a non-human animal that has ingested or otherwise comprises the cell line of any embodiment or combination of embodiments of the invention. In one embodiment, the non-human animal produces oocysts. Any suitable non-human animal model that produces oocysts can be used, including but not limited to cats. 
     In another aspect, the invention provides non-human animal models of apicomplexan parasitic infection, comprising a non-human animal that has ingested or otherwise comprises oocysts produced by the non-human animal model that has ingested or otherwise comprises the cell line of any embodiment or combination of embodiments of the invention. As described in detail in the examples that follow, oocysts given to non-human animal models such as mice created an illness and histopathology phenotypically characteristic for typical, virulent parasites causing dose related proliferation of the parasite (exemplified by  T. gondii ) with necrosis in terminal ileum, pneumonia at 9-10 days, with brain parasites by 17 days and dose-related mortality. Thus, the non-human animal models of this aspect of the invention are particularly useful in screening for drugs to treat the effects of apicomplexan parasite infection. 
     As will be understood by those of skill in the art, the oocysts do not need to be isolated prior to ingestion; they may be present, for example, in tissue (including but not limited to brain tissue) taken from the non-human animals that have ingested or otherwise comprise the cell lines of the invention, which then produce oocysts. Any suitable non-human animal model can be used, including but not limited to mice, rats, cats, zebrafish, non-human primates, cattle, sheep, and pigs. In one specific embodiment, the non-human animal is a mouse. 
     In another aspect the present invention provides methods of identifying compounds for treating an apicomplexan parasitic infection, comprising contacting one or more test compounds to the cell line of any embodiment or combination of embodiments of the invention, wherein those positive test compounds that reduce bradyzoite cyst amounts in the cell line are candidates to treat an apicomplexan parasitic infection. As disclosed above, the cell lines of the invention unexpectedly possess a true, dormant parasite phenotype in tissue culture and can be used to screen for drugs that can be used to treat apicomplexan parasitic infections. Any reduction in bradyzoite cyst amounts in the cell line indicates that the test compound may be useful for treating an apicomplexan parasitic infection. In various embodiments, positive test compounds are those that reduce bradyzoite cyst amounts by at least 5%, 10%, 15%, 20%, 25%, 50%, 75%, 90%, or more. 
     In another aspect the present invention provides methods of identifying compounds for treating an apicomplexan parasitic infection, comprising administering one or more test compounds to the animal model of any aspect or embodiment of the invention, wherein those positive test compounds that reduce one or more symptoms of the infection and/or reduce parasitic titer in the animal model are candidates to treat an apicomplexan parasitic infection. 
     In one embodiment, those positive test compounds that reduce oocyst production and/or reduce bradyzoite cyst amounts in the animal model are candidates to treat an apicomplexan parasitic infection. Any reduction in oocysts production and/or bradyzoite cyst amounts indicate that the test compound may be useful for treating an apicomplexan parasitic infection. In various embodiments, positive test compounds are those that reduce oocysts production and/or bradyzoite cyst amounts by at least 5%, 10%, 15%, 20%, 25%, 50%, 75%, 90%, or more. 
     In one embodiment of any of the methods of identifying compounds for treating an apicomplexan parasitic infection of the invention, positive test compounds are candidates for treating  Toxoplasma gondii  or  Plasmodium falciparum : infection, including drug resistant strains and or other plasmodial infections. The methods can be used to test any suitable type of candidate compound, including but not limited to polypeptides, antibodies, nucleic acids, organic compounds, etc. Treatment effects of the test compounds may be assessed relative to a suitable control, such as the cell lines or non-human animal models of the invention that are not treated with the test compound. It is well within the level of those of skill in the art to determine a suitable control in light of the teachings herein. 
     In one specific embodiment, the cell line, or non-human animal model that has ingested or otherwise comprises the cell line, comprises a G0 arrested parasite (such as RPS 13 delta) and is used to identify companion compounds for tetrahydroquinolones (THQ) that eliminate the G0 arrested stage of an apicomplexan parasite, such as  T. gondii , along with the active and the slowly growing bradyzoite stage. 
     RPS 13 Δ is a genetically engineered conditional knockout parasite that has a unique transcriptome documenting its G0 state, G1 arrest in the absence of tetracycline but grows normally in the presence of tetracycline which removes the repressor from the promoter. The method may utilize, for example, a system that when there is no anhydrotetracycline to remove the engineered tetracycline responsive repressor from the 4 tetracycline response elements engineered in tandem in the promoter; these parasites persist in tissue culture for long times (months). This embodiment is based on the observation that this conditional knockout RPS13 delta parasite when it is in its arrested in G1 state is not susceptible to the effect of any inhibitors that effect processes essential to the tachyzoite or bradyzoite form including those tested in vitro so far. In this embodiment the conditional knockout RPS13 delta parasite is amenable to testing inhibitors of hypnozoite like organisms by culturing them without tetracycline in the presence of the compound and determining whether any parasites can be rescued by adding tetracycline to determine whether they are still capable of persisting and becoming tachyzoites that grow rapidly in the presence of tetracycline. Furthermore, the methods may comprise testing RPS13 delta in mice, and involves the observations that when RPS13 delta is administered to wild type mice without tetracycline the RPS13 delta parasite induces a protective immune response as a vaccine dependent on interferon gamma and has no adverse effect on the mice, nor can it be rescued with tetracycline or inhibitors of iNOS (intracellular nitrogen oxide synthase) such as LNAME (L-N G -Nitroarginine methyl ester) which abrogate effects of interferon gamma after 7 days. For example, that in interferon gamma knock out mice or mice treated with antibody to interferon, RPS13 delta is lethal for the mice, where the attenuated organism persists, can be observed, until mice succumb slowly. Another example may be a SCID mouse or a steroid treated mouse that is more susceptible due to immune compromise. 
     In another embodiment, RPS13 delta can be used to test compounds in vitro against this G0 truly dormant stage, and against compounds that can target the hypnozoite state but that must be metabolized in the liver to produce toxic electron containing compounds in vivo. 
     In all these embodiments, the methods can be used to determine if compounds have parasiticidal effects on hypnozoite forms and be used in conjunction with THQ compounds, such as tafenoquine, known in primate models and in humans as the only compound besides primaquine which has a lethal effect on the malaria hypnozoite in primates or in humans. However, tafenoquine is not active against actively proliferating organisms and requires a compound that is effective against more rapidly and slowly growing forms to produce radical cure of malaria. 
     In another embodiment, the THQ compound may be primaquine, a compound that has a similar effect when metabolized and is ineffective against  T. gondii  tachyzoites in tissue culture and can therefore be utilized in the same manner as tafenoquine to inhibit the hypnozoite form of apicomplexan parasites to produce radical cure. 
     Compounds identified using the methods of these various embodiment of the invention can be used together the THQ compound(s) to treat/cure the active tachyzoite, the slowly growing bradyzoite, and the G0 arrested hypnozoite-like phase of the apicomplexan infections the active tachyzoite, the slowly growing bradyzoite, and the G0 arrested hypnozoite-like phase of the apicomplexan infections 
     As described in detail in the examples that follow, the inventors carried out transcriptome analysis of both the apicomplexan parasite and the host cells after parasite infection of the host cells. The resulting transcriptomes provide a signature for apicomplexan parasites (such as  T. gondii  strains EGS), which helps in identification of targets for drug development, as well as a signature for infected host cells (such as human foreskin fibroblasts (HFF) human monocytic cells (ex: MM6), and human primary neuronal stem cells (NSC)), which helps in identification of targets for treating apicomplexan infection. As shown in the examples, EGS transcription was influenced by host cell type ( FIGS.  1 A- 1 D ). Transcriptomics using host mRNA and miR profiling of EGS cultures in MM6, and NSC cells for 18 hours demonstrated that this parasite modulates host transcripts involved in protein misfolding, neurodegeneration, endoplasmic reticulum stress, spliceosome alteration, ribosome biogenesis, cell cycle, epilepsy, and brain cancer among others ( FIGS.  1 A- 1 D ). The number of genes significantly up or down regulated in MM6 and NSC cells compared to uninfected controls are depicted in  FIGS.  1 A- 1 D . Overexpressed genes differ from those of GT1, ME49 and VEG tachyzoite-infected human NSC cells, but modify the same or connected pathways. Hsa-miR-708-5p was the most affected miRNA (down-modulated) by EGS ( FIG.  1 D . miR-708-5p is a regulator that promotes apoptosis in neuronal and retinal cells, which could maintain a niche for EGS-like encysted bradyzoites to persist. 
     The genes identified in the host transcriptome study are thus targets for anti-parasite therapy, as well as markers of apicomplexan parasite infection (such as  T. gondii  infection). In various embodiments, the invention may thus comprise methods for treating an apicomplexan parasite infection (such as a  T. gondii  infection), comprising administering to a subject in need thereof an amount effective to treat the infection of an inhibitor (of up-regulated genes) or an activator (of down-regulated genes) of 1 or more (i.e.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) of the up-regulated genes listed discussed herein (protein encoding genes or miRNA). In various non-limiting embodiments, the inhibitor is selected from the group consisting of a target-specific inhibitory antibody, aptamer, siRNA, shRNA, antisense oligonucleotide, or small molecule. 
     In one embodiment, the target is miR-708-5p. In various further embodiments the targets are one or more of the genes listed in Table 1 below, or as discussed herein, which provide a more complete list of up-regulated or down-regulated genes involved in specific host cell pathways or indications. The table shows up-regulated or down-regulated genes involved in specific host cell pathways or indications (“KEGG pathway”), such as systemic lupus erythematosus, (SLE), Parkinson&#39;s disease, etc. In an exemplary embodiment, the methods comprise administering to the subject in need thereof an inhibitor (of up-regulated genes) or an activator (of down-regulated genes) of one or more (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or all 13) of genes HIST2H2AA3, HIST1H2AC, HIST1H2BC, ACTN4, SNRPD3, ELANE, ClR, HIST1H2BK, H2AFZ, SNRPB, H2AFX, CTSG, and HIST1H4H, to treat apicomplexan parasite infection-associated SLE. One of skill in the art will understand from the table that the methods may be used to treat apicomplexan parasite infection-associated Parkinson&#39;s, Huntington&#39;s disease, Alzheimer&#39;s disease, etc. using an inhibitor (of up-regulated genes) or an activator (of down-regulated genes) against 1 or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more, such as all) of the target genes listed for the specific indication. Similarly, one of skill in the art will understand from the table that the methods may be used to treat apicomplexan parasite infection-associated disorders relating to ribosomal assembly, spliceosome assembly, oxidative phosphorylation, etc. using an inhibitor (of up-regulated genes) or an activator (of down-regulated genes) against 1 or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more, such as all) of the target genes listed for the specific indication. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 KEGG id 
                 KEGG pathway 
                 P-value 
                 Genes 
               
               
                   
               
             
            
               
                 hsa03010 
                 Ribosome 
                 4.6E−07 
                 RPL35A, RPL36A, RPL35, RPS9, RPL27, 
               
               
                   
                   
                   
                 RPS27L, RPL38, RPS25, RPS27, RPL30, 
               
               
                   
                   
                   
                 RPL23, RPS29, RPL21, RPS20, RPS21, UBA52, 
               
               
                   
                   
                   
                 RPL36AL 
               
               
                 hsa05322 
                 Systemic lupus 
                 0.00082 
                 HIST2H2AA3, HIST1H2AC, HIST1H2BC, 
               
               
                   
                 erythematosus 
                   
                 ACTN4, SNRPD3, ELANE, C1R, HIST1H2BK, 
               
               
                   
                   
                   
                 H2AFZ, SNRPB, H2AFX, CTSG, HIST1H4H 
               
               
                 hsa04621 
                 NOD-like receptor 
                 0.01458 
                 IL6, CCL2, XIAP, NFKBIB, NFKBIA, 
               
               
                   
                 signalling pathway 
                   
                 TNFAIP3, BIRC3, CCL5 
               
               
                 hsa03040 
                 Spliceosome 
                 4.1E−06 
                 SNRPA1, CCDC12, MAGOH, SNRPD3, LSM6, 
               
               
                   
                   
                   
                 LSM7, SNRPB2, SNRPD2, PPIH, SNRPB, 
               
               
                   
                   
                   
                 PQBP1, SYF2, LSM5, U2AF1, MAGOHB, 
               
               
                   
                   
                   
                 THOC2, SNRPF, SNRPE, SNRPG 
               
               
                 hsa00190 
                 Oxidative 
                 6.4E−16 
                 ATP5E, NDUFB4, ATP6V0E1, NDUFB6, 
               
               
                   
                 phosphorylation 
                   
                 NDUFB9, COX7C, ATP6V1G1, ATP5G1, 
               
               
                   
                   
                   
                 UQCRQ, NDUFB1, NDUFB2, NDUFS5, 
               
               
                   
                   
                   
                 NDUFS4, ATP5L, NDUFS3, COX17, ATP5H, 
               
               
                   
                   
                   
                 ATP5J, NDUFA4, NDUFA5, NDUFA2, 
               
               
                   
                   
                   
                 NDUFA3, COX7A1, NDUFA6, COX8A, 
               
               
                   
                   
                   
                 NDUFC2, NDUFC1, NDUFA1, ATP6V1F, 
               
               
                   
                   
                   
                 NDUFV2, COX6A1, UQCRB 
               
               
                 hsa05012 
                 Parkinson&#39;s 
                 2.4E−14 
                 ATP5E, NDUFB4, NDUFB6, NDUFB9, 
               
               
                   
                 disease 
                   
                 COX7C, ATP5G1, UQCRQ, NDUFB1, 
               
               
                   
                   
                   
                 NDUFB2, NDUFS5, NDUFS4, HTRA2, 
               
               
                   
                   
                   
                 NDUFS3, ATP5H, ATP5J, NDUFA4, NDUFA5, 
               
               
                   
                   
                   
                 NDUFA2, NDUFA3, COX7A1, NDUFA6, 
               
               
                   
                   
                   
                 COX8A, NDUFC2, NDUFC1, UBE2L3, 
               
               
                   
                   
                   
                 NDUFA1, VDAC3, NDUFV2, COX6A1, 
               
               
                   
                   
                   
                 UQCRB 
               
               
                 hsa05016 
                 Huntington&#39;s 
                 2.2E−13 
                 ATP5E, NDUFB4, POLR2F, NDUFB6, 
               
               
                   
                 disease 
                   
                 POLR2K, NDUFB9, POLR2J, COX7C, 
               
               
                   
                   
                   
                 ATP5G1, UQCRQ, NDUFB1, NDUFB2, 
               
               
                   
                   
                   
                 NDUFS5, NDUFS4, TGM2, CREB3L1, 
               
               
                   
                   
                   
                 NDUFS3, ATP5H, ATP5J, NDUFA4, NDUFA5, 
               
               
                   
                   
                   
                 NDUFA2, NDUFA3, COX7A1, NDUFA6, 
               
               
                   
                   
                   
                 COX8A, NDUFC2, NDUFC1, NDUFA1, 
               
               
                   
                   
                   
                 VDAC3, SOD2, NDUFV2, COX6A1, UQCRB 
               
               
                 hsa05010 
                 Alzheimer&#39;s 
                   9E−11 
                 ATP5E, NDUFB4, NDUFB6, NDUFB9, 
               
               
                   
                 disease 
                   
                 COX7C, ATP5G1, UQCRQ, NDUFB1, 
               
               
                   
                   
                   
                 NDUFB2, NDUFS5, NDUFS4, PPP3CA, 
               
               
                   
                   
                   
                 NDUFS3, ATP5H, ATP5J, NDUFA4, NDUFA5, 
               
               
                   
                   
                   
                 NDUFA2, NDUFA3, COX7A1, NDUFA6, 
               
               
                   
                   
                   
                 COX8A, NDUFC2, NDUFC1, ITPR3, NDUFA1, 
               
               
                   
                   
                   
                 NDUFV2, COX6A1, UQCRB 
               
               
                 hsa04623 
                 Cytosolic DNA- 
                 0.0077  
                 MAVS, IL6, POLR3K, NFKBIB, IRF7, 
               
               
                   
                 sensing pathway 
                   
                 NFKBIA, POLR1C, CCL5 
               
               
                   
               
            
           
         
       
     
     In one embodiment, the invention provides methods for treating an apicomplexan parasite infection, comprising treating a subject with an apicomplexan parasite infection an amount effective to inhibit activity or expression from the apicomplexan parasite of one or more proteins as discussed herein. 
     In another embodiment, the invention provides methods for identifying a compound to treat an apicomplexan infection, comprising identifying a compound that inhibits activity or expression of one or more proteins as discussed herein from an apicoimplexan parasite present in an infected host cell. 
     Certain proteins as discussed herein are believed to be particularly important for apicomplexan parasite bradyzoite development and/or survival in the host. Thus, targeting expression and/or activity of these proteins from the apicomplexan parasite will be effective to inhibit bradyzoite development and/or survival in the host. 
     EGS transcripts in HHF, MM6, and NSC cells were enriched for genes transcribed in bradyzoites, including known bradyzoite transcripts, certain Apetela 2s and cytochrome b and other cytochromes. Among transcripts with the most increased fold change in EGS across all three cell lines were: cytochrome b; cytochrome c oxidase subunit III subfamily protein; apocytochrome b; cytochrome b, putative; and cytochrome b (N-terminal)/b6/petB subfamily protein. Other over-expressed genes include bradyzoite transcription factor AP2IX-9 and plant-like heat-shock protein BAG1 ( FIG.  2 A ). The up- or down-regulated genes identified in the parasite transcriptome study are thus targets against which to identify drugs for anti-apicomplexan parasite (such as  T. gondii ) therapy, by identifying test compounds that reduce expression of over-expressed genes, or promote expression of down-regulated genes. In various embodiments, positive test compounds are those that reduce expression (for up-regulated genes), or decrease expression (for down-regulated genes) of 1 or more (i.e.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 50, 100, or more) of the up-regulated apicomplexan parasite genes as discussed herein after host cell infection by at least 5%, 10%, 15%, 20%, 25%, 50%, 75%, 90%, or more. The drug screening assays may employ the cell lines and non-human animal models of the present invention. In one embodiment, the methods comprise identifying test compounds that reduce expression from the apicomplexan parasite after cell infection of 1 or more of cytochrome b; cytochrome c oxidase subunit III subfamily protein; apocytochrome b, cytochrome b, putative, cytochrome b (N-terminal)/b6/petB subfamily protein, bradyzoite transcription factor AP2IX-9 and plant-like heat-shock protein BAG1. 
     In another aspect, the invention provides compositions comprising a plurality of isolated probes that in total selectively bind to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 100, 150, 200, 250, 500, or all of certain markers as discussed herein, complements thereof, or their expression products, or functional equivalents thereof wherein at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or all of the probes in total are selective for markers that are upregulated in the EGS strain of  T. gondii  after infection of human fibroblasts, neuronal stem cells or monocytic lineage cells. 
     Functional equivalents are allelic variants of the recited marker from other  T. gondii  strains. In one embodiment, the markers include two or more of apetela 2 transcription factors, cytochrome b, cytochrome oxidase, or functional equivalents thereof. The markers may further comprise one or more of enolase 1, lactate dehydrogenase 2, bradyzoite antigen 1 and cyst wall protein, or functional equivalents thereof. In another embodiment, 
     In a further aspect, the invention provides a plurality of isolated probes that in total selectively bind to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 100, 150, 200, 250, 500, or all of certain markers as discussed herein, complements thereof, or their expression products, or functional equivalents thereof, wherein at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or all of the probes in total are selective for markers that are upregulated in human fibroblasts, neuronal stem cells or monocytic lineage cells after infection with  T. gondii , including but not limited to infection with the EGS strain of  T. gondii.    
     In one embodiment of each of these aspects, the plurality of isolated probes comprises polynucleotide probes. In another embodiment, the plurality of isolated probes comprises antibody probes. In all of the above embodiments, the isolated probes can be labelled with a detectable label. Methods for detecting the label include, but are not limited to spectroscopic, photochemical, biochemical, immunochemical, physical or chemical techniques. Any suitable detectable label can be used. 
     The compositions can be stored frozen, in lyophilized form, or as a solution. In one embodiment, the compositions can be placed on a solid support, such as in a microarray or microplate format; this embodiment facilitates use of the compositions in various detection assays. 
     The compositions of the invention can be used, for example, to test patient samples for up-regulation or down-regulation of the one or more markers disclosed in the figures, to assist in diagnosing a subject as having an apicomplexan parasite infection (such as  T. gondii ) or to monitor treatment of a subject receiving therapy for an apicomplexan-associated disorder. In one embodiment, such methods comprise testing the patient samples for increased expression of at least 1, 2, 3, 4, 5, 6, or all 7 of apetela 2 transcription factors, cytochrome b, cytochrome oxidase, enolase 1, lactate dehydrogenase 2, bradyzoite antigen 1 and cyst wall protein, or functional equivalents thereof. 
     In one embodiment, the transcriptome provides the signature of cytochrome b as an important part of the bradyzoite transcriptional pathways and a signature that demonstrates effective inhibition of cytochrome b with abrogation of the signature when treatment is with an inhibitor of cytochrome b, which when used early after infection can confirm selectivity of compound. Cytochrome b functions for pyrimidine synthesis in  Plasmodium falciparum  so that it will be synergistic or additive in effect with inhibitors of DHODH. 
     The invention thus also provides pathway to improved inhibitors of cytochrome b through co-crystallography that defines the chemical space and pi stacking which facilitates design of improved medicines and their delivery into tachyzoites and bradyzoites using molecular transporters such as octaargine, or carbonate, and also improves their solubility and access to encysted bradyzoites. 
     In various embodiments, the methods for monitoring treatment of an apicomplexan parasitic infection (such as a  T. gondii  infection), comprising monitoring expression, protein in serum or plasma, and/or activity of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of certain markers as discussed herein (such as a human subject) being treated for an apicomplexan parasitic infection, wherein a decrease or increase in expression and/or presence and/or activity of the one or more markers indicates that the treatment is effective. In one exemplary embodiment, infection is in the subject&#39;s brain or other neurologic tissue. 
     In another aspect, the present disclosure provides compounds having the structure of Formula (I): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, 
     wherein
         ring A combines with Y 1  and Y 2  to form a C 3-7 cycloalkenyl or heteroaryl ring,
           wherein the C 3-7 cycloalkenyl or heteroaryl is optionally substituted by halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, cyano or phenyl;   
           Y 1  is C or N;   Y 2  is C or N;   X 1  is C(R x1 ) or N,
           wherein R x1  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 2  is C(R x2 ) or N,
           wherein R x2  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 3  is O, N(R), S or C 1-3 alkyl;   X 4  is C or N;   X 5  is C or N;   R 1  is hydrogen or C 1-3 alkyl;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   n is 0, 1, 2, 3 or 4;   each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane; and   each R is independently hydrogen or C 1-3 alkyl.       

     The compounds of the invention have been demonstrated in the examples herein as useful, for example, in treating diseases associated with apicomplexan parasite infection. 
     In some embodiments, the compounds are of Formula (Ia): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, 
     wherein
         ring A combines with Y 1  and Y 2  to form a C 3-7 cycloalkenyl or heteroaryl ring,
           wherein the C 3-7 cycloalkenyl or heteroaryl is optionally substituted by halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, cyano or phenyl;   
           Y 1  is C or N;   Y 2  is C or N;   X 1  is C(R x1 ) or N,
           wherein R x1  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 2  is C(R x2 ) or N,
           wherein R x2  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 3  is O, N(R), S or C 1-3 alkyl;   R 1  is hydrogen or C 1-3 alkyl;   R 2  is hydrogen, C 1-3 alkyl or —C(O)OR;   n is 0, 1, 2, 3 or 4;   each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ; and   each R is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the compounds are of Formula (Ib): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of Formula (Ic): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of Formula (II): 
     
       
         
         
             
             
         
       
     
     wherein
         ring A combines with the carbon atoms with which it is attached to form a C 3-7 cycloalkenyl.       

     In some embodiments, the compounds are of Formula (IIa): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of Formula (IIa-1): 
     
       
         
         
             
             
         
       
     
     wherein 
     R 3  is hydrogen, halogen, C 1-3 alkyl or C 1-3 haloalkyl. 
     In some embodiments, the compounds are of Formula (III): 
     
       
         
         
             
             
         
       
     
     wherein
         ring A combines with the nitrogen atom and carbon atom with which it is attached to form a heteroaryl ring.       

     In some embodiments, the compounds are of Formula (IIIa): 
     
       
         
         
             
             
         
       
     
     wherein
         Y 3  is C(R 5 ) or N; and   R 4  and R 5  are independently hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, cyano or phenyl.       

     In some embodiments, the compounds are of Formula (IIIb): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of R 4  is hydrogen or C 1-3 alkyl. 
     In some embodiments, the compounds are of Formula (IIIb-1): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of Formula (IIIc): 
     
       
         
         
             
             
         
       
     
     In some embodiments, 
     R 4  is hydrogen or C 1-3 alkyl or phenyl; and
 
R 5  is hydrogen or cyano.
 
     In some embodiments, the compounds are of Formula (IIIc-1): 
     
       
         
         
             
             
         
       
     
     In some embodiments, the compounds are of Formula (IV): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, 
     wherein
         ring A combines with Y 1  and Y 2  to form a C 3-7 cycloalkenyl or heteroaryl ring, wherein the C 3-7 cycloalkenyl or heteroaryl is optionally substituted by halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, cyano or phenyl;   Y 1  is C or N;   Y 2  is C or N;   X 1  is C(R x1 ) or N,
           wherein R x1  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 2  is C(R x2 ) or N,
           wherein R x2  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   
           X 3  is O, N(R), S or C 1-3 alkyl;   X 5  is C or N;   R 1  is hydrogen or C 1-3 alkyl;   R2 is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   n is 0, 1, 2, 3 or 4;   each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ; and   each R is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the compounds are of Formula (IVa): 
     
       
         
         
             
             
         
       
     
     wherein
         ring A combines with the carbon atoms with which it is attached to form a C 3-7 cycloalkenyl.       

     In some embodiments, the compounds are of Formula (IVb): 
     
       
         
         
             
             
         
       
     
     In some embodiments, Y 1  is C. In other embodiments, Y 1  is N. 
     In some embodiments, Y 2  is C. In other embodiments, Y 2  is N. 
     In some embodiments, Y 1  is C. In other embodiments, Y 1  is N. 
     In some embodiments, X 1  is C(R x1 ) wherein R x1  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl. In other embodiments, X 1  is N. 
     In some embodiments, X 1  is C(R x1 ) wherein R x1  is selected from any of groups (1a)-(1x):
         (1a) hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   (1b) halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   (1c) hydrogen;   (1d) halogen or C 1-3 haloalkyl;   (1e) halogen or C 1-3 alkyl;   (1f) C 1-3 alkyl;   (1g) hydrogen, methyl or ethyl;   (1h) methyl or ethyl;   (1i) methyl;   (1j) ethyl;   (1k) propyl;   (1l) hydrogen, methyl or propyl;   (1m) methyl or propyl;   (1n) hydrogen, ethyl or propyl;   (1o) ethyl or propyl;   (1p) C 1-3 haloalkyl;   (1q) C 1-3 fluoroalkyl;   (1r) fluoromethyl   (1s) difluoromethyl   (1t) trifluoromethyl   (1u) fluoromethyl   (1v) fluoropropyl   (1w) —CH 2 OH;   (1x) —CH 2 OR;       

     In some embodiments, X 2  is C(R x2 ) wherein R x2  is hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl. In other embodiments, X 2  is N. 
     In some embodiments, X 2  is C(R x2 ) wherein R x2  is selected from any of groups (2a)-(2x):
         (2a) hydrogen, halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   (2b) halogen, C 1-3 alkyl, C 1-3 alkoxy or C 1-3 haloalkyl;   (2c) hydrogen;   (2d) halogen or C 1-3 haloalkyl;   (2e) halogen or C 1-3 alkyl;   (2f) C 1-3 alkyl;   (2g) hydrogen, methyl or ethyl;   (2h) methyl or ethyl;   (2i) methyl;   (2j) ethyl;   (2k) propyl;   (21) hydrogen, methyl or propyl;   (2m) methyl or propyl;   (2n) hydrogen, ethyl or propyl;   (2o) ethyl or propyl;   (2p) C 1-3 haloalkyl;   (2q) C 1-3 fluoroalkyl;   (2r) fluoromethyl   (2s) difluoromethyl   (2t) trifluoromethyl   (2u) fluoromethyl   (2v) fluoropropyl   (2w) —CH 2 OH;   (2x) —CH 2 OR;       

     In some embodiments, X 3  is selected from any of groups (3a)-(3p):
         (3a) O, N(R), S or C 1-3 alkyl;   (3b) O, N(R) or S;   (3c) O or N(R);   (3d) O;   (3e) N(R);   (3f) S or C 1-3 alkyl;   (3g) O, N(R), or C 1-3 alkyl;   (3h) O or C 1-3 alkyl;   (3i) N(R), S or C 1-3 alkyl;   (3j) N(R) or C 1-3 alkyl;   (3k) O or C 1-3 alkyl;   (31) C 1-3 alkyl;   (3m) methylene   (3n) ethylene;   (3o) propylene;   (3p) NH.       

     In some embodiments, X 4  is C. In other embodiments, X 4  is N. 
     In some embodiments, X 5  is C. In other embodiments, X 5  is N. 
     In some embodiments, R 1  is selected from any of groups (4a)-(41):
         (4a) hydrogen or C 1-3 alkyl;   (4b) hydrogen;   (4c) C 1-3 alkyl;   (4d) hydrogen, methyl or ethyl;   (4e) methyl or ethyl;   (4f) methyl;   (4g) ethyl;   (4h) propyl;   (4i) hydrogen, methyl or propyl;   (4j) methyl or propyl;   (4k) hydrogen, ethyl or propyl;   (4l) ethyl or propyl;       

     In some embodiments, R2 is selected from any of groups (5a)-(5gg):
         (5a) hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   (5b) C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   (5c) hydrogen, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   (5d) hydrogen, C 1-3 alkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   (5e) hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OR or —C(O)OR;   (5f) hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, or —C(O)OR;   (5g) hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, or —CH 2 OR;   (5h) hydrogen or C 1-3 alkyl;   (5i) hydrogen;   (5j) C 1-3 alkyl;   (5k) hydrogen, methyl or ethyl;   (5l) methyl or ethyl;   (5m) methyl;   (5n) ethyl;   (5o) propyl;   (5p) hydrogen, methyl or propyl;   (5q) methyl or propyl;   (5r) hydrogen, ethyl or propyl;   (5s) ethyl or propyl;   (5t) C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR or —C(O)OR;   (5u) C 1-3 haloalkyl;   (5v) C 1-3 fluoroalkyl;   (5w) fluoromethyl   (5x) difluoromethyl   (5y) trifluoromethyl   (5z) fluoromethyl   (5aa) fluoropropyl   (5bb) —CH 2 OH;   (5cc) —CH 2 OR;   (5dd) —C(O)OR;   (5ee) —C(O)OH;   (5ff) —C(O)OMe;   (5gg) —C(O)OEt       

     In some embodiments, n is selected from any of groups (6a)-(6k):
         (6a) n is 1, 2, 3, or 4.   (6b) n is 0, 1, 2, or 3.   (6c) n is 0, 1, or 2.   (6d) n is 0 or 1.   (6e) n is 1 or 2.   (60 n is 2 or 3.   (6g) n is 1.   (6h) n is 2.   (6i) n is 3.   (6j) n is 4.   (6k) n is 0.       

     In some embodiments, R 3  is selected from any of groups (7a)-(7cc):
         (7a) each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR, SF 5 , or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7b) each R 3  is independently C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7c) each R 3  is independently halogen, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7d) each R 3  is independently halogen, C 1-3 alkyl, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7e) each R 3  is independently halogen, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7f) each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7g) each R 3  is independently C 1-3 alkyl, C 1-3 alkoxy, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7h) each R 3  is independently —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7i) each R 3  is independently halogen, C 1-3 alkyl, C 1-3 alkoxy, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —S—C 1-3 haloalkyl, —C(O)OR or SF 5 ;   (7j) each R 3  is independently halogen, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —C(O)OR, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7k) each R 3  is independently halogen, C 1 haloalkyl, —O-C 1 haloalkyl, —C(O)OR, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7l) each R 3  is independently fluoro, chloro, C 1-3 haloalkyl, —O—C 1-3 haloalkyl, —C(O)OR, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7m) each R 3  is independently fluoro, chloro, trifluoromethyl, —O—C 1-3 haloalkyl, —C(O)OR, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7n) each R 3  is independently fluoro, chloro, trifluoromethyl, —OCF 3 , —C(O)OR, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7o) each R 3  is independently fluoro, chloro, trifluoromethyl, —OCF 3 , —C(O)OH, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7p) each R 3  is independently trifluoromethyl, —OCF 3 , —C(O)OH, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7q) each R 3  is independently fluoro, chloro, —OCF 3 , —C(O)OH, or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7r) each R 3  is independently fluoro, chloro, trifluoromethyl, —OCF 3 , or two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;   (7s) each R 3  is independently fluoro, chloro, trifluoromethyl or —OCF 3 ;   (7t) each R 3  is independently fluoro, chloro, trifluoromethyl, —OCF 3  or —C(O)OH;   (7u) each R 3  is independently fluoro, chloro, trifluoromethyl or —OCF 3 ;   (7v) each R 3  is independently fluoro, chloro or trifluoromethyl;   (7w) each R 3  is independently fluoro or chloro;   (7x) each R 3  is independently fluoro;   (7y) each R 3  is independently chloro;   (7z) each R 3  is trifluoromethyl;   (7aa) each R 3  is —OCF 3 ;   (7bb) each R 3  is —C(O)OH;   (7cc) two R 3  groups, together with the carbons to which they are attached, form a 1,3-dioxolane;       

     In some embodiments, R is selected from any of groups (8a)-(8l):
         (8a) hydrogen or C 1-3 alkyl;   (8b) hydrogen;   (8c) C 1-3 alkyl;   (8d) hydrogen, methyl or ethyl;   (8e) methyl or ethyl;   (8f) methyl;   (8g) ethyl;   (8h) propyl;   (8i) hydrogen, methyl or propyl;   (8j) methyl or propyl;   (8k) hydrogen, ethyl or propyl;   (8l) ethyl or propyl;       

     In some embodiments, the compound is of Formula (I), (Ia), (Ib) or (Ic), and X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l). 
     In some embodiments, the compound is of Formula (II), (IIa) or (IIa-1), and X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l). 
     In some embodiments, the compound is of Formula (III), (IIIa), (IIIb), (IIIb-1), (IIIc) or (IIIc-1), and X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l). 
     In some embodiments, the compound is of Formula (IV), (IVa) or (IVb) and X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l). 
     In some embodiments, the compound is: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                 No. 
                 ID 
                 Structure 
                 Name 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 ELQ-type systems 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 PA1 
                 MJM102/ MJM113 (ELQ- 271) 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(4- (trifluoromethoxy)phenoxy)phenyl) quinolin-4(1H)-one 
               
               
                   
               
               
                 PA2 
                 MJM 129 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4- phenoxyphenyl)quinolin-4(1H)-one 
               
               
                   
               
               
                 PA3 
                 JM10 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1-ethyl-2-methyl-3-(4- phenoxyphenyl)quinolin-4(1H)-one 
               
               
                   
               
               
                 PA4 
                 RG38 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-chlorophenoxy)-3- hydroxyphenyl)-2-methylquinolin- 4(1H)-one 
               
               
                   
               
            
           
           
               
            
               
                 5,6-fused pyridone systems 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 1 
                 MJM136 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- [1,2,4]triazolo[1,5-a]pyrimidin-7(4H)- one 
               
               
                   
               
               
                 2 
                 MJM141 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl) pyrazolo[1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 3 
                 JAG006 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2,5-dimethyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl) pyrazolo[1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 4 
                 JAG013 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-2-(methylthio)-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- [1,2,4]triazolo[1,5-a]pyrimidin-7(4H)- one 
               
               
                   
               
               
                 5 
                 JAG014 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-7-oxo-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 4,7-dihydropyrazolo[1,5-a]pyrimidine- 3-carbonitrile 
               
               
                   
               
               
                 6 
                 JAG015 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-2-phenyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl) pyrazolo[1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
            
           
           
               
            
               
                 Tetrahydroquinolones (THQ) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 7 
                 MJM170 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-phenoxyphenyl)- 5,6,7,8-tetrahydroquino1in-4(1H)-one 
               
               
                   
               
               
                 8 
                 JAG21 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 9 
                 JAG039 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 4-((5-(2-methyl-4-oxo-1,4,5,6,7,8- hexahydroquinolin-3-yl)pyridin-2- yl)oxy)benzoic acid 
               
               
                   
               
               
                 10 
                 JAG046 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 4-(4-(2-methyl-4-oxo-1,4,5,6,7,8- hexahydroquinolin-3- yl)phenoxy)benzoic acid 
               
               
                   
               
               
                 11 
                 JAG047 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(2-methyl-4-oxo-1,4,5,6,7,8- hexahydroquinolin-3- yl)phenoxy)benzoic acid 
               
               
                   
               
               
                 12 
                 JAG50 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-chlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 13 
                 JAG58 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-fluorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 14 
                 JAG63 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(4- (trifluoromethyl)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 15 
                 JAG062 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3-chlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 16 
                 JAG067 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3-fluorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 17 
                 JAG023 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1,2-dimethyl-3-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 18 
                 JAG077 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-chlorophenoxy)phenyl)-1,2- dimethyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 19 
                 AS006 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(3- (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 20 
                 AS0012 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(3- (trifluoromethyl)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 21 
                 AS021 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3,5-dichlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 22 
                 AS022 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3-chloro-4- fluorophenoxy)phenyl)-2-methyl- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
            
           
         
       
     
     or a stereoisomer thereof or a pharmaceutically acceptable salt thereof. 
     In some embodiments, the compound is: 
     
       
         
           
               
               
               
             
               
                   
               
               
                 ID 
                 Structure 
                 Name 
               
               
                   
               
             
            
               
                 MJM136 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- [1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 MJM141 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)pyrazolo [1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 JAG006 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2,5-dimethyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)pyrazolo [1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 JAG013 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-2-(methylthio)-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- [1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one 
               
               
                   
               
               
                 JAG014 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-7-oxo-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)-4,7- dihydropyrazolo[1,5-a]pyrimidine-3- carbonitrile. 
               
               
                   
               
               
                 JAG015 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 5-methyl-2-phenyl-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)pyrazolo [1,5-a]pyrimidin-7(4H)-one. 
               
               
                   
               
               
                 MJM170 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-phenoxyphenyl)-5,6,7,8- tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG21 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-methyl-3-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG039 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 methyl 3-((5-(4-ethoxy-2-methyl-5,6,7,8- tetrahydroquinolin-3-yl)pyridin-2-yl)oxy) benzoate 
               
               
                   
               
               
                 JAG046 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 4-(4-(2-methyl-4-oxo-1,4,5,6,7,8- hexahydroquinolin-3-yl)phenoxy)benzoic acid 
               
               
                   
               
               
                 JAG047 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(2-methyl-4-oxo-1,4,5,6,7,8- hexahydroquinolin-3-yl)phenoxy)benzoic acid 
               
               
                   
               
               
                 JAG50 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-chlorophenoxy)phenyl)-2-methyl- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG58 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(4-Fluorophenoxy)phenyl)-2-methyl- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG63 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 2-Methyl-3-(4-(4- (trifluoromethyl)phenoxy)phenyl)-5,6,7,8- tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG062 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3-Chlorophenoxy)phenyl)-2-methyl- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG069 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3-Fluorophenoxy)phenyl)-2-methyl- 5,6,7,8-tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JAG023 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1,2-dimethyl-3-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4-one 
               
               
                   
               
               
                 AS006/ JAG143 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3,4-Dichlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin-4(1H)- one 
               
               
                   
               
               
                 AS012/ JAG144 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3,4-Dichlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin-4(1H)- one 
               
               
                   
               
               
                 AS021/ JAG145 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-[4-(3-chloro-4-fluorophenoxy)phenyl]-2- methyl-5,6,7,8-tetrahydro-1H-quinolin-4- one 
               
               
                   
               
               
                 AS034/ JAG148 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-{4-[(2,6-dichloropyridin-4- yl)oxy]phenyl}-2-methyl-5,6,7,8- tetrahydro-1H-quinolin-4-one 
               
               
                   
               
               
                 AS022 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-[4-(3,5-dichlorophenoxy)phenyl]-2- methyl-5,6,7,8-tetrahydro-1H-quinolin- 4(1H)-one 
               
               
                   
               
               
                 JAG084 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-(3,4-Dichlorophenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin-4(1H)- one 
               
               
                   
               
               
                 JAG091 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3(4-(4-Trifluoromethoxyphenoxy)phenyl)- 2-(carboxylate)-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 JAG092 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(6-(4-Trifluoromethoxyphenoxy)pyrdin- 3-yl)-2-methyl-5,6,7,8-tetrahydroquinolin- (4)-one 
               
               
                   
               
               
                 JAG095 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-(4-Phenonxyphenyl)-1,2,3,4,5,6,7,8- octahydroquinazoline-2,4,dione 
               
               
                   
               
               
                 JAG099 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3(4-(4-Trifluoromethoxyphenoxy)phenyl)- 2-(methylhydroxy)-5,6,7,8- tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 AS032 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3-[4-(2H-1,3-benzodioxo1-5- yloxy)phenyl]-2-methyl-5,6,7,8- tetrahydro-1H-quinolin-4-one 
               
               
                   
               
               
                 JAG100 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 6-Ethyl-3-(4-(4- trifluoromethoxyphenoxy)phenyl)-2- methyl-5,6,7,8-tetrahydroquinolin-4(1H)- one 
               
               
                   
               
               
                 JAG106 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3(4-(4-Trifluoromethoxyphenoxy)phenyl)- 2,6-dimethyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 JAG107 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3(4-(4-Trifluoromethoxyphenoxy)phenyl)- 2,7-dimethyl-5,6,7,8-tetrahydroquinolin- 4(1H)-one 
               
               
                   
               
               
                 JAG121 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 7-Ethyl-2-methyl-3(4-(4- trifluoromethoxyphenoxy)phenyl)-5,6,7,8- tetrahydroquinolin-4(1H)-one 
               
               
                   
               
               
                 JA129 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 3(4-(4-trifluoromethoxyphenoxy)phenyl)- 2-methyl-1,7-napthyrid-4(1H)-one 
               
               
                   
               
               
                 JAG162 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 7-Trifluromethyl-2-methyl-3(4-(4- trifluoromethoxyphenoxy)phenyl)-5,6,7,8- tetrahydroquinolin-4(1H)-one 
               
               
                   
               
            
           
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof. 
     In another aspect, the invention provides prodrugs of a compound of Formula (I). The term “prodrug” is intended to represent covalently bonded carriers, which are capable of releasing the active ingredient when the prodrug is administered to a mammalian subject. Release of the active ingredient occurs in vivo. Prodrugs can be prepared by techniques known to one skilled in the art. These techniques generally modify appropriate functional groups in a given compound. These modified functional groups however regenerate original functional groups by routine manipulation or in vivo. Prodrugs of compounds of the invention include compounds wherein an amino, hydroxy, carboxylic or a similar group is modified. Examples of prodrugs include, but are not limited to esters (e.g., acetate, formate, and benzoate), carbamates (e.g., N,N-dimethylaminocarbonyl), amides (e.g., trifluoroacetylamino, acetylamino, and the like), and the like. A complete discussion of prodrugs is found in Huttunen, K. M. and Rautio J.  Current Topics in Medicinal Chemistry,  2011, 11, 2265-2287 and Stella, V. J. et al. (2007).  Prodrugs: Challenges and Awards Part  1. New York: Springer. The disclosure of both references is herein incorporated by reference in its entirety. 
     In some embodiments, the prodrug of a compound of Formula (I) has the structure of Formula (I-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, Y 1 , Y 2 , X 1 , X 2 , X 3 , X 4 , X 5 , R, R 3  and n are as described above;   R2 is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (Ia-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, Y 1 , Y 2 , X 1 , X 2 , X 3 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (Ib-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, Y 1 , Y 2 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (Ic-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, Y 1 , Y 2 , R and R 3  are as described above; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (II-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, X 1 , X 2 , X 3 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIa-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 1 , X 2 , X 3 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIa-1-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIa-2-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIa-3-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (III-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, X 1 , X 2 , X 3 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIIa-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         Y 3 , X, X 2 , X 3 , R, R 2 , R 3 , R 4  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIIb-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 1 , X 2 , X 3 , R, R 2 , R 3 , R 4  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIIb-1-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 3 , R, R 2 , R 3 , R 4  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIIc-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 1 , X 2 , X 3 , R, R 2 , R 3 , R 4 , R 5  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IIIc-1-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 3 , R, R 2 , R 3 , R 4 , R 5  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IV-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, Y 1 , Y 2 , X 1 , X 2 , X 3 , X 5 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IVa-p): 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         ring A, X 1 , X 2 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the prodrug is a compound of Formula (IVb-p 
     
       
         
         
             
             
         
       
     
     or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein
         X 1 , X 2 , X 3 , R, R 2 , R 3  and n are as described above;   R 2  is hydrogen, C 1-3 alkyl, C 1-3 haloalkyl, —CH 2 OH, —CH 2 OR, —C(O)OR or —CH 2 OP; and   P is —C(O)OR′, —C(O)R′, —C(O)NR′ 2  or —OP(O)(OR′)OR′, wherein each R′ is independently hydrogen or C 1-3 alkyl.       

     In some embodiments, the compound is of any of Formulae (I-p), (Ia-p), (Ib-p), (Ic-p), (II-p), (Ia-p), (IIa-1-p), (IIa-2-p), (IIa-3-p), (III-p), (IIIa-p), (IIIb-p), (IIIb-1-p), (IIIc-p), (IIIc-1-p), (IV-p), (Iva-p) or (IVb-p), and X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l). 
     In some embodiments, the compound is of Formulae (I-p), (Ia-p), (Ib-p), (Ic-p), (II-p), (Ia-p), (IIa-1-p), (IIa-2-p), (IIa-3-p), (III-p), (IIIa-p), (IIIb-p), (IIIb-1-p), (IIIc-p), (IIIc-1-p), (IV-p), (Iva-p) or (IVb-p), X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l), and P is —C(O) 2 R′. 
     In some embodiments, the compound is of Formulae (I-p), (Ia-p), (Ib-p), (Ic-p), (II-p), (Ia-p), (IIa-1-p), (IIa-2-p), (IIa-3-p), (III-p), (IIIa-p), (IIIb-p), (IIIb-1-p), (IIIc-p), (IIIc-1-p), (IV-p), (Iva-p) or (IVb-p), X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l), and P is —C(O)R′. 
     In some embodiments, the compound is of Formulae (I-p), (Ia-p), (Ib-p), (Ic-p), (II-p), (Ia-p), (IIa-1-p), (IIa-2-p), (IIa-3-p), (III-p), (IIIa-p), (IIIb-p), (IIIb-1-p), (IIIc-p), (IIIc-1-p), (IV-p), (Iva-p) or (IVb-p), X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l), and P is —C(O)NR′ 2 . 
     In some embodiments, the compound is of Formulae (I-p), (Ia-p), (Ib-p), (Ic-p), (II-p), (Ia-p), (IIa-1-p), (IIa-2-p), (IIa-3-p), (III-p), (IIIa-p), (IIIb-p), (IIIb-1-p), (IIIc-p), (IIIc-1-p), (IV-p), (Iva-p) or (IVb-p), X 1 , X 2 , X 3 , R 1 , R 2 , R 3  and n are selected from any combination of groups (1a)-(8l), and P is —OP(O)(OR′)OR′. 
     In another aspect, the invention provides a pharmaceutical composition comprising a compound of Formula (I-p) and a pharmaceutically acceptable diluent, excipient, or carrier. 
     In some embodiments, the pharmaceutical composition is a combination comprising a compound of Formula (I), an 8-Aminoquinoline drug and a pharmaceutically acceptable diluent, excipient, or carrier. 
     In some embodiments, the pharmaceutical composition is a combination comprising a compound of Formula (I), tafenoquine and a pharmaceutically acceptable diluent, excipient, or carrier. 
     In some embodiments, the pharmaceutical composition is a combination comprising a compound of Formula (I-p), an 8-Aminoquinoline drug and a pharmaceutically acceptable diluent, excipient, or carrier. 
     In some embodiments, the pharmaceutical composition is a combination comprising a compound of Formula (I-p), tafenoquine and a pharmaceutically acceptable diluent, excipient, or carrier. 
     In another aspect, the invention provides a pharmaceutical composition comprising a compound of claim Formula (I) and a pharmaceutically acceptable diluent, excipient, or carrier. In another aspect, the invention provides a method for treating an apicomplexan parasitic infection, comprising administering to a subject (such as a human subject) in need thereof an amount effective to treat the infection of the compound of Formula (I) or a pharmaceutical composition comprising a compound of Formula (I). In some embodiments of the method, the infection comprises a  Toxoplasma gondii  infection and/or a  Plasmodium falciparum  infection. In some embodiments of the method, the infection comprises an infection in the subject&#39;s brain and/or the subject&#39;s eye. In some embodiments of the method, the compound is a prodrug of Formula (I-p). 
     In another aspect, the invention provides a method for treating an apicomplexan parasitic infection, comprising administering to a subject (such as a human subject) in need thereof an amount effective to treat the infection of a a combination comprising a compound of Formula (I) and a 8-Aminoquinoline drug or a pharmaceutical composition comprising a compound of Formula (I) and a 8-Aminoquinoline drug. In some embodiments of the method, the infection comprises a  Toxoplasma gondii  infection and/or a  Plasmodium falciparum  infection. In some embodiments of the method, the infection comprises an infection in the subject&#39;s brain and/or the subject&#39;s eye. In some embodiments of the method, the compound is a prodrug of Formula (I-p). In some embodiments of the method, the 8-Aminoquinoline drug is tafenoquine. 
     In some embodiments of the method, the subject is immune compromised. In some embodiments of the method, the subject is immune compromised due to cancer/cancer treatment, autoimmune disease, and/or AIDS. In some embodiments of the method, the subject has malaria, and the treating comprises reducing severity of one or more symptoms of malaria, and/or reducing recurrence of symptoms of malaria. In some embodiments of the method, the subject has toxoplasmosis, and the treating comprises reducing severity of one or more symptoms of toxoplasmosis, and/or reducing recurrence of symptoms of toxoplasmosis. In some embodiments of the method, the treating comprises reducing parasitic load in the subject. In some embodiments of the method, the treating comprises reducing the bradyzoite form and/or the tachyzoite form of the parasite in the subject. In some embodiments of the method, the method further comprises administering to the subject one or more additional compounds in an amount effective to treat the infection. In some embodiments of the method, the one or more additional compounds are selected from the group consisting of pyrimethamine, sulfadiazine, cycloguanil, inhibitors of kcalcium kinases or dense granules or vacuolar atpases, atovoquone, and bulky cytochrome Qi inhibitors, itraconazole and other inhibitors of  T. gondii.    
     In another aspect, the invention provides a method for monitoring treatment of an apicomplexan parasitic infection (including but not limited to any of the treatments of claims  23 - 33 ), comprising monitoring expression, protein in serum or plasma, and/or activity of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the markers listed in Table and figures in Example 8/ FIGS.  3 A- 3 B  in the Appendix in a subject (such as a human subject) being treated for an apicomplexan parasitic infection, wherein a decrease or increase in expression and/or presence and/or activity of the one or more markers indicates that the treatment is effective. 
     In some embodiments of the method, the infection is a  T. gondii  infection. In some embodiments of the method, the infection is in the subject&#39;s brain or other neurologic tissue. 
     Definitions 
     Terms used herein may be preceded and/or followed by a single dash, “-”, or a double dash, “=”, to indicate the bond order of the bond between the named substituent and its parent moiety; a single dash indicates a single bond and a double dash indicates a double bond or a pair of single bonds in the case of a spiro-substituent. In the absence of a single or double dash it is understood that a single bond is formed between the substituent and its parent moiety; further, substituents are intended to be read “left to right” unless a dash indicates otherwise. For example, alkyl, alkyl-, and -alkyl indicate the same functionality. 
     Further, certain terms herein may be used as both monovalent and divalent linking radicals as would be familiar to those skilled in the art, and by their presentation linking between two other moieties. For example, an alkyl group can be both a monovalent radical or divalent radical; in the latter case, it would be apparent to one skilled in the art that an additional hydrogen atom is removed from a monovalent alkyl radical to provide a suitable divalent moiety. 
     The term “alkoxy” as used herein, means an alkyl group, as defined herein, appended to the parent molecular moiety through an oxygen atom. Representative examples of alkoxy include, but are not limited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy, pentyloxy, and hexyloxy. 
     The term “alkyl” as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n-heptyl, n-octyl, n-nonyl, and n-decyl. When an “alkyl” group is a linking group between two other moieties, then it may also be a straight or branched chain; examples include, but are not limited to —CH 2 —, —CH 2 CH 2 —, —CH 2 CH 2 CHC(CH 3 )—, —CH 2 CH(CH 2 CH 3 )CH 2 —. 
     The terms “cyano” and “nitrile” as used herein, mean a —CN group. “Cycloalkenyl” as used herein refers to a monocyclic or a bicyclic cycloalkenyl ring system. Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon-carbon double bond), but not aromatic. Examples of monocyclic ring systems include cyclopentenyl and cyclohexenyl. Bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form —(CH 2 ) w —, where w is 1, 2, or 3). Representative examples of bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct-2-enyl. Fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The bridged or fused bicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkenyl ring. 
     Cycloalkenyl groups are optionally substituted with one or two groups which are independently oxo or thia. 
     The term “halo” or “halogen” as used herein, means —Cl, —Br, —I or —F. 
     The term “haloalkyl” as used herein, means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl. 
     The term “heteroaryl,” as used herein, means a monocyclic heteroaryl or a bicyclic ring system containing at least one heteroaromatic ring. The monocyclic heteroaryl can be a 5 or 6 membered ring. The 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom. The 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms. The 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl. Representative examples of monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl. The bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia. When the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system. When the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system. Representative examples of bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5,6-dihydroquinolin-2-yl, 5,6-dihydroisoquinolin-1-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroisoquinolin-1-yl, thienopyridinyl, 4,5,6,7-tetrahydrobenzo[c][1,2,5]oxadiazolyl, and 6,7-dihydrobenzo[c][1,2,5]oxadiazol-4(5H)-onyl. In certain embodiments, the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. 
     The term “hydroxy” as used herein, means an —OH group. 
     The term “nitro” as used herein, means a —NO 2  group. 
     The term “oxo” as used herein means a ═O group. 
     The term “saturated” as used herein means the referenced chemical structure does not contain any multiple carbon-carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like. 
     The term “thia” as used herein means a ═S group. 
     The term “unsaturated” as used herein means the referenced chemical structure contains at least one multiple carbon-carbon bond, but is not aromatic. For example, a unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like. 
     As used herein, the term “cell” is meant to refer to a cell that is in vitro, ex vivo or in vivo. In some embodiments, an ex vivo cell can be part of a tissue sample excised from an organism such as a mammal. In some embodiments, an in vitro cell can be a cell in a cell culture. In some embodiments, an in vivo cell is a cell living in an organism such as a mammal. 
     As used herein, the term “contacting” refers to the bringing together of indicated moieties in an in vitro system or an in vivo system. For example, “contacting” a parasite with a compound includes the administration of a compound described herein to an individual or patient, such as a human, infected with the parasite, as well as, for example, introducing a compound into a sample containing a cellular or purified preparation containing the parasite. 
     In another aspect, the invention provides methods for monitoring  T. gondii  infection in a subject, comprising monitoring levels in a blood sample from the subject of one or more markers selected from the group consisting of clusterin, oxytocin, PGLYRP2 (N-acetylmuramoyl-L-alanine amidase), Apolipoprotein A1 (apoA1), miR-17-92, and miR-124, wherein a change in levels of the one or more circulating markers compared to control correlates with  T. gondii  infection in the subject. The inventors have discovered these specific markers of active  T. gondii  infection, as described in the examples that follow. 
     The blood sample can be whole blood, serum, blood plasma, or any other suitable blood sample in which circulating IgG from a person with toxoplasmosis may be present. For example, the blood sample may be a plasma sample. As used herein, a “plasma sample” means blood plasma, the liquid component of blood, and is prepared, for example, by centrifugation of whole blood to remove blood cells. As used herein, a plasma sample also includes a blood serum sample, in which blood clotting factors have been removed. 
     Any suitable control can be used, including but not limited to a reference value obtained from one or more subjects that either do not have a  T. gondii  infection, or that are known to have a  T. gondii  infection, a previous blood sample obtained from the same subject, or any other suitable control. It is well within the level of those of skill in the art to determine an appropriate control for an intended use in light of the teachings herein. The change in level from control that correlates with  T. gondii  infection in the subject may be a difference of 10%, 25%, 50%, 100%, or more. In one embodiment, the difference is a statistically significant increase as judged by standard statistical analysis. 
     The level (e.g., quantity or amount) of a particular biomarker can be measured in the blood sample using a variety of methods known to those of skill in the art. Such methods include, but are not limited to, flow cytometry, ELISA using red blood cell, platelet, or white blood cell lysates (e.g., lymphocyte lysates), and radioimmunoassay. 
     In one embodiment, the method is used to monitor effect on the subject of a therapy for  T. gondii  infection. In this embodiment, the subject is receiving therapy for a  T. gondii  infection, and the methods permit attending medical personnel to assess efficacy of the therapy. In this embodiment, the blood sample test may, for example, be carried out periodically over time during the course of therapy. In another embodiment, the method is used to diagnose whether the subject is suffering from a  T. gondii  infection. In this embodiment, the subject is suspected of suffering from a  T. gondii  infection based on the presence of one or more symptoms, and the methods can be used to assist in providing a more definitive diagnostic, along with all other factors to be considered by an attending physician. 
     In various embodiments of these methods: 
     (a) an increase in level of one or more of clusterin, oxytocin, miR-17-92, or miR-124 compared to control correlates with active  T. gondii  infection; and/or 
     (b) a decrease in level of one or more of PGLYRP2 or ApoA1 compared to control correlates with active  T. gondii  infection. 
     In further embodiments of these methods: 
     (a) a decrease in level of one or more of clusterin, oxytocin, miR-17-92, or miR-124 compared to a level of the one or more markers in a serum sample obtained from the subject at an earlier time point correlates with a positive effect of the therapy in treating active  T. gondii  infection; and/or 
     (b) an increase in level of one or more of PGLYRP2 or ApoA1 compared to a level of the one or more markers in a serum sample obtained from the subject at an earlier time point correlates with a positive effect of the therapy in treating correlates with active  T. gondii  infection. 
     In one embodiment, the  T. gondii  infection involves neuronal damage and/or retinal damage in the subject. For example, the  T. gondii  infection may involve neuronal damage selected from the group consisting of neurodegeneration and/or seizures. 
     In another aspect, the invention provides methods for treating a  T. gondii  infection, comprising administering to a subject with a  T. gondii  infection an amount effective to treat the infection of ApoA1. As shown in the examples that follow, a reduction in apoA1 closely correlates with active  T. gondii  infection. The apoA1 may be administered as a protein therapeutic, or may be administered in an expression construct (such as a recombinant viral vector, etc.) that expresses apoA1 (i.e.: gene therapy). 
     In one embodiment, the subject to be treated has a decreased level of serum ApoA1 compared to control. 
     
       
         
           
               
               
            
               
                   
                 UniProtKB-P02647 (APOA1_HUMAN) 
               
               
                   
                 (SEQ ID NO: 4) 
               
               
                   
                 MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT 
               
               
                   
                   
               
               
                   
                 VYVDVLKDSG RDYVSQFEGS ALGKQLNLKL LDNWDSVTST 
               
               
                   
                   
               
               
                   
                 FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK 
               
               
                   
                   
               
               
                   
                 VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE 
               
               
                   
                   
               
               
                   
                 LQEKLSPLGE EMRDRARAHV DALRTHLAPY SDELRQRLAA 
               
               
                   
                   
               
               
                   
                 RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ 
               
               
                   
                   
               
               
                   
                 GLLPVLESFK VSFLSALEEY TKKLNTQ. 
               
            
           
         
       
     
     As used herein, the term “individual” or “patient,” or “subject” used interchangeably, refers to any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, and most preferably humans. 
     As used herein, the phrase “amount effective”, “therapeutically effective amount” or “effective to treat” refers to the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician. 
     In certain embodiments, a therapeutically effective amount can be an amount suitable for (1) preventing the disease; for example, preventing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease; 
     (2) inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder; or
 
(3) ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing the pathology and/or symptomatology) such as decreasing the severity of disease.
 
     As used here, the terms “treatment” and “treating” means (i) ameliorating the referenced disease state, for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing or improving the pathology and/or symptomatology) such as decreasing the severity of disease; or (ii) eliciting the referenced biological effect (e.g., reducing parasitic loador adverse effects the parasite is causing in the human it infects). 
     As used herein, the phrase “pharmaceutically acceptable salt” refers to both pharmaceutically acceptable acid and base addition salts and solvates. Such pharmaceutically acceptable salts include salts of acids such as hydrochloric, phosphoric, hydrobromic, sulfuric, sulfinic, formic, toluenesulfonic, methanesulfonic, nitric, benzoic, citric, tartaric, maleic, hydroiodic, alkanoic such as acetic, HOOC—(CH 2 ) n —COOH where n is 0-4, and the like. Non-toxic pharmaceutical base addition salts include salts of bases such as sodium, potassium, calcium, ammonium, and the like. Those skilled in the art will recognize a wide variety of non-toxic pharmaceutically acceptable addition salts. 
     Example 1. New Paradigms for Understanding and Step Changes in Treating Active and Chronic, Persistent Apicomplexan Infections 
     Abstract 
       Toxoplasma gondii , the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain  T. gondii  forms cysts in vitro that induce oocysts in cats, the gold standard criterion for cysts. These cysts highly express cytochrome b. Using these models, we envisioned, and then created, novel 4-(1H)-quinolone scaffolds that target the cytochrome bc 1  complex Q i  site, of which, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC 50 , 30 nM) and cysts (IC 50 , 4 μM) in vitro, and in vivo (25 mg/kg), and drug resistant  Plasmodium falciparum : (IC50, &lt;30 nM), with clinically relevant synergy. Mutant yeast and co-crystallographic studies demonstrate binding to the bc 1  complex Q i  site. Our results have direct impact on improving outcomes for those with toxoplasmosis, malaria, and ˜2 billion persons chronically infected with encysted bradyzoites. 
       Toxoplasma gondii  infections can cause systemic symptoms, damage and destroy tissues 1-1 , especially eye and brain 1-10  and cause fatalities S1-20  Primary infections may be asymptomatic, or cause fever, headache, malaise, lymphadenopathy, and rarely meningoencephalitis, myocarditis, or pericarditis 9,11,12 . Retinochoroiditis and retinal scars develop in up to 30% of infected persons 1,7,13  and epilepsy may occur 6,14  In immune-compromised and congenitally infected persons, active infection frequently is harmful 1-10 . Recrudescence arises from incurable, dormant cysts throughout life 6,7,9,10  In rodents, chronic infection alters fear, smell, reward pathways, neurotransmitters such as GABA and dopamine, and causes abnormal neurologic functions 15 . Although this parasite is present in the brains of 2-3 billion persons worldwide, consequences are unknown. Neurobehavioral abnormalities and differences in serum cytokines, chemokines, and growth factors were associated with seropositivity in humans 16, 17 . 
     Current treatments against active  T. gondii  tachyzoites can have side effects such as hypersensitivity, kidney stones, and bone marrow suppression, limiting their use 10 . Latent bradyzoites are not significantly affected by any medicines 6 . Atovaquone partially, and transiently, limits cyst burden in mice 18 , but resistance develops with clinical use 19 -2 4 . Thus,  T. gondii  infection is incurable with recrudescence from latent parasites posing a continual threat. Estimates of costs for available, suboptimal medicines to treat active, primary ocular, gestational and congenital infections, in just the U.S. and Brazil, exceed $5 billion per year. Improved medicines are needed urgently. Molecular targets shared by  T. gondii  and Plasmodia make re-purposing compounds a productive strategy. 
     Critical flaws and limitations of available methods and models for developing medicines to cure  T. gondii  infections include lack of in vitro culture systems for cysts and scalable, easy to use animal models for screening compounds. To address these challenges, we characterized the EGS parasite, isolated in 1994 from amniotic fluid of a congenitally infected Brazilian fetus 24a , that form cyst-like structures in vitro 25 . In our characterization of EGS in vitro, herein, we discovered that true cysts develop, making EGS especially useful for drug development. EGS parasites can infect zebrafish, and we have characterized this, as well as a fluorescent tachyzoite and cyst assay in this new model 26 . Further, cytochrome bc 1  expression is markedly increased in encysted EGS bradyzoites suggesting cytochrome bc 1  might be a viable drug target for this life stage. This mitochondrial membrane bound protein complex cytochome bc 1 , part of the electron transport chain responsible for generating ubiquinone for pyrimidine biosynthesis in  Plasmodium , is the molecular target of the naphthoquinone, atovaquone 27-52 . Partial efficacy, rapid emergence of drug resistance in malaria and toxoplasmosis limit clinical usefulness of atovaquone. We present new 4-(1H)-quinolone scaffolds that target the Q i  site of cytochrome bc1 in apicomplexan parasites. Our lead 5,6,7,8-tetrahydroquinolin-4-one compound, MJM170, is highly effective against apicomplexan parasites and has substantially enhanced solubility compared with other reported quinolones due to its&#39; new scaffold. Direct visualisation in the crystallographic structure opens the way to design a new generation of compounds for both parasites. 
     Results 
     Characterization of EGS Strain Develops Novel In Vitro Models to Test Compounds. 
     Genotyping and Phylogenetic Analysis of EGS: We isolated and sequenced genomic DNA from the EGS 25  (25) parasite, which formed cysts when grown in human foreskin fibroblasts (HFF) in culture. Phylogenetic analysis based on 796,168 SNPs across 62  T. gondii  genomes revealed that EGS is closely related to other Brazilian strains including TgCatBr1, TgCatBr18 and TgCatBr25 and ancient South American MAS. All these grouped to clade B, haplogroup 4 and 8. Full genome sequence analysis of EGS compared with canonical and geographically closely related parasite genomic sequences reveal a non-synonymous mutation and disordered c terminal sequence in Apetela 2 (AP2) IV-iv, a bradyzoite repressor. EGS differs from other isolates by non-synonymous SNPs in Apetela 2 IV-iv, M=&gt;I (570) and a disordered area beginning at 821, GGNRPHYHVAKQEWRVRYYMNGKRKMRTYSAKFY GYETAHTMAEDFAHYVDKHE (SEQ ID NO: 1). AP2 IV-iv is a member of the plant-like transcription factor family unique to apicomplexan parasites. This AP2 represses tachyzoite to bradyyzoite conversion, 56  among other differences. Because AP2 IV-iv is a bradyzoite gene expression repressor 56 , a mutation could create a parasite like EGS that remains as an encysted bradyzoite. 
     Phenotypes of EGS in Human cells in vitro, and in Cats and Mice: 
     EGS in human foreskin fibroblasts (HFF). In vitro, these EGS parasites form cysts that enlarge over ˜48-96 hours and then destroy monolayers as single cell organisms. This created novel, useful in vitro models. Cyst walls are thick in electron micrographs (data not shown). Cyst-like structures&#39; perimeters demonstrate dolichos, with bradyzoites within them staining with BAG1 and nuclei with Dapi. Kinetic analysis of EGS in HFF cultures, 2, 18, and 72 hours after infection, RNA-seq and MiR-seq results demonstrated varied expression signatures over time in culture with expression of bradyzoite markers by 18 hours and Apetela 2 signatures by 2 hours. 
     Cats fed EGS in HFF cultures or mouse brain produce oocysts. When HFF tissue cultures with these cyst structures were fed to cats, they developed the classic, gold standard bradyzoite phenotype of producing oocysts in two replicate experiments. All other  T. gondii  strains cultured for more than 30 passages, as EGS was since the 1990s, lose the ability to produce oocysts when fed to cats (JP Dubey, personal observations). This experiment established that these were true bradyzoites in cysts formed in vitro under standard culture conditions. Oocysts also formed 10 days after feeding cats mouse brains infected with EGS stably transfected with tachyzoite SAG1 promoter-driven mcherry, and bradyzoite BAG1 promoter-driven green fluorescent protein (GFP), and merozoite promoter-driven blue fluorescent protein, engineered to facilitate creation of automated, scalable in vitro and in vivo assays. In vitro, these promoters did not provide a fluorescence signal robust enough to detect differences between 2×10 5  and 650 parasites useful in scalable assays (data not shown). 
     EGS is virulent in Mice. When these EGS oocysts were fed to mice they produced disease indistinguishable from other virulent Brazilian strains. Oocysts given to mice per-orally created an illness and histopathology phenotypically characteristic for typical, virulent parasites causing dose related proliferation of  T. gondii  with necrosis in terminal ileum, pneumonia at 9-10 days, with brain parasites by 17 days and dose-related mortality. 
     EGS has a bradyzoite/cyst morphology and alters the transcriptomes of the biologically relevant human monocytic cell line MM6 and human primary neuronal stem cells (NSC). Human cells particularly relevant to human toxoplasmosis were infected with different strains of  T. gondii  to better characterize EGS parasites. Immunofluorescence staining of EGS-infected MM6 and NSC cultures revealed the development of cysts ( FIG.  1 A ) and accordingly, EGS gene expression resembled that of bradyzoites when compared to equivalent infections done with GT1, ME49 or VEG strains. Interestingly, EGS transcription was influenced by host cell type ( FIGS.  1 A- 1 D ). Transcriptomics using host mRNA and miR profiling of EGS cultures in MM6, and NSC cells for 18 hours demonstrated that this parasite modulates host transcripts involved in protein misfolding, neurodegeneration, endoplasmic reticulum stress, spliceosome alteration, ribosome biogenesis, cell cycle, epilepsy, and brain cancer among others ( FIGS.  1 A- 1 D ). The number of genes significantly up or down regulated in MM6 and NSC cells compared to uninfected controls are depicted in  FIGS.  1 A- 1 D . Overexpressed genes differ from those of GT1, ME49 and VEG tachyzoite-infected human NSC cells ( FIG.  2 A ), but modify the same or connected pathways (McLeod et al, unpublished observations). Hsa-miR-708-5p was the most affected miRNA (down-modulated) by EGS ( FIG.  1 D ). miR-708-5p is a regulator that promotes apoptosis in neuronal and retinal cells, which could maintain a niche for EGS-like encysted bradyzoites to persist. 
     EGS transcripts demonstrate importance of cytochromes and key Apetela 2 transcription factors in this life cycle stage. EGS transcripts in HHF, MM6, and NSC cells were enriched for genes transcribed in bradyzoites, including known bradyzoite transcripts, certain Apetela 2s and cytochrome b and other cytochromes. Among transcripts with the most increased fold change in EGS across all three cell lines were: cytochrome b; cytochrome c oxidase subunit III subfamily protein; apocytochrome b; cytochrome b, putative; and cytochrome b (N-terminal)/b6/petB subfamily protein. Other over-expressed genes include bradyzoite transcription factor AP2IX-9 and plant-like heat-shock protein BAG1 ( FIG.  2 A ). 
     Identifying Novel and Efficacious Compounds Against  T. gondii  Cytochrome bc 1 , 
     Increased expression of cytochromes in EGS made it pertinent to synthesize and test an endochin-like quinolone (ELQ) 271, which was previously reported to inhibit  T. gondii  cytochrome bc 1  Q i  site and reduce, but not eliminate, brain cyst numbers in mice 27 . ELQ271 also inhibited EGS in vitro ( FIG.  2 B  bottom) demonstrating that our in vitro model correlates with previously reported partial activity of ELQ271 against bradyzoites in cysts in mouse brain. Vivoporter-PMOs inhibiting cytochrome bc 1  had a modest effect on tachyzoite replication and a small effect on size and number of EGS cysts ( FIG.  2 B  top). Minimal effect might be related to limited entry of vivoporter into cysts or mitochondria. 
     ELQs have been a focus for drug development for malaria (ELQ 300) and toxoplasmosis (ELQ 271 and 316) as they were reported to be potent and selective (versus human cytochrome bc 1 ) inhibitors of  P. falciparum  cytochrome bc 1  at nanomolar concentrations 27 . ELQs are part of the 4-(1H)-quinolone class of cytochrome bc 1  inhibitor 36,42,40,45,49,52,53,54,56-62  and (Dogget et al, 13th International Toxoplasmosis Meeting Abstract. Gettysburg Pa., June 2015), a scaffold that suffers from limited aqueous solubility. Another aspect of inhibitor design for this system is minimizing the inhibition of mammalian cytochrome bc 1 , which shares ˜40% sequence identity to the  T. gondii  ortholog within the Q substrate sites. Thus, we set out to design potent and selective inhibitors of  T. gondii  cytochrome bc 1  with improved solubility ( FIGS.  3 A and  3 B ) compared to known quinolone-based inhibitors. Noting the previous work of GSK on the preclinical development of Clopidol derivatives which led to terminating studies secondary to toxicity in the rat models, as another serious deficiency 63  and the incorporation of the diphenyl ether group onto the central 4-(1H)-quinolone core as reported by Riscoe et al. 27 , we focused on the central core ring system. Doggett, Riscoe et al&#39;s 27  ELQ 271 ( FIGS.  3 A and  3 B ) was reported to be ineffective against yeast with a mutation in the Q i  site. Nonetheless, it recently was shown that ELQs can bind both Q i  and Q o  depending on subtle chemical changes 61-3 . As a result of our initial efforts, a 5,6,7,8-tetrahydroquinolone (MJM170, 2) displayed promising results. ( FIGS.  3 A and  3 B ; Table 2). We chose ELQ271 for comparison because it had the greatest activity at the lowest dose (5 mg/kg) in the mouse model of Doggett despite the higher cytotoxicity toward human fibroblasts in the in vitro toxicity studies. 27    
     MJM170 is a potent inhibitor of  T. gondii  tachyzoites (RH—YFP strain, IC 50  0.03 μM) and bradyzoites (EGS strain, IC 50  4 μM), equipotent to ELQ271 (Table 2,  FIG.  4 A- 4 E ). MJM170 showed 10-fold improved aqueous kinetic solubility (pH 7.4) over ELQ 271 (Table 2), 3-fold improved FaSSIF/FeSSIF (pH 6.5) solubility, with similar human microsomal stability profiles (146 vs 172 minutes). A different method from that in reference 49  was used. MJM170 has a significantly decreased mouse microsomal stability compared to ELQ 271 (20 vs&gt;200 minutes). MJM170 was further evaluated with MDCK-MDR1 cells (a measure of blood-brain barrier permeability) and results suggest that MJM170 could cross the blood brain barrier and not suffer from P-glycoprotein efflux These data highlight the potential of the 5,6,7,8-tetrahydroquinolin-4-one scaffold for further hit-to-lead development. 
     
       
         
           
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 Comparison of ELQ 271 and MJM170 in our biological assays: inhibition of 
               
               
                 apicomplexan parasites and ADME/Tox. ELQ 271 was synthesised in-house. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                 Compound 
                 ELQ 271 
                 MJM170 
               
               
                   
               
               
                 Structure 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 
                   
                     
                     
                         
                         
                     
                   
                 
               
               
                   
               
               
                 Mol. Wt. 
                 411.4 
                 331.4 
               
               
                 
                   T. 
                   gondii 
                 
                   
                   
               
               
                 Tachyzoite IC 50  μM 
                 0.03 
                 0.03 
               
               
                 
                   T. 
                   gondii 
                 
                 1 
                 4 
               
               
                 Bradyzoite IC 50  μM 
                   
                   
               
               
                 
                   P. 
                   falciparum 
                 
                 0.03 (D6) 0.09 (TM91C235) 0.10 
                 0.01 (D6) 0.03 (TM91C235) 0.03 
               
               
                 IC 50  μM a   
                 (W2) 0.13 (C2B) 
                 (W2) 0.01 (C2B) 
               
               
                 HFF Toxicity CC 50  μM 
                 20 
                 20 
               
               
                 Kinetic Solubility 
                 0.15 
                 1.97 
               
               
                 PBS pH 7.4 μM  b   
                   
                   
               
               
                 FaSSIF Solubility 
                 3.4 
                 9.8 
               
               
                 pH 6.5 μM  b   
                   
                   
               
               
                 Human microsomal 
                 171.9 
                 146.3 
               
               
                 stability T 1/2  mins  b   
                   
                   
               
               
                 Mouse microsomal 
                 &gt;200 
                 21.0 
               
               
                 stability T 1/2  mins  b   
                   
                   
               
               
                 MDCK-MDR1 
                 N.D. 
                 32.1 
               
               
                 P app A-B × 10 6  cm/s  b   
                   
                   
               
               
                 MDCK-MDR1 
                 N. D. 
                 1.23 
               
               
                 Efflux Ratio  b   
               
               
                   
               
               
                   a The D6 strain (Sierra Leone) is drug sensitive, the TM91C235 (Thailand) is multi-drug resistant, the W2 strain (Thailand) is chloroquine resistant, and the C2B strain is multi-drug resistant with pronounced resistance to atovaquone. 
               
               
                   b  ADME carried out by ChemPartner Shanghai Ltd. N.D. not determined. Human and mouse microsomal stability differs as is known to occur for other compounds such as TMP/SMX. 
               
            
           
         
       
     
     MJM 170 is effective in vivo against tachyzoites, and modestly against bradyzoites in cysts of mice, and development of a scalable zebrafish assay. MJM170 was highly efficacious against RH ( FIG.  5 A ) and Prugniaud ( FIG.  5 B ) strain tachyzoites in mice at 25 mg/kg without toxicity for 5 days (p&lt;0.00), and modestly reduced numbers of Me49 strain cysts established &gt;2 months earlier when treated with 12.5-25 mg mg/kg for 17 days (p&lt;0.002) ( FIG.  5 C ). In analysis of parallel histopathology, there was a similar trend (data not shown). Translucent zebra fish can be infected with EGS, other  T. gondii  that make cysts, and RH YFP preparing for a novel model for scalable screening ( FIG.  5 D ). 
     Cytochrome bc 1  Q i  is the binding site of MJM170 which is potent against  Plasmodium falciparum : and yeast. Tetrahydroquinolone binds to the Q i  site of cytochrome bc 1 : Studies to determine whether cytochrome bc 1  Q i  is the molecular target of MJM170 initially included studies of resistance of yeast and  P. falciparum  with known cytochrome b Q i  mutations predicted to cause a steric clash with MJM170 ( FIGS.  6 A- 6 G ). Recently, we reported co-crystal structures of GSK&#39;s cytochrome bc 1  inhibitors bound to bovine cytochrome bc 1  at the Q i  site 52  demonstrating that these pyridone inhibitors and other structurally related inhibitors bind to an alternative site to atovaquone on cytochrome bc 1 . This structure allowed us to model MJM170 within the Q i  site using the Maestro Suite from Schrödinger. This molecular modelling predicted steric clashes in mutant yeast and  P. falciparum  cytochrome bc 1  with MJM170 ( FIG.  6 A ). 
     Co-crystallization of MJM170 with bovine cytochrome bc 1  and modelling of the  T. gondii  enzyme confirm the target. Co-crystallization validates predictions made with modelling and confirmed using assays with  S. cerevesiae  mutants ( FIG.  6 D ). There was no steric clash for  P. falciparum —model based upon this crystal structure, consistent with in vitro assays ( FIGS.  6 E- 6 F ). MJM170 was co-crystallized with bovine cytochrome bc 1  and the resulting good quality electron density maps allowed for unambiguous placement of MJM170 within the Q i  site ( FIG.  6 F ). The planar region of the quinolone group is held between heme b H  and Phe220 and the additional ring further extends into the hydrophobic cavity at the apex of the binding site towards Pro24 and Ile27. The carbonyl group of the compound is surrounded by Ser35, Asp228 and the carbonyl of Trp31, while its amine moiety lies between His201 and Ser205. The diphenyl ether group extends outwards towards the hydrophobic residues Ile39 and Ile42 and forms a stacking interaction with Phe18 ( FIG.  6 G ). 
     Surrogate assays demonstrate efficacy of compounds, providing target validation and added value as MJM170 is effective against wild type but not M221Q(F) mutant yeast. Mutants of  S. cerevesiae  were used to further confirm the molecular target of MJM170 ( FIG.  6 D ), and documented that the Q i  domain in cytochrome b is essential for its efficacy. This approach provided insight into binding of compounds to the enzyme. Crystallographic structure of bovine cytochrome bc 1  with GSK932121 52  indicates that certain amino acids are critical in tetrahydroquinolone binding and explains why there is inhibition by certain compounds. Previous studies reported that no cross-resistance is observed between ELQs and atovaquone in  P. falciparum . This is rationalised as atovaquone binds the Q o  site on cytochrome bc 1 . A yeast M221Q substitution within the Q i  site displayed resistance to ELQ inhibition further confirming that this to be the target site 27 . MJM170 and ELQ271 were effective against  S. cerevisiae  wild type parental AD1-9 strain at 1 mM, 100, 5 and 1 μM when grown on non-fermentable, glycerol medium forcing reliance on ATP production for respiration. Yeast strains with point mutations in the cytochrome b gene that substitute methionine by glutamine (M221Q) or phenylalanine (M221F) at position 221 in the Q i  site predicted to yield a steric clash upon inhibitor binding were resistant to MJM170 ( FIG.  6 D ). 
     Tetrahydroquinolones are potent against wild type  P. falciparum , and  P. falciparum  G33A/V and other drug resistant mutants but not DHODH mutant. MJM170 is highly effective against  P. falciparum  (Table 2) including multiple strains resistant to available antimicrobials and a cytochrome bc 1  Q i  mutant ( FIGS.  7 A- 7 C ). Resistance against transgenic  P. falciparum  yeast DHODH mutant strain indicates MJM170 affects mitochondria suggesting that the mode of action against  P. falciparum  is through inhibition of electron transport ( FIG.  7 A ). 
     Potentially clinically useful combinations with tetrahydroquinolone demonstrated in synergy studies. To determine whether there might be clinically relevant synergies and additive effects, combinations of MJM170 with other clinically available and useful compounds also were tested. Earlier, we had found cycloguanil and related biguanide tnazines 64  were active against  T. gondii  tachyzoites and  P. falciparum  making it relevant to test them in combination with MJM170. We observed modest synergy in vitro for atovaquone, additive effect with cycloguanil, and antagonism with BRD6323, a Q i  inhibitor for  P. falciparum  ( FIG.  7 B ). Combining atovaquone with proguanil (active component cycloguanil) as Malarone R  for malaria provides an approach to reduce selection of drug resistant  plasmodium  mutants. 
     DISCUSSION 
     The results presented here offer a molecular understanding and therapeutic strategies for one of the most common parasitic infections of human brain and eye, and that persists across lifetimes in around 2 billion people worldwide. We have developed new models to facilitate discovery of curative treatments for toxoplasmosis. We have characterized the Brazilian  T. gondii  isolate called EGS that was known to be morphologically similar to encysted bradyzoites in tissue culture. We further validate the cystic nature of these EGS infected cultures, since they are able to induce the intra-intestinal life cycle when fed to cats ultimately resulting in oocyst secretion. This is the first such description of this phenotype and provides definitive proof that this unique parasite has a true cyst phenotype when maintained in vitro. Our data also provide a number of other major conceptual advances on EGS by demonstrating the following: (i) Genome sequencing of this EGS isolate demonstrates that EGS has a typical Brazilian virulent genotype and phylogeny, (ii) EGS is a haplogroup 4  T. gondii . Consistent with a genotype that is known to be pathogenic and virulent for mice, we demonstrate that EGS oocyst induced infection is similar to that of other virulent Brazilian parasites. For example, mice fed EGS oocysts demonstrated ileal parasites causing necrosis, as well as pneumonitis, encephalitis and systemic infection leading to death. This indicates that the ability to form cysts in culture does not alter the pathogenicity of EGS in mice. However, potentially relevant to its in vitro bradyzoite phenotype, full genome sequencing revealed that it has nonsynonymous single nucleotide repeat sequence differences from other Brazilian and canonical U.S. and European parasites which do not share its in vitro bradyzoite phenotype. EGS has a non-synonymous mutation in a bradyzoite repressor, Apetela 2 (AP2) IV-iv, plant like transcription factor. AP2s interact with HATs and HDACs to modulate transcriptional signatures in apicomplexan parasites 55 . This Apetela 2, plant-like transcription factor gene, AP2IV-4, represses bradyzoite genes during the tachyzoite cell cycle, thereby preventing commitment to the bradyzoite developmental pathway 56 . If the observed substitution or disordered N terminus results in a defective or non-functional molecule, this could provide an explanation for the observed bradyzoite phenotype of EGS parasites. This is consistent with our findings that EGS in HFF forms cysts by 24 hours, characterized by BAG1, and  Dolichos  staining at 24, 48, and 96 hours after infection. These cysts gradually enlarge until 48-96 hrs in culture, when single  T. gondii  begin to destroy HFF monolayers. These are the cultures of bradyzoites in cysts that when fed to cats ˜48 hours after infection form oocysts which are virulent in mice, providing definitive proof of an in vitro bradyzoite phenotype for the EGS strain of  T. gondii.    
     The transcriptomic studies with this EGS isolate have provided critical insights into host cell mechanisms that are a prominent part of the ability of the encysted parasite to persist in this untreatable life cycle stage, and biologic consequences of such persistent infection. RNAseq and miR seq of EGS infected human host cells included human fibroblasts, monocytic and neuronal stem cells with this encysted EGS strain parasite. These provide an understanding of the types of perturbations of biologically relevant host cells this bradyzoite life cycle stage can cause, providing insights into unique aspects of pathogenesis of this infection with untreatable cysts and its consequences. We found that EGS modifies critical host cell pathways. For example we find in vitro modulations of host cell pathways in human, primary neuronal stem cells are the same as those associated with modulation of host cell replication as seen with malignancies, and in neurodegenerative diseases. Further, it is noteworthy that the level of a microRNA that specifies apoptosis in eye and brain cells is markedly down modulated by this EGS bradyzoite which would inhibit host protective apoptotic mechanisms allowing parasites to persist in brain and eye without a critical protective mechanism. EGS, as an encysted bradyzoite, clearly alters biologic processes including cell cycle, cell death, alternative splicing, protein synthesis, protein folding and ubiquitination and down regulates hsa-miR-708-5p that specifies apoptosis in neuronal and retinal cells 65 . 
     RNA and MiR sequencing and transcriptomic analyses of the EGS parasites also identified molecular targets that are critical for the bradyzoite life cycle stage in the parasite as well. These molecular targets include cytochrome b, as critically increased in dormant, encysted parasites. Cytochrome b was increased along with known cyst constituents like enolase 1, Cyst wall protein, Lactate dehydrogenase 2, bradyzoite antigen 1, Apetela 2 plant like transcription factors not present in animals, such as AP2 IX-ix, and cytochrome oxidase. Our work provides a new means to identify stage specific molecular targets, and emphasizes that cytochrome be 1 complex is a critical target. The transcriptome of EGS parasites in HFF over time are similar to those of in vivo bradyzoites in terms of known critical genes modified. Finally, EGS presents a much-needed assay for identifying novel molecular targets present in bradyzoites in vitro. EGS was also useful to evaluate the effect of inhibitors on encysted bradyzoites in vitro. 
     Recent crystallographic studies with the bovine cytochrome bc 1  complex allowed us to rationally design a novel compound to target the Q i  site of cytochrome b. Our novel compound was designed to address issues with poor solubility of existing quinolone/pyridone Q i  inhibitors. One of these compounds MJM170, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC 50  30 nM) and cysts (IC 50  4 μM) in vitro, and in vivo (25 mg/kg). It is predicted to cross the blood brain barrier with no efflux as demonstrated in an in vitro MDR1-MDCK permeability assay (Table 2), indicating this class of compounds have promise for treatment of central nervous system infections. When we tested MJM170 against wild type and multi-drug resistant  P. falciparum , we found it was also potent (IC50&lt;30 nM against all strains). In combination studies, MJM170 was identified as additive with cycloguanil and modestly synergistic with atovoquone. Studies of yeast and malaria mutants, as surrogate assays, and co-crystallography studies with bovine cytochrome bc 1  confirm the mechanism of action/target for MJM170. The co-crystal structure of MJM170 in complex with bovine cytochrome bc 1  reveals a clear binding mode within the Q i  site. Using homology models of the apicomplexan Q i  sites, there are clear differences between the binding sites of the apicomplexan and mammalian orthologs which can be used to fine-tune the selectivity of our scaffold towards apicomplexan bc 1 . The larger binding pocket of the apicomplexan versus the mammalian bc 1  may provide a way forward to increase selectivity. Our work provides a conceptual and a practical step change forward that provides a foundation for further testing and improvements to efficacy, toxicity, solubility, oral absorption, large animal toxicology that will be needed to reach the clinic. Our work reported herein not only provides new and important insights into the biology of  T. gondii , especially the bradyzoite life cycle stage and the remarkable effects of this parasite on its human host&#39;s cells, but also provides critical molecular targets and new methods to identify others. Armed with this information, a novel scaffold with intrinsically higher solubility than the equivalent quinolone has been designed with holds promise towards developing a much-needed curative medicine for those with toxoplasmosis, malaria, and ˜2 billion persons chronically infected with presently incurable, encysted bradyzoites which persist and can recrudesce lifelong. 
     Methods 
     All methods were carried out in accordance with approved guidelines set at the University of Leeds by the Education &amp; Training Resources office and all experimental protocols were approved by the IRB committees; University of Chicago Institutional Animal Care and Use Committee (IACUC) and all experimental protocols were approved by the IRB committee; United States Department of Agriculture IACUC and all experimental protocols were approved by the IRB committees; J Craig Venter Institute Research ethics committee; University of Liverpool UK Office for Research Integrity (UKRIO) and all experimental protocols were approved by the IRB committees; Harvard School of Public Health HMS IACUC and all experimental protocols were approved by the IRB committees; The Broad Institute IACUC and all experimental protocols were approved by the IRB committees; Walter Reed Army Institute of Research Division of Human Subjects Protection (DHSP) and all experimental protocols were approved by the IRB committees; Oregon State University IACUC and all experimental protocols were approved by the IRB committees; Institute for Systems Biology ethics committee; Albert Einstein College of Medicine IACUC and all experimental protocols were approved by the IRB committees; Strathclyde University Ethics Committee (UEC) and all experimental protocols were approved by the IRB committees; Institute for Integrative Biology of the Cell IACUC and all experimental protocols were approved by the IRB committees, and the Centre national de 1a recherche scientifique IACUC and all experimental protocols were approved by the IRB committees. 
     Cells and Parasites for Work with  T. gondii    
     Cells: The cells utilized for  T. gondii  assays included human foreskin fibroblasts (HFF), Human MonoMac 6 cells (MM6), and Neuronal Stem cells (NSC) from a temporal lobe biopsy. 
       Toxoplasma gondii . The strains of  T. gondii  utilized in this work were: RH—YFP Tachyzoites of the RH—YFP strain were passaged in human foreskin fibroblasts (HFF cells); EGS-Bradyzoite assays use the EGS strain, isolated from amniotic fluid of human with congenital toxoplasmosis; Other strains used are: Me49; Prugniaud; Beverly; Veg; GT1. All other than EGS are  T. gondii  tachyzoites. These parasites are passaged in HFF. 
     Isolation of DNA and RNA. EGS single celled organisms were grown in Human Foreskin Fibroblasts, filtered free of host cells. gDNA was isolated and processed for sequencing as described. For isolation of RNA RIN scores were &gt;8. 
     Gene Sequencing, Genomics, RNA and MiR Sequencing, Systems Analysis, Metabolomics 
     Genome sequencing of  T. gondii  EGS strain. A single Illumina paired-end barcoded library was prepared from tachyzoite gDNA with Illumina TrueSeq library preparation kit. The library was then sequenced using 100 bp pared-end reads in one ninth of a lane of an Illumina HiSeq 2000 machine to generate ˜2 Gbp of genome sequence. 
     Single nucleotide polymorphism (SNP) identification and annotation. Illumina genome sequencing reads from EGS or downloaded from GenBank SRA database for GT1 (SRR516419), VEG (SRR516406) and TgCatBr1 (SRR350737) were aligned to the  T. gondii  ME49 reference genome assembly (ABPA02000000, ToxoDB release 13.0) with Bowtie2 and realigned around gaps using the GATK toolkit. SNP calls were done simultaneously across all four strains with samtools utility mpileup, requiring a minimum SNP coverage of 5 reads and an alternative allele frequency of 0.8 or higher, given the haploid nature of these genomes. Thereafter, SnpEff and a gff3 file containing the annotation of  T. gondii  ME49 downloaded from ToxoDB v13.0 were used to classify the different types of mutations identified in each strain. Allelic variants that were different between EGS and the rest of the strain were considered EGS-specific. 
     Phylogenetic network analysis. A total of 790,168 single nucleotide polymorphisms spanning the entire  T. gondii  genome from 62 different strains representing all major haplogroups were downloaded from ToxoDB, combined with SNP data from the same sites from the EGS strain and directly incorporated as a FASTA file into SplitsTree v4.13.1 to generate unrooted phylogenetic networks using a neighbor-net method. 
     Differential gene expression (DGE) analysis. Total RNA extracted from human cell cultures infected (or not) with a number of  T. gondii  strains for 2 h, 18 h or 48 h was treated with miRNeasy Mini Kit columns (Qiagen) following manufacturer instructions to separate mRNA and miRNA fractions. Afterwards, Illumina barcoded sequencing libraries were constructed with TruSeq RNA Sample Preparation Kits v2 (Illumina) for mRNA and miRNA TruSeq Small RNA Library Preparation Kit (Illumina) for miRNA. Libraries were sequenced as 100 bp single reads with Illumina HiSeq 2000 apparatus in pulls of 6 or 9 samples per lane for mRNA (yield ˜3 Gbp per sample) and miRNA (yield ˜2 Gbp per sample) libraries respectively. For protein coding genes, reads were mapped to the human (release GRCh38) and  T. gondii  ME49 strain (ToxoDB release 13.0) reference genome assemblies and annotations with CLC Genomic Workbench software (CLC Bio-Qiagen, Aarhus, Denmark) and raw read counts per gene were then analyzed with the R package EdgeR using a generalized linear model likelihood ratio test to identify genes that are differentially expressed among samples. 
     For miRNA DGE analysis, reads were depleted of adaptor and primer sequences and mapped to the human reference genome assembly (GRCh38) and the miRNA annotation from miRBase v21 (see the mirbase web site) with CLC Genomic Workbench software. Identification of human miRNA genes that are differentially expressed across treatments was carried out with EdgeR from raw read counts per miRNA gene using a generalized linear model likelihood ratio test. 
     For both mRNA and miRNA DGE analyses p-values were adjusted for multiple hypotheses testing using the False Discovery Rate method. MDS plots and heat maps were generated with the plotMDS tool from EdgeR and the R tool heatmap. Differentially expressed genes (DEGs) in MM6 and NSC cell lines infected with EGS parasites were identified under the criteria of 1% FDR and absolute log 2-fold-change &gt;1.5 (i.e. fold-change &gt;2 and &lt;0.5 for up- and down-regulated genes, respectively). 
     Functional enrichment analysis GO enrichment analyses were performed for up- or down-regulated genes, by using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7. GO slim enrichment analysis was performed for genes carrying potential change-of-function mutations in EGS that were absent in strains ME49, VAND or TgCatBr1. GO slim database was downloaded from QuickGO provided by EMBL-EBI. Using taxonomy id “508771” for the ME49 strain, relevant GO slim terms were retrieved. GO slim enrichment analysis was performed with Fisher&#39;s exact test based on the GO slim terms. 
     Assay for oocyst development in cats. Oocysts were collected from feces of  Toxoplasma -free cats 3-14 days after feeding infected cell cultures or infected mouse brains. Oocysts were separated from feces by sugar floatation, sporulated in 2% sulfuric acid by aeration at room temperature for 1 week. After removing sulfuric acid oocysts were inoculated orally in to Swiss Webster albino mice. All tissues of mice that died or euthanized were studied histologically after staining with hematoxylin and eosin and by BAG1 antibodies to  T. gondii  as described. (Dubey J P, Ferreira L R, Martins J, McLeod R. Oral oocyst-induced mouse model of toxoplasmosis: effect of infection with  Toxoplasma gondii  strains of different genotypes, dose, and mouse strains (transgenic, out-bred, inbred) on pathogenesis and mortality. Parasitology 139:1-13, Epub 2011. PMID: 22078010; also referred t herein as S39) 
     Chemical Synthesis. Final compounds had &gt;95% purity determined by high performance liquid chromatography (HPLC) and 300 and/or 500 MHz NMR spectrometers. Liquid chromatography-mass spectrometry (LC-MS) and high resolution mass spectrometers (HRMS) analytical systems were used to determine integrity and purity of all intermediates and final compounds. 
     Synthesis of 2-methyl-5,6,7,8-tetrahydroquinolin-4-one (6) Platinum oxide (100 mg, 10 mol %) was added to a solution of 4-hydroxy-2-methylquinoline (5, 1.00 g, 6.28 mmol, 1.00 eq) in glacial acetic acid (10.0 ml). The heterogeneous mixture was catalytically hydrogenated under a balloon of hydrogen. After 22 hrs, TLC (10% MeOH-DCM) confirmed complete reaction. The mixture was filtered through celite under vacuum, washing thoroughly with EtOAc. The filtrate was concentrated and the resulting residue purified by column chromatography (10% MeOH-DCM) to give the desired product as a pale yellow oil (917 mg, 5.65 mmol, 89%); Rr 0.14 (10% MeOH-DCM); δ H  (300 MHz, CDCl 3 ) 1.74-1.76 (4H, m, CH 2 ), 2.29 (3H, s, Me), 2.49-2.52 (2H, m, CH 2 ), 2.67-2.70 (2H, m, CH 2 ), 6.16 (1H, s, Ar—H); δ C  (125 MHz, CDCl 3 ) 19.0 (Me), 21.8 (CH 2 ), 22.1 (CH 2 ), 27.1 (CH 2 ), 112.5 (CH), 122.4 (Cq), 146.4 (Cq), 147.0 (Cq), 178.3 (Cq); Spectroscopic data consistent with literature values (JMC, 1993, 36, 1245-54). 
     Synthesis of 2-methyl-3-iodo-5,6,7,8-tetrahydroquinolin-4-one (7) Butylamine (6.20 ml, 62.8 mmol, 10.0 eq) was added to a suspension of 2-methyl-5,6,7,8-tetrahydroquinolin-4-one (6, 1.02 g, 6.28 mmol, 1.00 eq) in DMF (10.0 ml). To this heterogeneous mixture was added 12 (1.60 g, 6.28 mmol, 1.00 eq) in a saturated solution of KI (6.00 ml). After 20 hrs stirring at R.T., a precipitate formed in the orange solution, Excess iodine was quenched with 0.1 M sodium thiosulfate solution. The precipitate was filtered by vacuum filtration, washed with distilled H 2 O and dried (Na 2 SO 4 ) to give the desired product as a colourless solid (1.76 g, 6.09 mmol, quantative yield); δ H  (300 MHz, DMSO-d 6 ) 1.61-1.70 (4H, m, CH 2 ), 2.29 (2H, t, J 6.0, CH 2 ), 2.43 (2H, s, CH 2 ), CH 3  under DMSO peak. 
     Synthesis of 2-methyl-3-iodo-4-ethoxy-5,6,7,8-tetrahydroquinoline (8) Potassium carbonate (1.53 g, 11.1 mmol, 2.00 eq) was added to a heterogeneous mixture of 2-methyl-3-iodo-5,6,7,8-tetrahydroquinolin-4-one (7, 1.60 g, 5.56 mmol, 1.00 eq) in DMF (15.0 ml), and the reaction heated to 50° C. for 30 mins. The R.B. flask was removed from the heating mantle and ethyl iodide was added dropwise. The reaction was then heated at 50° C. for 18 hrs. The reaction was cooled to R.T., quenched with water (40 ml). The resulting emulsion formed which was extracted with EtOAc (50 ml). EtOAc layer were washed with water (3×30 ml), brine (3×30 ml), dried (Na 2 SO 4 ) and concentrated to give a pale yellow oil (1.09 g, 3.44 mmol, 61%); Rr 0.88 (1:1 Pet-EtOAc); HPLC (RT=1.67 mins); LCMS (Method A), (RT=1.6 min, m z (ES) Found MH +  318.0); δ H  (500 MHz, CDCl 3 ) 1.49 (3H, t, J 7.0, ethoxy CH 3 ), 1.73-1.78 (2H, m, CH 2 ) 1.84-1.88 (2H, m, CH 2 ), 2.78-2.69 (5H, m, CH 2  &amp; CH 3 ), 2.84 (2H, t, J 6.5, CH 2 ), 3.97 (2H, q, J 7.0, OCH 2 ); δ C  (125 MHz, CDCl 3 ) 15.6 (CH 3 ), 22.3 (CH 2 ), 22.8 (CH 2 ), 23.6 (CH 2 ), 29.3 (CH 3 ), 32.0 (CH 2 ), 68.4 (OCH 2 ), 90.9 (Cq), 124.5 (Cq), 158.3 (Cq), 158.9 (Cq), 163.9 (Cq). 
     Synthesis of 2-methyl-3-(4-phenoxyphenyl)-4-ethoxy-5,6,7,8-tetrahydroquinoline (10) 2-Methyl-3-iodo-4-ethoxy-5,6,7,8-tetrahydroquinoline (8, 0.266 g, 0.839 mmol, 1.00 eq), Pd(PPh 3 ) 4  (0.048 mg, 0.0419 mmol, 5 mol %) and 4-phenoxyphenylboronic acid (9, 0.270 mg, 1.26 mmol, 1.50 eq) were charged to a R.B. flask under N 2 (g) 49 . Degassed DMF (10.0 ml) was added to the flask followed by 2M K 2 CO 3  (1.60 ml). The flask was heated to 85° C. under N 2 (g). After 15 mins, TLC (4:1 Pet-EtOAc) confirmed reaction was complete. The reaction was cooled and diluted with EtOAc (15 ml), filtered through celite and partitioned between EtOAc (10 ml) and H 2 O (25 ml). Combined organics were washed with H 2 O (3×30 ml), then brine (3×30 ml), dried (Na 2 SO 4 ) and concentrated to give a red oil which was purified by column chromatography (3:1 Pet-EtOAc), to give the desired product as a pale yellow oil (0.235 mg, 0.655 mmol, 78%); Rr 0.31 (3:1 Pet-EtOAc); HPLC (RT=3.08 mins); δ H  (300 MHz, CDCl 3 ) 1.04 (3H, t, J 7.0, ethoxy CH 3 ), 1.76-1.93 (4H, m, 2×CH 2 ), 2.32 (3H, s, CH 3 ) 2.72 (2H, t, J 6.0, CH 2 ), 2.91 (2H, t, J 6.5, CH 2 ), 3.50 (2H, q, J 7.0, OCH 2 ), 7.05-7.16 (5H, m, Ar—H), 7.20-7.29 (2H, m, Ar—H), 7.31-7.43 (2H, m, Ar—H); δ C  (125 MHz, CDCl 3 ) 15.7 (CH 3 ), 22.5 (CH 2 ), 23.0 (CH 3 ), 23.3 (CH 2 ), 23.4 (CH 2 ), 32.7 (CH 2 ), 68.2 (OCH 2 ), 118.6 (CH), 118.9 (CH), 123.4 (CH), 126.8 (Cq), 129.8 (CH), 131.5 (CH), 154.9 (Cq), 156.5 (Cq), 157.1 (Cq), 157.3 (Cq); m/z (ES) (Found: MH + , 360.1973. C 24 H 26 NO 2  requires MH, 360.1964). 
     Synthesis of 2-methyl-3-(4-phenoxyphenyl)-4-ethoxy-5,6,7,8-tetrahydroquinoline (MJM170, 4) 49  Aqueous hydrobromic acid (&gt;48%) (1.00 ml) was added to a solution of 2-methyl-3-(4-phenoxyphenyl)-4-ethoxy-5,6,7,8-tetrahydroquinoline (10, 0.226 mg, 0.630 mmol, 1.00 eq) in glacial acetic acid (2 ml). The reaction was stirred at 90° C. for 5 days, monitoring by LMCS. The reaction was cooled to R.T. and the pH adjusted to pH5 with 2M NaOH. The precipitate was collected by vacuum filtration and recrystallized from MeOH:H 2 O to give the desired product as an off-white solid (0.155 g, 0.467 mmol, 74%); HPLC (RT=2.56 mins); δ H  (500 MHz, DMSO-d 6 ) 1.66-1.72 (4H, m, 2×CH 2 ), 2.08 (3H, s, CH 3 ) 2.31 (2H, t, J 6.0, CH 2 ), 2.56 (2H, t, J 6.0, CH 2 ), 6.99 (2H, d, J 8.5, Ar—H), 7.06 (2H, d, J 7.5, Ar—H), 7.14-7.18 (3H, m, Ar—H), 7.40-7.43 (2H, m, Ar—H), 11.0 (1H, s, NH); δ C  (125 MHz, DMSO-d 6 ) 17.7 (CH 3 ), 21.5 (CH 2 ), 21.8 (CH 2 ), 21.9 (CH 2 ), 26.2 (CH 2 ), 117.8 (CH), 118.6 (CH), 121.2 (Cq), 123.3 (CH), 123.7 (Cq), 130.0 (CH), 131.4 (Cq), 132.3 (CH), 142.3 (Cq), 143.2 (Cq), 155.0 (Cq), 156.8 (Cq), 175.4 (Cq); nm/z (ES) (Found: MH + , 332.1654. C 22 H 22 NO 2  requires MH, 332.1645). 
     ADME studies of inhibitors: Compounds that were highly effective in vitro (IC 50  &lt;1 μM) were tested for ADME profiling S43-5 s by Shanghai ChemPartner Ltd. Initial studies focused on aqueous kinetic solubility pH 7.4, microsomal metabolic stability (human and mouse) and Blood-Brain Barrier (BBB) permeability (performed with MDCK-MDR1 cells as described). 
     In Vitro Assays 
     Cytotoxicity Assay 
     Toxicity Analysis. Lack of toxicity for mammalian host cells was demonstrated first by visual inspection of monolayers following giemsa staining, in separate methods by incorporation of a mitochondrial cell death reagent called WST we used successfully for this purpose and in separate experiments. 
     Toxicity assays were conducted using WST-1 cell proliferation reagent (Roche). HFF were grown on a flat, clear-bottomed, black 96-well plate. Confluent HFF were treated with inhibitory compounds at concentrations equal to those being tested in challenge assays. Compounds were diluted in IMDM-C, and 20 μl were added to each designated well, with triplicates for each condition. A gradient of 2 fold-decreasing concentrations of DMSO in clear IMDM-C was used as a control. The plate was incubated for 72 hours at 37° C. 10 μl of WST-1 reagent (Roche) were added to each well and the cells were incubated for 30 to 60 minutes. Absorbance was read using a fluorometer at 420 nm. A higher degree of color change (and absorbance) indicated mitochondrial activity and cell viability. 
     In Vitro Cellular Assays for Effects on  T. gondii    
     Vivo PMO: Vivo-PMO (Vivo porter linked to morpholinos) to knock down cytochrome b and an off-target PPMO (Vivo porter) were utilized at concentrations of 5 and 10 μM as previously described with both cultures of RH—YFP tachyzoites and EGS. Morpholino sequence for cytochrome b/c knockdown is 5′ AGTGTTCTCGAAACCATGCTAACAC 3′ (SEQ ID NO: 5), and for unrelated sequence, off target, is 5′ CCTCTTACCTCAGTTACAATTTATA 3′ (SEQ ID NO: 6). 
     Tetrahydroquinolone Compounds: Compounds synthesized at the University of Leeds were initially prepared in 10 mM Stock solutions made with 100% Dimethyl Sulfoxide (DMSO) [Sigma Aldrich], and working concentrations were made with IMDM-C (1×, [+]glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS) [Gibco, Denmark]). 
     Tachyzoite Assays: 
     Type 1 parasites. Human foreskin fibroblasts (HFF) were cultured on a flat, clear-bottomed, black 96-well plate to 90% to 100% confluence. IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C (1×, [+] glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS)[Gibco, Denmark]). Type I RH parasites expressing Yellow Fluorescent Protein (RH—YFP) were lysed from host cells by double passage through a 27-gauge needle. Parasites were counted and diluted to 32,000/mL in IMDM-C. Fibroblast cultures were infected with 3200 tachyzoites of the Type I RH—YFP strain and returned to incubator at 37° C. for 1-2 hours to allow for infection. Diluted solutions of the compounds were made using IMDM-C, and 20 μl were added to each designated well, with triplicates for each condition. Controls included pyrimethamine/sulfadiazine (current standard of treatment), DMSO only, fibroblast only, and an untreated YFP gradient with 2 fold dilutions of the parasite. Cells were incubated at 37° C. for 72 hours. The plates were read using a fluorimeter (Synergy H4 Hybrid Reader, BioTek) To ascertain the amount of yellow fluorescent protein, in relative fluorescence units (RFU), as a measure of parasite burden after treatment. Compounds were not considered effective or pursued for further analysis if there were no signs of inhibition at 1 μM. Data was collected using Gen5 software and analyzed with Excel. 
     Type Hparasites. To test type II parasites,  T. gondii  ME49 and Prugneaud parasites expressing luciferase or GFP. We tested them in vitro and in vivo as we have described. 
     EGS strain Bradyzoite Assay. HFF cells were grown in IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS, [Gibco, Denmark]) on removable, sterile glass disks in the bottom of a clear, flat-bottomed 24-well plate. Cultures were infected with 3×10 4  parasites (EGS strain) per well, in 0.5 mL media and plate was returned to incubator at 37° C. overnight. The following day, the media was removed and clear IMDM and compounds were added to making various concentrations of the drug, to a total volume of 0.5 mL. Two wells were filled with media only, as a control. Plates were returned to the 37° C. incubator for 72 hours. 
     Efficacy was determined following fixation. Staining was used to determine the numbers of cysts in cultures without and with treatment with the test compounds. Cells were fixed using 4% paraformaldehyde and stained with Fluorescein-labeled  Dolichos biflorus  Agglutinin, DAPI, and anti-BAG1, and anti-SAG1. Disks were removed and mounted onto glass slides and visualized using microscopy (Nikon T17). Slides were also scanned using a CRi Pannoramic Scan Whole Slide Scanner and viewed using Panoramic Viewer Software. 
     When cysts that had dolichos in their cyst wall were eliminated or markedly reduced in size and number, a compound was considered efficacious against bradyzoites in cysts. 
     Statistical Analyses. Significance of differences were determined using Student&#39;s t-test. P&lt;0.05 was considered significant. Every experiment was replicated at least twice. A Pearson test was used to confirm a correlation between increasing dose and increasing inhibition. An ANOVA and subsequent pair wise comparison with Dunnett correction was used to determine whether or not inhibition or toxicity at a given concentration was statistically significant. Stata/SE 12.1 was used for this analysis. This study was approved by the University of Chicago IRB, IBC, and IACUC. 
     In Vivo Analysis (Mice and Zebrafish): 
     Initial screening with tachyzoites using IVIS, fluorescence, and histopathology: Ability of compounds to abrogate tachyzoites multiplication was assessed using an in vivo imaging system (IVIS). To facilitate this we have  T. gondii  strains from each of the 3 major lineages expressing the luciferase gene. In these studies mice are injected intraperitoneally with tachyzoites and parasite proliferation followed up to 30 days post infection. Removal of brains at 30 days allows parasite quantitation by bioluminescence ex vivo using the IVIS. As an alternative method to improve screening efficiency and scalability it is possible for initial screening to use zebrafish with histopathology and visualization as shown in  FIGS.  1 A- 1 D . Quantitation also was performed using QT PCR as described for mice or in translucent Casper zebrafish with parasites with fluors or luciferase to screen rapidly. Tachyzoites and bradyzoites in cysts were used for IP infection and compounds given intraperitoneally. 
     Type II parasites. To test type II parasites, we used  T. gondii  Me49 and Prugneaud parasites S39 . 
     Encephalitis: The ability of compounds to reduce cyst burden and prevent encephalitis induced by the Type II strain of  T. gondii  were tested. Encephalitis was assessed by histological analyses and parasite burdens evaluated by quantitation of cysts. 
     Oocyst induced disease: The oocyst challenge model is ideal for this study because oocysts can be diluted at one time and stored at 4° C. for 12 months without loss of infectivity titer. For treatment of chronic infection there were 5 to 10 mice per group treated 2 months after infection was established by compound in DMSO for parenteral administration administered once per day. Treatment was for 17 days. 
     Zebrafish Zebrafish were acclimatized to 37 degrees a degree a day and then infected with tachyzoites or cysts of RH YFP, Me49, Veg  T. gondii  as described. The use of RH YFP was performed for the first time herein in order to develop a rapidly scalable assay for drug development. This is the initial demonstration of cyst formation by 10 days in Zebrafish. 
     Tissue processing and histopathology: All organs including eyes and brains were fixed in 0.1M phosphate buffer (pH 7.4) containing 4% formaldehyde. Sections were cut from paraffin-embedded tissues and stained with Hematoxylin and Eosin (H&amp;E) or immunoperoxidase stained. All sections were examined and assessed without knowledge of the group from which they originated S39 . 
     Testing of Cytochrome b Q i  Mutant Yeast 
     Target Validation with Mutant  S. cerevisiae  (Growth Inhibition): 
     Three  S. cerevisiae  strains were used: M221Q and M221F cytochrome b mutants and wild type. They share the same nuclear genetic background deriving from AD1-9 (kindly given by M. Ghislain, UCL, Belgium). AD1-9 harbors multiple deletions in the ABC transporter genes that render the strain more sensitive to drugs than standard yeast strainss S65 . 
     Cytochrome b mutant M221F was generated by mitochondrial transformation as described. M221Q was selected as suppressor from a respiratory deficient mutant. Analysis of revertants from respiratory deficient mutants within the center N of cytochrome b in  Saccharomyces cerevisiae.    
     Protocol: Yeast strains were grown over 48 hours at 33° C. in liquid YPG medium [1% yeast extract, 2% (wt/vol) peptone, and 3% (vol/vol) glycerol). Cultures were diluted to an OD 600  of 0.05 and grown for 2 hrs. Cultures were then combined with YPG containing 6% melted agar for a total volume of 15-20 mL and poured onto OmniTray single-well rectangular plates that measured 86 mm by 128 mm (ThermoScientific). Filter paper disks (7 mm diameter, 3 um thick) were placed onto the cooled agar plates. Compounds were dissolved in DMSO in diluted concentrations (1 mM, 500 μM, 100 μM, and 10 μM) and 10 microliters were applied to a disk. A single disk with DMSO on each plate was used as a control. Plates were incubated at 33° C. Images were obtained after 4 days using GelDoc XR Imaging System (BioRad) and Quantity One software. Drug effect was assessed by the presence and size of a zone of inhibition around the disks. 
     Testing of  P. falciparum : D6 is a drug sensitive strain from Sierra Leone, C235 is a multi-drug resistant strain from Thailand, W2 is a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. 
     Testing of  P. falciparum  Cytochrome b Q i  and DHODH Mutants and Drug Combinations for  P. falciparum    
     Parasite Strains and Culture Maintenance. We used the following parasite line from the MR4 repository of the American Type Culture Collection (ATCC): Dd2 (MRA-156). Mutant Dd2 parasites harboring a G33A or G33V substitution in cytochrome b were as reported. Dd2 parasites with a G131S mutation in cytochrome b and transgenic lines expressing a chromosomally integrated copy of the  S. cerevisiae  DHODH were utilized as previously described. Parasites were cultured by standard methods in RPMI media supplemented with 5% human O +  serum and 0.25% AlbuMAX® II (Life Technologies 11021-045). 
     In Vitro Drug Sensitivity and EC 50  Determinations 
     Drug susceptibility was measured using the SYBR Green method. Twelve point curves based on 2-fold dilutions of the test compound were carried out in triplicate each day and replicated on at least three different days. EC 50  values were calculated using a nonlinear regression curve fit in Prism 6.0 for Mac (GraphPad Software, Inc.). 
     Studies of compound, drug combinations in vitro. Isobologram experiments were performed in similar fashion utilizing the modified fixed ratio methodology. Briefly, MJM170 and either atovaquone or cycloguanil or BRD6323 were mixed at multiple fixed volumetric ratios (10:0, 8:2, 6:4, 4:6, 2:8, and 0:10) and then serially diluted in 12-point 2-fold dilutions and dispensed in triplicate to 384-well assay plates and replicated on three different days. EC 50  values were calculated as above, and FICs were calculated for each drug combination as described S76 . Synergy was defined as an FIC&lt;1.0, additivity as FIC=1.0, and antagonism as FIC&gt;1.0. 
     Molecular Modelling/Chemogenomics. X-ray structures of the cytochrome bc 1  complex are available from the Protein DataBank S80 . An Homology model of the  T. gondii  cytochrome bc 1  complex was generated using the Phyre webserver. Molecular modelling and docking was performed on high performance Linux clusters at the University of Leeds, using specialist software: SPROUT S82  &amp; eHiTs S83  (SymBioSis), Maestro &amp; Glide S84  (Schrodinger), AutoDock (Scripps Institute), ROCS/EON S85  &amp; VIDA S86  (OpenEye) and the Marvin/JChem suites (ChemAxon). 
     X-ray crystallography: Cytochrome bc 1  was purified usig standard techniques. Crude bovine mitochondria were isolated from fresh cow heart and solubilised in DDM. The solution was clarified by ultracentrifugation at 200,000 g for 1 hour at 4° C. and the supernatant applied to a DEAE CL-6B sepharose column ca. 50 ml pre-equilibrated in 50 mM KPi (pH 7.5), 250 mM NaCl, 3 mM NaN 3 , 0.1 g/L DDM, washed with two CV and eluted along a gradient from 250 mM to 500 mM NaCl. Cyt. bc 1  containing fractions were pooled and concentrated before loading on a Sepharose S300 column ca. 120 ml equilibrated with 20 mM KMOPS (pH 7.2), 100 mM NaCl, 0.5 mM EDTA, 0.1 g/L DDM at 0.5 ml/min. 10 mM MJM170 stock in DMSO was added to the eluted protein in a two-fold molar excess and allowed to incubate at 4° C. for 1 hour. Increasing amounts of PEG4000 were then added to precipitate cyt. bc 1  and separate remaining contaminants. The cyt. bc 1  was then resuspended before buffer exchange into a final buffer (25 mM KPi (pH 7.5), 3 mM NaN 3 , 0.015% DDM) and concentrated to 40 mg/ml. 1.6% HECAMEG was added to the protein solution prior tp crystals growing by the hanging drop vapour diffusion method against a reservoir of 50 mM KPi (pH 6.8), 100 mM NaCl, 3 mM NaN 3 , 9% PEG4000, 0.16% HECMAEG. Crystals were flash frozen in 23% glycerol in reservoir solution as a cryoprotectant. Multiple wedges of data were collected at 100K from different points on the same crystal at 124 Diamond Light Source using 0.9686 A X-rays with a Pilatus3 6M detector. 
     Datasets were processed in iMosfim and combined using Blend to produce a complete merged dataset. Refinement was carried out with Refmac using Prosmart to generate secondary structure restraints to assist in the low-resolution refinement. The ligand MJM170 was produced using JLigand S92  and modelled in the Q i  site of cyt. bc 1  using Coot. Cycles of alternating Refmac5 and manual modelling resulted in a completed model. Data collection and refinement statistics are summarised In table 1A. For 3715 residues 95.2% are Ramachandran favored, 4.6% allowed and 0.3% outliers. 
     Interpretation of Data and Statistical Analyses 
     (1) Sample size and number of experiments. There were 3 replicate samples per group for in vitro experiments. All experiments were performed with sufficient sample sizes to have an 80% power to detect differences at the 5% level of significance. 
     (2) Statistics. Groups included untreated or mock treated controls. Results were compared using students T test, Chi square analysis or Fisher&#39;s exact test as appropriate for the data set. When there were more than two groups, pairwise comparisons were made only when F-test for the ANOVA was significant at the 5% levels using protected least significant difference (LSD) test approach. 
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     Example 2. Potent anti-apicomplexan tetrahydroquinolone 
     Summary: Apicomplexan infections cause substantial morbidity and mortality. Herein, we created a next generation tetrahydroquinolone that we found to be an anti-apicomplexan, mature, lead compound. We utilized sphere-like 3D space and predicted flexibility conferred by eliminating double bonds in this lead compound. This was to optimize ADMET and create a compound, JAG21, that is potent against  Toxoplasma gondii  tachyzoites (IC 90&lt;125 nM) and bradyzoites (IC 90 500 nM), and drug resistant  Plasmodium falciparum  in vitro (IC 90&lt;50 nM), not toxic to human HepG cells (&gt;17 μM). Further, we demonstrate metabolic stability with assays for human and mouse liver microsomal activity and logs improved aqueous solubility at pH 7.4. This compound displays a balanced set of physicochemical and pharmacologic properties, including clean hERG, CYP profile, and a long (days in humans), predicted half-life and predicted ability to cross blood brain barrier. This allowed progression towards in vivo studies. In vivo  Toxoplasma  tachyzoites were cleared from mice at a dose of 5 mg/kg/day (IP). JAG21 acted in conjunction with tafenoquine (3 mg/kg single dose) to protect against a G0 arrested parasite that could persist in interferon   knockout mice similar to the effect of tafenoquine for malaria hypnozoites. There was cure with oral dosing, 0.625 mg/kg, 3 oral doses of JAG21, and cure with a single dose of 2.5 mg/kg, of  P. berghei  sporozoite, blood and liver stages in mice. There was no parasitemia and 100% survival at 30 days. This mature lead compound has improved solubility and diminished toxicity relative to other cytochrome b Qi inhibitors, without formulation as a pro-drug. Selectivity for apicomplexan enzyme relative to mammalian enzymes was demonstrated with co-crystallography, binding and enzyme assays. This compound has real promise as a mature, lead compound. 
     Malaria results in death of one child every eleven seconds and 1 million children a year, with drug resistance eliminating usefulness of successive generations of new medicines each decade. The related apicomplexan parasite,  Toxoplasma gondii , is the most frequent parasitic infection of humans, in the world. It is the second most frequent, single cause of food born associated death in the United States; It is the most frequent infectious cause of destruction of the back of the human eye; It is a cause of death and illness from recrudescent disease from its latent form in those who are immune compromised or immunologically immature; It has been estimated that in a ten year period, there are 1.9 million new cases of this congenital infection globally, causing 12 million disability adjusted life years from damage to the fetal brain and eye. This is a neglected, rarely diagnosed, and thus often untreated or mistreated disease. There are approximately 2 billion people throughout the world who have this parasite in their brain lifelong. No medicine eliminates this chronic encysted form of the parasite which causes epilepsy and may contribute to neurodegenerative disease. Certainly, new and improved medicines are greatly needed for both these diseases, These two apicomplexan parasites,  Plasmodia  and  Toxopalsma , often share molecular targets inhibited by the same inhibitory compounds. 
     Herein we identify a mature lead compound that is highly efficacious against  T. gondii  tachyzoites and bradyzoites in vitro, tachyzoites in vivo, likely to be active against cysts in vivo with experiments ongoing, all drug resistant forms of  Plasmodium falciparum, Plasmodium berghei  in mouse model in single or three doses at low amounts against the sporozoite, blood and liver stages of plasmodium when administered orally at 2.5 mg/kg and at 1.25 mg kg for 100% of mice with three doses. It was found to add to protection in conjunction with tafenoquine in immune compromised mice infected with a G0/tachyzoite form of  T. gondii  which resembles the malaria hypnozoite when treated with tafenoquine in conjunction with anti-blood stage parasite compounds. The data which follow present the creation and characterization of this broad spectrum anti-apicomplexan lead compound. 
     Materials and Methods 
     
       Toxoplasma gondii  
     
     Tachyzoites of the RH—YFP strain were passaged in human foreskin fibroblasts (HFF cells)(15). Bradyzoite assays use the EGS strain, isolated from a human with congenital toxoplasmosis (16,17). These parasites are also passaged in human foreskin fibroblasts. RPS13 delta was prepared and utilized as described (Hutson, McLeod et al 2010) 
     Tetrahydroquinolone (THQ) Compounds 
     The THQ compounds were synthesized at the University of Leeds as described in Example 3. 10 mM stock solutions were made with 100% Dimethyl Sulfoxide (DMSO) [Sigma Aldrich] and working concentrations were made with IMDM-C (1×, [+] glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS)[Gibco, Denmark]). Compounds are shown herein. 
     In Vitro Challenge Assay for  Toxoplasma  Tachyzoites 
     Protocol adapted from Fomovska, et. al. (18,19). Human foreskin fibroblasts (HFF) were cultured on a flat, clear-bottomed, black 96-well plate to 90% to 100% confluence. IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C (1×, [+] glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS)[gibco, Denmark]). Type I RH parasites expressing Yellow Fluorescent Protein (RH—YFP) were lysed from host cells by double passage through a 27-gauge needle. Parasites were counted and diluted to 32,000/mL in IMDM-C. Fibroblast cultures were infected with 3200 tachyzoites of the Type I RH strain expressing Yellow Fluorescent Protein (RH—YFP) and returned to incubator at 37° C. for 1-2 hours to allow for infection (15). Various concentrations of the compounds were made using IMDM-C, and 20 μl were added to each designated well, with triplicates for each condition. Controls included pyrimethamine/sulfadiazine (current standard of treatment), 0.1% DMSO only, fibroblast only, and an untreated YFP gradient with 2 fold dilutions of the parasite. Cells were incubated at 37° C. for 72 hours. Plates were read using a fluorimeter (Synergy H4 Hybrid Reader, BioTek) to ascertain the amount of yellow fluorescent protein, in relative fluorescence units (RFU), as a measure of parasite burden after treatment. Data was collected using Gen5 software. IC 50  was calculated by graphical analysis in Excel. 
     An initial screening assay of 10 μM, 1 μM, 100 nM, and 10 nM was performed. Compounds were not considered effective or pursued for further analysis if there were no signs of inhibition of tachyzoites at 1 μM. If compounds did appear to be effective at 1 μM, another experiment was conducted to assess effect at 1 μM, 500 nM, 250 nM, 125 nM, 62.5 nM, and 31.25 nM. 
     Cytotoxicity Assay 
     Toxicity assays were conducted using WST-1 cell proliferation reagent (Roche) as described in Fomovska, et. al. (18,19). HFF were grown on a flat, clear-bottomed, black 96-well plate. Confluent HFF were treated with inhibitory compounds at concentrations of 10 μM and 50 μM. Compounds were diluted in IMDM-C, and 20 μl were added to each designated well, with triplicates for each condition. A gradient of 2 fold-decreasing concentrations of DMSO from 10% to 0% in clear IMDM-C was used as a control. The plate was incubated for 72 hours at 37° C. 10 μl of WST-1 reagent (Roche) were added to each well and the cells were incubated for 30 to 60 minutes. Absorbance was read using a fluorimeter at 420 nm. A higher degree of color change (and absorbance) indicated mitochondrial activity and cell viability. 
     In Vitro Challenge Assay for Bradyzoites 
     HFF cells were grown in IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS, [gibco, Denmark]) on removable, sterile glass disks in the bottom of a clear, flat-bottomed 24-well plate. Cultures were infected with 3×10 4  parasites (EGS strain) per well, in 0.5 mL media and plate was returned to incubator at 37° C. overnight. The following day, the media was removed and clear IMDM and compounds were added to making various concentrations of the drug, to a total volume of 0.5 mL. 2 wells were filled with media only, as a control. Plates were returned to the 37° C. incubator for 72 hours, and checked once every 24 hours. If tachyzoites were visible in the control before 72 hours, the cells were fixed and stained. 
     Cells were fixed using 4% paraformaldehyde and stained with Fluorescein-labeled  Dolichos biflorus  Agglutinin, DAPI, and BAG1. Disks were removed and mounted onto glass slides and visualized using microscopy (Nikon T17). Slides were scanned using a CRi Pannoramic Scan Whole Slide Scanner and viewed using Panoramic Viewer Software. Effects of the compounds were quantified by counting cysts in the controls and treated cells. Cysts and persisting organisms were counted in a representative field of view and then multiplied by a factor determined by the total area of the disk in order to estimate the number of cysts and organisms in each condition. 
     Assessment of Compound Degradation and Microbicidal Effect on  Toxoplasma    
     HFF were cultured in a 96-well plate and infected with RH—YFP as described above on Day 0, 20 μL of compound was added to 9 wells for each compound and concentration (3 conditions, 3 wells per condition). In condition I, media was removed and replaced with fresh media on Day 3. In condition II, media was removed and replaced with fresh media and more compound on Day 3. In condition III, media was not replaced on Day 3, nor was the compound refreshed. On Day 6, media was removed and replaced with clean media in all wells. On Day 3, 6, and 9 plate was read in the fluorimeter and analyzed graphically in Prism (GraphPad Software). 
       Toxoplasma  In Vivo 
     IVIS. Mice were infected intraperitoneally with 20×103  Toxoplasma gondii  (Pru strain expressing luciferase) tachyzoites. Treatment commenced 2 hours later with JAG21 (5 mg/kg) which was dissolved in DMSO and administered intraperitoneally in a total volume of 0.05 ml. Mice were imaged every second day starting on day 4 post infection using a IVIS Spectrum (Caliper Life Sciences) for a 1 minute exposures, with medium binning, 20 minutes post injection with 150 mg/kg of D-luciferin potassium salt solution. 
     Brain cysts: Mice were infected intraperitoneally with 20x 103 Treatment commenced 2 hours later with JAG21 (5 mg/kg) which was dissolved in DMSO and administered intraperitoneally in a total volume of 0.05 ml. After 30 days, treatment with JAG21 was begun each day for 14 days intraperitoneally. In experiments when tafenoquine was administered alone or with JAG21 in some groups 3 mg/kg tafenoquine was administered once on day −1. Cysts in brain were quantitated after concluding treatment 
     RPS13 Δ. This G0 arrested parasite persists in tissue culture for prolonged times in the absence of tetracycline. The design of this experiment is shown in  FIG.  13   . The parasite (x) was used to infect interferon gamma knockout mice. For the first y days no tetracycline was administered. After that time tetracycline was administered. Mice were observed and at the time they appeared ill or at the termination of the experiment they were euthanized and tissues fixed in formalin and stained with hematoxylin and eosin or immunoperoxidase stained and parasite burden was assessed. 
     Malaria Assays 
     Methods for enzyme assays 21-3 . Professor Giancarlo A. Biagini, Dr Richard S. Priestley, Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. 
     Materials 
       Plasmodium  falciparum: 3D7 strain was obtained from the Liverpool School of Tropical Medicine. Protease cocktail inhibitor was obtained from Roche. Bradford protein assay dye reagent was obtained from Bio-Rad. All other reagents were obtained from Sigma-Aldrich. Decylubiquinol was produced as per Fisher et al. (Fisher et al. 2004) 21 . In brief, 25 mg of decylubiquinone were dissolved in 400 μl of nitrogen-saturated hexane. An equal volume of aqueous 1 M sodium dithionite was added, and the mixture vortexed until colorless. The organic phase containing the decylubiquinol was collected, the solvent was evaporated under N 2  and the decylubiquinol finally dissolved in 100 μl of 96% ethanol (acidified with 10 mM HCl). Concentrations of decylubiquinol was determined spectrophotometrically on a Cary 300 Bio UV/visible spectrophotometer (Varian, UK) from absolute spectra, using 8288-320=8.1 mM-1 cm −1 . Decylubiquinol was stored at −80° C. and used within two weeks. 
       Plasmodium falciparum : Culture and Extract Preparation 
       Plasmodium falciparum : strain 3D7 blood-stage cultures were maintained by the method of Trager and Jensen (Trager &amp; Jensen 2005) 23 . Cultures contained a 2% suspension of O+ human erythrocytes in RPMI 1640 medium containing L-glutamine and sodium carbonate, and supplemented with 10% pooled human AB+ serum, 25 mM HEPES (pH 7.4) and 20 μM gentamicin sulphate. Cultures were grown under a gaseous headspace of 4% 02 and 3% CO 2  in N 2  at 37° C. Cultures were grown to a parasitaemia of 5% before use. 
     The protocol for the preparation of parasite extract was adapted from Fisher et al. (Fisher et al. 2009) 22 . Free parasites were prepared from infected erythrocytes pooled from five T75 flasks, by adding 5 volumes of 0.15% (w/v) saponin in phosphate-buffered saline (137 mM NaCl, 2.7 mM KCl, 1.76 mM K 2 HPO 4 , 8.0 mM Na 2 HPO 4 , 5.5 mM D-glucose, pH 7.4) for 5 min, followed by three washes by centrifugation in RPMI containing HEPES (25 mM), and a final resuspension in potassium phosphate buffer (50 mM K 2 HPO 4 , 50 mM KH 2 PO 4 , 2 mM EDTA, pH7.4) containing a protease inhibitor cocktail (Complete Mini; Roche). Parasite extract was then prepared by disruption with a sonicating probe for 5 s, followed by a 1 min rest period on ice to prevent the sample overheating. This process was performed three times. The parasite extract was used immediately. The protein concentration of the parasite extract was determined by Bradford protein assay (Bio-Rad). 
     Pfbc 1  Native Assay 
       Plasmodium falciparum : bc 1  complex cytochrome c reductase (Pfbc 1 ) activity was measured by monitoring cytochrome c reduction at 550 versus 542 nm using a Cary 300 Bio UV-Visible Spectrophotometer (Varian, UK), using a protocol adapted from Fisher et al. (Fisher et al. 2009) 21-23 . The assay was performed in potassium phosphate buffer in a quartz cuvette and in a final volume of 700 μL. Potassium cyanide (10 μM), oxidised cytochrome c (30 μM), parasite extract (100 μg protein) and compound/DMSO were added sequentially to the cuvette, with mixing between each addition. Test compounds were added to a final concentration of 1 μM. DMSO (0.1% v/v) and atovaquone (1 μM), a known malarial cytochrome bc 1  complex inhibitor, were used as negative and positive controls respectively. The reaction was initiated by the addition of 50 μM decylubiquinol and allowed to proceed for 3 min. 
     Data Analysis 
     Malaria 
     In vitro studies: D6 is a drug sensitive strain from Sierra Leone, C235 is a multi-drug resistant strain from Thailand, W2 is a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. These assays were performed as described. 
     Compound Activity Against  Plasmodium falciparum:    
     Compound activity against  P. falciparum , a causative agent of malaria, was tested using the Malaria SYBR Green I—Based Fluorescence (MSF) Assay. This; microtiter plate drug sensitivity assay uses the presence of malarial DNA as a measure of parasitic proliferation in the presence of antimalarial drugs or experimental compounds based on modifications of previously described methods by Plouffe et al (20) and Johnson et al. As the intercalation of SYBR Green I dye and its resulting fluorescence is relative to parasite growth, a test compound that inhibits the growth of the parasite will result in a lower fluorescence. 
     Selected compounds were examined for activity against four strains of  P. falciparum : D6 (CDC/Sierra Leone), a drug-sensitive strain readily killed by chloroquine, TM91-C235, a multi-drug resistant strain resistant to chloroquine, W2, a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. 
       P. berghei  Model Sporozoite, Blood Stage, and Liver Stage Model. 
       P. berghei  sporozoites. The methods that follow are taken directly from 24,25 : From laboratory-reared female  Anopheles stephensi , isolation, inoculation and viability check  Plasmodium berghei  sporozoites (luciferase expressing) were obtained and maintained at 18° C. for 17 to 22 days after feeding on malaria-infected Swiss CD-1/ICR mice. From malaria-infected mosquitoes, salivary glands were extracted and sporozoites obtained. Briefly, mosquitoes were separated into head/thorax and abdomen. Thoraxes and heads were triturated with a mortar and pestle and suspended in medium RPMI 1640 containing 1% C57BL/6 mouse serum (Rockland Co, Gilbertsville, Pa., USA). 50-80 heads with glands total were placed into a 0.5 ml Osaki tube on top of glass wool with enough dissection media to cover the heads. Until all mosquitoes had been dissected, the Osaki tube was kept on ice. Sporozoites that were isolated from the same batch of mosquitoes were inoculated into C57BL/6, 2D knock-out and 2D knock-out/2D6 knock-in C57BL/6 mice on the same day to control for biological variability in sporozoite preparations. On day 0, each mouse was inoculated intravenously in the tail vein with approximately 10,000 sporozoites suspended in 0.1 ml volume. They were stained with a vital dye containing fluorescein diacetate (50 mg/ml in acetone) and ethidium bromide (20 μg/ml in phosphate buffered saline; Sigma Chemical Co, St. Louis, Mo., USA) and counted in a haemocytometer to ensure that inoculated sporozoites were viable following the isolation procedure. Viability of the sporozoites ranged from 90 to 100%. 
     Animals 
     The mice used in these experiments were Swiss Webster females. The animals were acclimated for seven days (quarantine) on arrival. The animals were housed in a cage maintained in a room with 34-68% relative humidity, a temperature range of 64-79° F., and a 12-hr light/dark cycles. Water and food were provided during quarantine and throughout the study. The mice were fed a standard rodent maintenance diet. All animal studies were performed under protocols that are IACUC-approved. All animal care, handling, and use was performed in accordance with the current Guide for the Care and Use of Laboratory Animals (1996). 
     Test Compounds and Administration 
     At the time of preparation of the suspension solution, compounds tested in these experiments were dosed based on the body weight. The suspension solution of oral agents, using homogenizer (PRO Scientific Inc, Monroe, Conn., USA) with 10 mm open-slotted generator to homogenize drug powder mixture at 20,000-22,000 rpm for 5 min in ice bath, were prepared in 0.5% (w/v) hydroxyethyl cellulose and 0.2% (0.5% HECT, v/v) Tween-80 in distilled water. 
     A three consecutive day-treatment regimen (−1, 0, 1 day) or a once-a-day, one dose on day 0 was used in assessments. Drug suspensions were transferred to a 20-ml bottle, drawn into a 1-ml syringe, and delivered to the designated recipient via intragastric feeder (18 gauge). 
     1 hour after intravenous administration of 10,000  P. berghei  sporozoites, single dose causal prophylaxis in 5 C57BL/6 albino mice at 2.5 mpk dosed on day 0. In 5 C57BL/6 albino mice, 3 dose causal prophylaxis treatment at 0.6 mpk dosed on days −1, 0, and +1. 
     In Vivo Imaging System Spectrum 
     All of the in vivo imaging system (IVIS) methods utilized have been described previously [6]. Briefly TQ and NPC-1161B were administered orally on days −1, 0 and 1 with respect to sporozoite inoculation. All inoculated mice were tested using the Xenogen IVIS-200 Spectrum (Caliper Life Sciences, Hopkinton, Mass., USA) IVIS instrument at 24, 48 and 72 hr post-sporozoite infection. Additionally, using a flow cytometry system (FC500 MPL, Beckman Coulter, Miami, Fla., USA), blood-stage infections were measured. For the IVIS calibration in each test, positive and negative controls were used. D-Luciferin potassium salt, (Xenogen, Calif. and Goldbio, St Louis, Mo., USA), the luciferase substrate, was inoculated intraperitoneally into mice at a concentration of 200 mg/kg 15 min before luminescence analysis. Three min post-luciferin administration the mice were anesthetized using isoflurane. The mice, in the IVIS on the 37° C. platform, were then positioned ventral side up. Through nose cone delivery, the mice continued to receive isoflurane. The exposure time of the camera was 5 min for the 24, 48 and 72 hr time points with f-stop=1 and large binning setting. Using Living Image® 3.0 software, photons emitted from specific regions were quantified. 
     Parasitemia was measured after days of IVIS imaging. During a total of 30 days, mice were observed and parasitemia level determined using FACs analysis. (Pybus et al. Malaria Journal 2013, 12:212; Marcsisin et al. Malaria Journal 2014, 13:2). 
     Bovine Cytochrome bc1 Purification Protocol 
     Preparation of crude mitochondria: Whole bovine heart was collected directly from slaughter and transported on ice to the cold room. All work was carried out at 4° C. Fat and other tissues were removed leaving only lean muscle that was then cut into small cubes. The cubes were then transferred to a waring blender and homogenisation buffer (250 mM sucrose; 20 mM K 2 HPO 4 ; 2 mM succinic acid; 0.5 mM EDTA) was added at a ration of 2.6 L buffer per 1 L of muscle tissue. The solution was then homogenised. The resulting homogenate was adjusted to pH 7.8 using 2 M Tris and PMSF was added to a concentration of 0.1 mM. The homogenate was then centrifuged in a Sorvall GS-3 rotor at 3000 rpm for 20 mins. The resulting supernatant was then transferred to a Sorvall GSA rotor and centrifuged at 12,000 rpm for 20 mins. The pellet was then re-suspended and washed in buffer 1 (50 mM KPi (pH 7.5); 0.1 mM PMSF) before centrifugation under the same conditions again. The pellet was collected and frozen at −80° C. for use later. 
     Solubilisation of membrane proteins: The frozen mitochondria were thawed and re-suspended in buffer 2 (50 mM KPi (pH 7.5); 150 mM NaCl; 3 mM NaN 3 ; 0.1 mM PMSF) and a sample taken for a BCA assay. The remaining sample was centrifuged at 42,000 rpm in a Beckman Ti70 rotor for 60 mins. The pellet was re-suspended in the same wash buffer to a volume of 70 ml with the addition 0.1 mg DDM per 1 mg of protein and centrifuged at 42,000 rpm in a Beckman Ti70 rotor for 60 mins. The pellet was then re-suspended in the same wash buffer to a final volume of 215 ml with the addition of 0.9 mg DDM per 1 mg of protein and centrifuged for a final time at 42,000 rpm in a Beckman Ti70 rotor for 60 mins. The supernatant was collected. 
     Purification of cytochrome bc 1 : Whilst being purified, the presence of protein was determined using 280 nm absorbance and the presence of haem was determined using 415 nm soret band peak and 462 nm absorbance. The solubilised protein solution was first applied to a DEAE-Sepharose CL-6B column (ca. 50 ml) pre-equilibrated in buffer A (50 mM KPi (pH 7.5); 150 mM NaCl; 0.03% DDM; 3 mM NaN 3 ) washed with 2 CV buffer A and eluted along a gradient with buffer B (50 mM KPi (pH 7.5); 350 mM NaCl; 0.03% DDM; 3 mM NaN 3 ). The collected protein was pooled and diluted twofold with buffer C (50 mM KPi (pH 7.5); 0.03% DDM; 3 mM NaN 3 ) before application to a hydroxyapatite column (ca. 15 ml) pre-equilibrated with buffer C. The column was washed with 10 CV of buffer C before elution along a gradient with Buffer C* (1000 mM KPi (pH 7.5); 0.03% DDM; 3 mM NaN 3 ). Fractions containing cytochrome bc 1 , as identified by 415 nm absorbance, were then collected, pooled and concentrated to 1.5 ml using an Amicon Ultra-15 (Amicon, MWCO 100,000). The sample was then applied to a Sephacryl-S300 column (ca. 120 ml) pre-equilibrated in buffer D (25 mM KPi (pH 7.5); 100 mM NaCl; 0.015% DDM; 3 mM NaN 3 ) and ran at a flow rate of 0.5 ml/min. Purified cytochrome bc 1  fractions were then collected and concentrated to 30 mg/m. 
     Bovine Enzyme crystallography: Compounds designed using structure-based analyses of cytochrome b co-crystalized with JAG21 as described un Example 1 26 . This was done to optimize medicine-like properties using structure activity principles and analyses. Compounds synthesized as above were used in these assays as follows: 0.10 mM stock solutions were made with 100% Dimethyl Sulfoxide (DMSO) [Sigma Aldrich] and working concentrations were made with IMDM-C (1×, [+] glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS)[gibco, Denmark]). 
     StatisticalAnalysis: A Pearson test was used to confirm a correlation between increasing dose and increasing inhibition. An ANOVA and subsequent pairwise comparison with Dunnett correction was used to determine whether or not inhibition or toxicity at a given concentration was statistically significant. Stata/SE 12.1 was used for this analysis. 
     Results 
     Tetrahydroquinolone Compounds: 
     In Vitro Challenge Assay for Tachyzoites: Seven compounds (Table 1) were tested and each compound was tested at least twice. JAG021 and JAG050 demonstrated effect below 1 μM, and were tested at lower concentrations. A representative graph of this data is shown in  FIG.  8   . JAG050 and JAG021 were identified as lead compounds because the IC 50  values were 55 and 188 nM respectively. Correlation between concentration of compound and inhibition of parasite growth and activity (as measured by fluorescence) was observed for all compounds except JAG046. 
     Cytotoxicity Assay using HFF and WST-1 and IC50 with HEP G cells: Because  T. gondii  grows inside cells, if a compound was toxic to host Human Foreskin Fibroblast Cells (HFF), then it would make the compound appear to be spuriously effective; in actuality only toxicity for the host cell would be measured. Cytotoxicity to human foreskin fibroblasts was therefore assessed for all compounds at 10 μM and 50 μM. Results of this experiment are in  FIG.  9    and Table 3. A two-way ANOVA and subsequent pairwise comparison found none of the differences in absorbance, compared to the controls, to be statistically significant (p&gt;0.05). This suggests that these compounds are not toxic at 10 μM or 50 μM and that toxicity to cells is attributed to DMSO in the solution, not the compound. IC50 with HEP G cells was performed as described and toxicity was: HEP G2 IC50 17.70 microM (r 2 =0.97) JAG 21; JAG 50 7.1 microM r 2 =0.98. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Cytotoxicity to human foreskin fibroblasts was therefore assessed for all compounds 
               
               
                 at 10 μM and 50 μM. Graph is representative of replicate experiment. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                 JAG050 
                 JAG050 
                 JAG021 
                 JAG021 
               
               
                 Observation 
                 Control 
                 10 μM 
                 1 μM 
                 10 μM 
                 1 μM 
               
               
                   
               
            
           
           
               
            
               
                 a 
               
            
           
           
               
               
               
               
               
               
            
               
                 True Cysts 
                 4.67 ± 3.06 
                   1 ± 0.82 
                 0.25 ± 0.5  
                 0.25 ± 0.5 
                 0.5 ± 0.6 
               
               
                   
                 [2-8] 
                 [0-2] 
                 [0-1] 
                 [0-1] 
                 [0-1] 
               
               
                 Pseudocysts 
                 40.3 ± 11.4 
                 20.5 ± 2.9  
                 23.25 ± 10.31 
                 25.5 ± 5.1 
                 29 ± 6  
               
               
                   
                 [31-53] 
                 [17-24] 
                 [14-38] 
                 [19-30] 
                 [21-34] 
               
               
                 Small 
                 1600 ± 436  
                 31 ± 16 
                 58 ± 24 
                 73.25 ± 30.9 
                 90.5 ± 33.5 
               
               
                 organisms 
                 [1100-1900] 
                  [8-43] 
                 [27-85] 
                  [30-101] 
                  [63-137] 
               
            
           
           
               
            
               
                 b 
               
            
           
           
               
               
               
               
               
               
            
               
                 True Cysts 
                 452 
                 88 
                 29 
                 22 
                 54 
               
               
                 Pseudocysts 
                 3884 
                 1921 
                 2269 
                 2638 
                 2955 
               
               
                 Small organisms 
                 16404 
                 3018 
                 5086 
                 7309 
                 9734 
               
               
                   
               
            
           
         
       
     
     In Vitro Challenge Assay for Bradyzoites 
     Lead compounds JAG050 and JAG021 were tested against EGS because of their effects on tachyzoites (RH—YFP). Under immunofluorescence microscopy, the following forms were observed: “true cysts” with a dolichos-staining wall, “pseudocysts” or tight clusters of parasites, and small organisms. If there were fewer than four parasites visible in a cluster, the organisms were counted individually (as “small organisms”). A statistically significant reduction in the number of true cysts and small organisms was observed at 1 μM and 10 μM for both compounds (p&lt;0.05, p&lt;0.005,  FIGS.  10 A- 10 C ). 
     ADMEproperties of THQs. In vitro ADME analyse of the THQ compounds were outsourced to ChemPartner Shanghai Ltd. ELQ-271 was tested as a comparison. THQs which were potent inhibitors of  T. gondii  tachyzoites were assessed for their kinetic solubility, metabolic stability in human and mouse liver microsomes, and their ability to permeate across MDCK-MDK1 cell membranes (in vitro measure of blood-brain barrier (BBB) permeability). Solubility, half-life and BBB permeability/efflux results are shown in Table 4. The kinetic solubility (PBS, pH 7.4) of compounds JAG021 and JAG050, 7 and 16 μM respectively, were higher than MJM170 (2 μM) and ELQ-271 (0.2 μM). JAG021 was the most metabolically stable compound in human liver microsomes (&gt;99% remaining after 45 mins) compared with other THQs and ELQ-271, although it displayed a much shorter half-life of 101 mins in mouse liver microsomes. All THQs tested in the MDK1 (MJM170, JAG021 and JAG050) MDCK-MDK1 system exhibit high permeability (P app  &gt;10×10 6  cm/s) and low efflux (efflux ratio &lt;1.5). 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Chart compares properties of solubility and half-life of JAG050 
               
               
                 and JAG021 to parent compounds ELQ 271 and MJM170. 
               
            
           
           
               
               
               
               
            
               
                   
                 Solubility 
                 Human liver 
                 Mouse liver 
               
               
                 Compound 
                 (pH 7.4)* 
                 microsomes #   
                 microsomes #   
               
               
                   
               
               
                 ELQ271 
                 0.15 μM 
                 171.93 min 
                 448.13 min 
               
               
                 MJM170 
                 1.97 μM 
                 146.33 min 
                  20.97 min 
               
               
                 JAG021 
                 7.07 μM 
                 ∞ 
                 101.09 min 
               
               
                 JAG050 
                 16.41 μM  
                  99.04 min 
                  68.55 min 
               
               
                   
               
               
                 The test system was 100 mM Phosphate Buffer (pH 7.4).: 
               
               
                 &lt;10 μM is low solubility, 
               
               
                 10-80 μM is moderate solubility and 
               
               
                 &gt;80 μM is high solubility. 
               
               
                 A T 1/2   
               
               
                 &lt; 30 minutes indicates susceptibility to metabolism, 
               
               
                 between 30 and 120 minutes indicates moderate metabolism and 
               
               
                 &gt;120 minutes indicates stability in the liver. 
               
            
           
         
       
     
     Enzyme assays: Enzyme reduction of cytochrome c by the parasite extract is mediated by  P. falciparum  bc 1  complex cytochrome c reductase (Pfbc 1 ). All three compounds (1 μM) significantly inhibited the reduction of cytochrome c by the parasite extract, (JAG021=86.4±3.2; JAG099=81.3±6.0; MJM170=69.7±11.3% atovaquone response). This clearly demonstrates the compounds are inhibitors of Pfbc 1 . Additional data demonstrating effect on bovine and  Plasmodium falciparum  enzyme are shown in Table 5. There is selectivity for the malaria enzyme. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Inhibition of Pfbc 1  by compounds. 
               
            
           
           
               
               
            
               
                   
                 Inhibition of cytochrome c reduction 
               
               
                 Compound (1 μM) 
                 (% atovaquone response) 
               
               
                   
               
               
                 JAG021 
                 86.4 ± 3.2 
               
               
                 JAG099 
                 81.3 ± 6.0 
               
               
                 MJM170 
                 69.7 ± 11.3 
               
               
                   
               
               
                 Data shown are mean ± s.e.m. of 4 independent experiments performed in triplicate. 
               
            
           
         
       
     
     Binding assays and co crystallography. JAG021 has lower binding affinity to bovine cytochrome be in comparison with previous compounds that we have tested. JAG 21 inhibits&#39; Cytbc1 but not fully, indicating that it will be less toxic for bovine/human cyt bc ( FIG.  11   ) 
     Assessment of Compound Degradation and Microbicidal Effect on  Toxoplasma gondii  Compounds JAG050 and JAG021 were observed for degradation and microbicidal effect. Neither compound was found to be microbicidal; when media was replaced with clean media, the parasites appeared to resume activity and replication. In comparing the 6-day exposure with no addition of compound to the 6-day exposure with the addition of compound, it did not appear that the compound was being degraded over time. In condition II, in which the compound is refreshed, there appears to be a rise in fluorescence on day 6 in the 1 μM treatment group for both compounds. However, these differences were not found to be statistically significant (p&gt;0.05). 
     Effective of JAG21 on  Toxoplasma gondii . JAG21 at 5 mg/kg eliminates  T. gondii  tachyzoites seen in luminescence studies ( FIGS.  12 A- 12 D ). 
     JAG21 against G0 arrested and normal (no tet repressor)  Toxoplasma  RPS13 delta in Interferon gamma knockout mice plus and minus tetracycline. Our data show that the combination of JAG21 and tafenoquine treatment is superior to either alone against RPS13 A minus  tetracycline ( FIG.  13   ). The data indicates that this appears to be a dormant parasite that is less susceptible to JAG21 than either the slowly growing EGS bradyzoites or the rapidly proliferating tachyzoites. 
     Malaria: 
     In vitro. Results are shown in Table 6. JAG 21 is a 40-65 nM inhibitor of  Plasmodium falciparum  including effect against all drug resistant strains. The effects of the other compounds are also shown in this table and are in the range of 50-200 nM. 
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Inhibition of  P falciparum  in vitro including drug resistant isolates 
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                 SYBR 
                   
                 SYBR 
                   
                 SYBR 
                   
                 SYBR 
                   
               
               
                   
                 Green 
                   
                 Green 
                   
                 Green 
                   
                 Green 
                   
               
               
                   
                 D6 
                   
                 C235 
                 SYBR 
                 W2 
                   
                 C2B 
                   
               
               
                 Compound 
                 IC50 
                 SYBR 
                 IC50 
                 TM91C235 
                 IC50 
                 SYBR 
                 IC50 
                 SYBR 
               
               
                 ID 
                 (uM) 
                 D6 R 2   
                 (uM) 
                 R 2   
                 (uM) 
                 W2 R 2   
                 (uM) 
                 C2B R 2   
               
               
                   
               
               
                 JAG006 
                 0.29 
                 0.90 
                 0.88 
                 0.92 
                 2.46 
                 0.92 
                 1.66 
                 0.94 
               
               
                 JAG021 
                 0.01435 
                 0.9572 
                 0.06164 
                 0.9706 
                 0.05518 
                 0.9727 
                 0.04042 
                 0.9847 
               
               
                 JAG050 
                 0.04664 
                 0.9138 
                 0.06913 
                 0.9562 
                 0.03136 
                 0.9693 
                 0.03635 
                 0.9427 
               
               
                 JAG047 
                 3.746 
                 0.9738 
                 12.56 
                 0.9218 
                 9.072 
                 0.9358 
                 7.781 
                 0.9575 
               
               
                 JAG039 
                 9.595 
                 0.9532 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 JAG046 
                 6.716 
                 0.9844 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 RG38 
                 2.84 
                 0.8936 
                 13.66 
                 0.8338 
                 9.245 
                 0.7954 
                 &gt;20 
                 N/A 
               
               
                   
               
            
           
         
       
     
     In vivo. Single dose causal prophylaxis in 5 C57BL/6 albino mice at 2.5 mpk dosed on day 0, 1 hour after intravenous administration of 10,000  P. berghei  sporozoites. 3 dose causal prophylaxis treatment in 5 C57BL/6 albino mice at 0.6 mpk dosed on days −1, 0, and +1. A representative figure for higher dose (5 mg/kg) is shown, but all experiments with the amounts mentioned above had efficacy measured as cure measured as survival, luminesence and parasitemia quantitated by flow cytometry are similar to these. ( FIGS.  12 A- 12 D ) 
     Discussion 
     JAG050 and JAG021 were identified as lead compounds, demonstrating potent inhibition of tachyzoites and bradyzoites and no toxicity to human foreskin fibroblasts in our in vitro model. While compounds inhibited parasite replication and activity, there did not appear to be a microbicidal effect. 
     Toxoplasmosis is highly prevalent and the impact of this disease can be devastatingly severe. Current treatments have toxic side effects and are not curative. JAG050 and JAG021 are lead compounds in the search for a new curative medicine because they demonstrate effect on both life stages and were not toxic to the human cells in our in vitro model. 
     Experiments testing the compounds against the EGS strain had some surprising findings. While true cysts in vitro appeared to be completely eliminated by treatment, or their number significantly reduced, parasites did persist in tight, clustered, cyst-like structures, or pseudo-cysts, and small punctate life forms that resemble tachyzoites. One possible explanation is that the dolichos-staining organisms that remain 48 hours after treatment are in a separate, hypnozoite-like life stage that is not affected by the compounds. 
     JAG050 and JAG021 do not appear to have a microbicidal effect on the RH—YFP parasites. However, in comparing the two conditions in which cells and parasites were exposed to the drug for 6 days, it does not appear that the parasites or host cells are degrading the compounds. In order to cure toxoplasmosis, a companion drug that can work synergistically with the compounds of the present invention may be helpful. Primaquine and tafenoquine, which are the only medicines that can treat the hypnozoite stage of  Plasmodium vivax  and  P. ovale , may be potential candidates. We had demonstrated synergy with an earlier generation compound with atovaquone and additive effect with cycloguanil. 26    
     JAG21 demonstrated high efficacy against Toxopalsma tachyzoites in our vitro and in vivo models, low nanoM efficacy against drug resistant  P. falciparum , and single dose causal prophylaxis in a mouse model of  P. berghei  sporozoites infection 
     REFERENCES FOR EXAMPLE 2 
     
         
         1. CDC—Toxoplasmosis [Internet]. [cited 2015 Jul. 1]. 
         2. Montoya J, Liesenfeld O. Toxoplasmosis. The Lancet [Internet]. 2004 Jun. 12 [cited 2015 Jul. 1]; 363(9425):1965-76. 
         3. McLeod R, Vantubbergen C, Boyer K. Toxoplasmosis ( Toxoplasma gondii ). In: Nelson Textbook of Pediatrics. 20th ed. Elsevier; 2015. 
         4. Jones J L, Holland G N. Annual Burden of Ocular Toxoplasmosis in the United States. Am J Trop Med Hyg [Internet]. 2010 Mar. [cited 2015 Jul. 1]; 82(3):464-5. 
         5. Wallon M, Garweg J G, Abrahamowicz M, Cornu C, Vinault S, Quantin C, et al. Ophthalmic outcomes of congenital toxoplasmosis followed until adolescence. Pediatrics. 2014 March; 133(3):e601-8. 
         6. Roberts F, McLeod R. Pathogenesis of toxoplasmic retinochoroiditis. Parasitol Today Pers Ed. 1999 February; 15(2):51-7. 
         7. McLeod R, Khan A R, Noble G A, Latkany P, Jalbrzikowski J, Boyer K. SEVERE SULFADIAZINE HYPERSENSITIVITY IN A CHILD WITH REACTIVATED CONGENITAL TOXOPLASMIC CHORIORETINITIS: Pediatr Infect Dis J [Internet]. 2006 March [cited 2015 Jun. 16]; 25(3):270-2. 
         8. Waxman S, Herbert V. Mechanism of pyrimethamine-induced megaloblastosis in human bone marrow. N Engl J Med. 1969 Jun. 12; 280(24):1316-9. 
         9. Caumes E, Bocquet H, Guermonprez G, Rogeaux O, Bricaire F, Katlama C, et al. Adverse cutaneous reactions to pyrimethamine/sulfadiazine and pyrimethamine/clindamycin in patients with AIDS and toxoplasmic encephalitis. Clin Infect Dis Off Publ Infect Dis Soc Am. 1995 September; 21(3):656-8. 
         10. Phan L, Kasza K, Jalbrzikowski J, Noble A G, Latkany P, Kuo A, et al. Longitudinal study of new eye lesions in children with toxoplasmosis who were not treated during the first year of life. Am J Ophthalmol. 2008 September; 146(3). 
         11. Vercesi A E, Rodrigues C O, Uyemura S A, Zhong L, Moreno S N J. Respiration and Oxidative Phosphorylation in the Apicomplexan Parasite  Toxoplasma gondii . J Biol Chem [Internet]. 1998 Nov. 20 [cited 2015 Jun. 16]; 273(47):31040-7. 
         12. Khan A A, Nasr M, Araujo F G. Two 2-hydroxy-3-alkyl-1,4-naphthoquinones with in vitro and in vivo activities against  Toxoplasma gondii . Antimicrob Agents Chemother. 1998 September; 42(9):2284-9. 
         13. Doggett J S, Nilsen A, Forquer I, Wegmann K W, Jones-Brando L, Yolken R H, et al. Endochin-like quinolones are highly efficacious against acute and latent experimental toxoplasmosis. Proc Natl Acad Sci USA. 2012 Sep. 25; 109(39):15936-41. 
         14. Capper M J, O&#39;Neill P M, Fisher N, Strange R W, Moss D, Ward S A, et al. Antimalarial 4(1H)-pyridones bind to the Qi site of cytochrome bc1. Proc Natl Acad Sci USA. 2015 Jan. 20; 112(3):755-60. 
         15. Gubbels M-J, Li C, Striepen B. High-Throughput Growth Assay for  Toxoplasma gondii  Using Yellow Fluorescent Protein. Antimicrob Agents Chemother [Internet]. 2003 January [cited 2015 Jul. 8]; 47(1):309-16. 
         16. Vidigal P V T, Santos D V V, Castro F C, Couto J C de F, Vitor R W de A, Brasileiro Filho G. Prenatal toxoplasmosis diagnosis from amniotic fluid by PCR. Rev Soc Bras Med Trop [Internet]. 2002 February [cited 2015 Jul. 8]; 35(1):1-6. 
         17. Silva L A, Brandao G P, Pinheiro B V, Vitor R W A. Immunosuppression with cyclophosphamide favors reinfection with recombinant  Toxoplasma gondii  strains. Parasite J Societe Fr Parasitol [Internet]. 2012 August [cited 2015 Jul. 8]; 19(3):249-57. 
         18. Fomovska A, Huang Q, El Bissati K, Mui E J, Witola W H, Cheng G, et al. Novel N-Benzoyl-2-Hydroxybenzamide Disrupts Unique Parasite Secretory Pathway. Antimicrob Agents Chemother [Internet]. 2012 May [cited 2015 Jul. 8]; 56(5):2666-82. 
         19. Fomovska A, Wood R D, Mui E, Dubey J P, Ferreira L R, Hickman M R, et al. Salicylanilide inhibitors of  Toxoplasma gondii . J Med Chem. 2012 Oct. 11; 55(19):8375-91. 
         20. Galen P. Miley, Sovitj Pou, Rolf Winter, Aaron Nilsen, Yuexin Li, Jane X. Kelly, Allison M. Stickles, Michael W. Mather, c Isaac P. Forquer, a April M. Pershing, Karen White, David Shackleford, Jessica Saunders, Gong Chen, Li-Min Ting, Kami Kim, N. Zakharov, Cristina Donini, Jeremy N. Burrows, Akhil B. Vaidya Susan A. Charman, Michael K. Risco, ELQ-300 Prodrugs for Enhanced Delivery and Single-Dose Cure of Malaria 2015 AAC 59: 5555-556 
         21. Fisher, N. et al., 2009. Chapter 17 Type II NADH: Quinone Oxidoreductases of  Plasmodium Falciparum  and  Mycobacterium Tuberculosis : Kinetic and High-Throughput Assays. In B. T.-M. in Enzymology, ed.  Mitochondrial Function, Part A: Mitochondrial Electron Transport Complexes and Reactive Oxygen Species . Academic Press, pp. 303-320. 
         22. Fisher, N. et al., 2004. Human disease-related mutations in cytochrome b studied in yeast.  The Journal of biological chemistry,  279(13), pp. 12951-12958. 
         23. Trager, W. &amp; Jensen, J. B., 2005. Human malaria parasites in continuous culture. 1976 . The Journal of parasitology,  91(3), pp. 484-486. 
         24. Pybus et al. Malaria Journal 2013, 12:212. 
         25. Marcsisin et al. Malaria Journal 2014, 13:2. 
         26. McPhillie M SREP(Nature) Jume 2016 
       
    
     Example 3: Synthesis and Activity of Compounds 
     All reagents and solvents were purchased from commercial sources. All commercial reagents and solvents were used as received without further purification. The reactions were monitored using analytical thin layer chromatography (TLC) with 0.25 mm EM Science silica gel plates (60F-254). The developed TLC plates were visualized by short wave UV light (254 nm) or immersion in potassium permanganate solution followed by heating on a hot plate. Flash chromatography was performed with Selecto Scientific silica gel, 32-63 μm particle sizes. All reactions were performed in flame or oven-dried glassware under a nitrogen atmosphere. All reactions were stirred magnetically at ambient temperature unless otherwise indicated.  1 H NMR spectra were obtained with a Bruker DRX400, Varian VXR400 or VXR300.  1 H NMR spectra were reported in parts per million (6) relative to TMS (0.0), DMSO-d6 (2.50) or CD 3 OD (4.80) as an internal reference. All  1 H NMR spectra were taken in CDCl3 unless otherwise indicated. 
     
       
         
         
             
             
         
       
     
     
       
         
         
             
             
         
       
     
     General Method A 
     2,2-Dimethyl-1,3-dioxane-4,6-dione (1.5 equiv.) was dissolved in trimethylorthoacetate (2 equiv.) and heated to 115° C. for 2 hrs. The reaction was cooled to allow the addition of the aniline (1 equiv.) before being heated to 115° C. for a further 2 hrs. The reaction mixture was then allowed to cool and was concentrated in vacuo, remaining solvent was washed off with cold methanol. The precipitate was then dissolved in minimum volume of Dowtherm A and refluxed at 250° C. for 1.5 hours. The reaction mixture was allowed to cool and the precipitate filtered followed by washing with hexane to afford the title compound. 
     2-Methyl-6-(trifluoromethyl)quinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised by general method A using 4-trifluoromethyl aniline (2.00 g, 12. 4 mmol) to yield the title compound as a white amorphous solid (466 mg, 2.05 mmol, 17%). 1 H NMR (300 MHz, MeOD) δ 8.42 (s, 1H), 7.81 (dd, J=8.8 Hz, 2.1 Hz, 1H), 7.60 (d, J=8.8 Hz, 1H), 6.16 (s, 1H), 2.40 (s, 3H); M/Z (ESI+); 228.06 (Found MH + 228.0634, C 11 H 8 F 3 NO requires 228.0630). 
     7-ethyl-2-methylquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure A from 3-ethylaniline (1.4 mL, 11.1 mmol). The title compound was isolated as a colourless solid (210 mg, 1.12 mmol, 10%). 1 H NMR (500 MHz, CDCl3) δ 9.72 (s, 1H), 8.17 (d, J=8.3 Hz, 1H), 7.16 (s, 1H), 7.10 (d, J=8.3 Hz, 1H), 6.07 (s, 1H), 2.66 (q, J=7.6 Hz, 2H), 2.33 (s, 3H), 1.18 (t, J=7.6 Hz, 3H); 
     2,7-Dimethylquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure A from 3-methylaniline (7.5 mL, 42 mmol). The title compound was isolated as a colourless solid (370 mg, 2.13 mmol, 5%). 1 H NMR (400 MHz, CDCl3) δ 9.58 (s, 1H), 8.24 (d, J=8.3 Hz, 1H), 7.22 (s, 1H), 7.16 (d, J=8.3 Hz, 1H), 6.15 (s, 1H), 2.46 (s, 3H), 2.41 (s, 3H). 
     7-trifluormethyl-2-methylquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure A from 3-trifluoromethyl-aniline (3 mL, 24 mmol). The title compound was isolated with its regiomer and separation was not achieved and so was carried forwards as a mixture (1.5 g). 
     
       
         
         
             
             
         
       
     
     General Method B 
     The 4-hydroxylquinolone (1 equiv.) was dissolved in acetic acid (10.0 mL) under inert conditions. platinum dioxide (5% weight equiv.) was added and a hydrogen balloon was attached. The reaction was left to proceed for 12 hours. The resulting suspension was filtered through a pad of Celite and washed with ethyl acetate (10.0 mL). The filtrate was concentrated in vacuo to afford a yellow/brown oil. Purification by column chromatography (10% methanol in chloroform) afforded the title compound. 
     2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     A solution of 4-hydroxyl 2-methyl-quinolone (1.00 g, 6.28 mmol) in acetic acid (10.0 mL) was catalytically hydrogenated over platinum dioxide (0.10 g, 0.44 mmol) for 12 hours. The resulting suspension was filtered through a pad of Celite and washed with ethyl acetate (10.0 mL). The filtrate was concentrated in vacuo to afford a yellow/brown oil. Purification by column chromatography (10% methanol in chloroform) afforded the title compound as a colourless amorphous solid. (1.02 g, 6.25 mmol, 99%). δ H NMR; (500 MHz, Chloroform-d); δ 6.29 (s, 1H), 2.71 (t, J=6.1 Hz, 2H), 2.48 (t, J=6.1 Hz, 2H), 2.32 (s, 3H), 1.78-1.69 (m, 4H); M/Z (ESI+); 164.1122 (Found MH+, 164.11 C 10 H 13 NO requires 164.1075). 
     2-Methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from 2-methyl-6-(trifluoromethyl)quinolin-4(1H)-one (466 mg, 2.0 mmol), The title compound was isolated as colourless solid (230 mg, 0.99 mmol, 49%).  1 H NMR (500 MHz, MeOD) δ 6.32 (s, 1H), 2.94 (dd, J=16.7, 5.1 Hz, 1H), 2.86 (dd, J=8.4, 4.1 Hz, 2H), 2.65-2.52 (m, 1H), 2.41 (dd, J=22.8, 11.5 Hz, 1H), 2.36 (s, 3H), 2.28-2.15 (m, 1H), 1.75 (tt, J=12.8, 9.1 Hz); M/Z (ESI+); 232.10 (Found MH + ; 232.0955, C 11 H 12 F 3 NO requires 232.0949). 
     2,6-Dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from 2,6-dimethyl-quinolin-4(1H)-one (1.0 g, 5.78 mmol), The title compound was isolated as a colourless solid (780 mg, 4.30 mmol, 76%).  1 H NMR (400 MHz, CDCl3) δ 12.26 (s, 1H), 6.09 (s, 1H), 2.88-2.64 (m, 3H), 2.30 (s, 3H), 1.98 (dd, J=16.9, 10.1 Hz, 1H), 1.87 (d, J=12.4 Hz, 1H), 1.77 (m, 1H), 1.39 (ddd, J=23.9, 11.1, 6.0 Hz, 1H), 1.08 (d, J=6.5 Hz, 3H); M/Z (ESI+); 178.13 (Found MH + ; 178.1280, C 11 H 15 NO requires 177.1154). 
     2,7-Dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from 2,7-Dimethyl-quinolin-4(1H)-one (350 mg, 2.0 mmol). The title compound was isolated as a colourless solid (311 mg, 1.75 mmol, 88%). 1 H NMR (500 MHz, MeOD) δ 6.31 (s, 1H), 2.78 (dd, J=17.0, 5.1 Hz), 2.73 (ddd, J=17.7, 5.2, 2.7 Hz), 2.45-2.31 (m, 2H), 2.00-1.87 (m, 2H), 2.37 (s, Me), 1.37 (m, 2H), 1.13 (d, J=6.6 Hz, 3H); M/Z (ESI+); 178.13 (Found MH + ; 178.1278, C 11 H15NO requires 177.1154). 
     7-ethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from 7-ethyl-2-methylquinolin-4(1H)-one (420 mg, 1.78 mmol). The title compound was isolated as a colourless solid (360 mg, 1.5 mmol, 84%). H NMR (400 MHz, CDCl3) δ 12.20 (s, 1H), 6.09 (s, 1H), 2.88-2.66 (m, 2H), 2.46-2.19 (m, 5H, 2-Me), 1.95 (d, J=13.0 Hz, 1H), 1.63 (s, 1H), 1.38 (td, J=13.9, 6.9 Hz, 2H), 1.33-1.22 (m, 1H) 0.94 (t, J=7.4, 3H); M/Z (ESI+); 192.14 (Found MH + ; 192.1378 C 12 H 17 NO requires 192.1383). 
     7-trifluormethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from a mixture of 7-trifluormethyl-2-methylquinolin-4(1H)-one &amp; 5-trifluormethyl-2-methylquinolin-4(1H)-one (1.5 g). The title compound was isolated as a colourless solid (495 mg, 2.14 mmol).  1 H NMR (500 MHz, CDCl 3 /MeOD, 1:1) δ 5.99 (s, 1H), 2.73-2.60 (m, 2H), 2.53 (dd, J=16.3, 12.0 Hz, 1H), 2.35 (s, 1H), 2.20 (ddd, J=17.7, 11.4, 5.9 Hz, 1H), 2.11 (s, 3H), 2.09-2.01 (m, 1H), 1.42 (ddd, J=25.0, 12.1, 5.7 Hz, 1H); M/Z (ESI+); 232.10 (Found MH + ; 232.0953, C 11 H 12 F 3 NO requires 232.0949). 
     
       
         
         
             
             
         
       
     
     General Method C 
     Potassium iodide solution (sat aq, 5.60 mL mmol −1 ) and n-butylamine (10 equiv.) were added to a solution of the tetrahydroquinolin-4(1H)-one (1 equiv.) and iodine (1 equiv.) in DMF (10.0 mL). The reaction mixture was stirred at room temperature for 16 hours. Observed colour change from dark purple to orange. Sodium thiosulphate (250 mg in 10.0 mL water) was then added causing precipitation of a colourless solid. Filtration (washed 2×10 mL water) afforded the title compound. 
     4(1H), 3-iodo-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     Saturated potassium iodide solution (sat aq, 5.60 mL) and n-butylamine (5.80 mL, 58.3 mmol) was added to a solution of 2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (0.95 g, 5.83 mmol) and iodine (1.48 g, 5.83 mmol) in DMF (10.0 mL). The reaction mixture was stirred at room temperature for 16 hours. Observed colour change from dark purple to orange. Sodium thiosulphate (250 mg in 10.0 mL water) was then added followed by filtration (washed 2×10 mL water) to afford the title compound (39) as colourless microcrystals (1.45 g, 5.02 mmol, 86%). 1H NMR (500 MHz, methanol-d4); δ 2.53 (t, J=6.1 Hz, 2H), 2.44 (s, 3H), 2.30 (t, J=6.1 Hz, 2H), 1.73-1.67 (m, 2H), 1.67-1.61 (m, 2H); M/Z (ESI+); 290.00 (Found MH+, 290.0037 C 10 H 12 INO requires 290.0036). 
     3-Iodo-2-methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure C from 2-methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one (230 mg, 1.0 mmol). The title compound was isolated as colourless solid (300 mg, 0.84 mmol, 84%).  1 H NMR (400 MHz, DMSO) δ 11.58 (s, 1H), 2.75 (d, J=5.6 Hz, 1H), 2.72-2.67 (m, 2H), 2.62 (dd, J=7.4, 5.8 Hz, 1H), 2.46 (s, 3H), 2.31 (d, J=22.7 Hz, 1H), 2.15 (dd, J=16.4, 11.1 Hz, 1H), 2.07 (dd, J=6.6, 5.4 Hz, 1H), 1.68-1.51 (m, 1H); M/Z (ESI+); 357.99 (Found MH + ; 357.9914, C 11 H 11 F 3 INO requires 357.9910). 
     3-Iodo-2·6-dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure C from 2,6-dimethyl-5,6,7,8-tetrahydro quinolin-4(1H)-one (750 mg, 4.24 mmol). The title compound was isolated as colourless solid (740 mg, 2.44 mmol, 58%).  1 H NMR (500 MHz, CDCl 3 /MeOD) δ 2.36 (dd, J=17.3, 4.8 Hz), 2.25 (d, J=4.8 Hz, 2H), 2.15 (s, 3H), 1.57 (dd, J=17.3, 10.4 Hz, 1H), 1.51 (d, J=10.9 Hz, 1H), 1.36 (s, 1H), 1.09-0.94 (m, 1H), 0.69 (d, J=6.6 Hz, 3H); M/Z (ESI+); 304.02 (Found MH + ; 304.0190, C 11 H 14 INO requires 304.0193). 
     3-Iodo-7-ethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure C from 7-ethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (110 mg, 0.57 mmol). The title compound was isolated as colourless solid (180 mg, 0.57 mmol, 99%).  1 H NMR (400 MHz, MeOD) δ 2.62 (dd, J=17.2, 4.4 Hz, 2H), 2.47 (s, 3H), 2.34-2.22 (m, 1H), 2.18 (dd, J=17.8, 9.6 Hz, 1H), 1.92-1.81 (m, 1H), 1.64-1.50 (m, 1H), 1.34 (dtd, J=14.1, 7.2, 2.2 Hz, 2H), 1.21 (ddd, J=24.1, 10.9, 5.6 Hz, 1H), 0.91 (t, J=7.4 Hz, 3H); M/Z (ESI+); 318.03 (Found MH + ; 318.0261, C 12 H 16 INO requires 318.0349). 
     3-Iodo-7-trifluormethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure C from 7-trifluormethyl-2-methylquinolin-4(1H)-one (480 mg, 2.10 mmol). The title compound was isolated as a colourless solid (688 mg, 1.92 mmol, 91%).  1 H NMR (500 MHz, CDCl 3 /MeOD, 1:1) δ 2.40 (dd, J=16.0, 4.9 Hz, 2H), 2.24 (dd, J=17.9, 8.3 Hz, 1H), 2.20-2.12 (m, 1H), 2.12 (s, 2H), 2.00-1.86 (m, 1H), 1.94 (s, 1H), 1.75 (s, 1H), 1.74 (dd, J=13.5, 5.9 Hz, 1H), 1.13 (ddd, J=19.4, 12.1, 5.8 Hz, 1H). M/Z (ESI+); 357.99 (Found MH + ; 357.9915, C 11 H 11 F3INO requires 357.9910). 
     
       
         
         
             
             
         
       
     
     General Procedure d 
     Copper (II) acetate (1 equiv.), triethylamine (5 equiv.), and pyridine (5 equiv.) was added to a solution of the boronic acid (1.5 equiv.) and phenol (1 equiv.) in dichloromethane (10 mL mmol −1 ) over heat-activated 4 Å molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HCl (0.5 M, 20 mL mmol −1 ) and filtered through a pad of Celite, followed by repeated washing with water (10 mL mmol −1 ). The organic layer was extracted with brine, dried over magnesium sulphate, and concentrated in vacuo. Purification by silica gel chromatography (ethyl acetate/hexane) afforded the title compound. 
     1-Bromo-4-(4-(trifluoromethoxy)phenoxy)benzene 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised, from 4-bromophenol (0.42 g, 2.43 mmol) and 4-trifluoromethoxy benzene boronic acid (1.00 g, 4.68 mmol), according to general procedure d as a colourless oil (70%, 0.53 g, 1.63 mmol). δ H NMR (500 MHz, Chloroform-d) δ 7.37 (d, J=9.0 Hz, 2H), 7.10 (d, J=9.1 Hz, 2H), 6.91 (d, J=9.1 Hz, 2H), 6.80 (d, J=9.0 Hz, 2H); 
     Methyl 3-(4-bromophenoxy)benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised, from 4-bromo-pehonl (0.42 g, 2.43 mmol) and 3-methoxycarbonyl phenyl boronic acid (0.43 g, 2.43 mmol), according to general procedure D. The title compound (43) was isolated as colourless glassy solid (0.21 g, 0.69 mmol, 28%).  1 H NMR (500 MHz, CDCl 3 ) δ 7.73 (dt, J=7.7, 1.2 Hz, 1H), 7.59-7.53 (m, 1H), 7.38 (d, J=9.0 Hz, 2H), 7.34 (t, J=8.4 Hz, 2H), 7.13 (ddd, J=8.4, 2.5, 0.9 Hz, 1H), 6.82 (d, J=9.0 Hz, 2H), 3.83 (s, 3H); M/Z (ESI+); 307.00 (Found MH + , 306.9962 C 14 H 11 BrO 3  requires; 306.9964). 
     1-bromo-4-(4-chlorophenoxy)benzene 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised, from 4-bromophenol (0.5 g, 2.80 mmol) and 4-trifluoromethoxy benzene boronic acid (0.6 g, 4.20 mmol), according to general procedure D. The title compound was isolated as a colourless needles (160 mg, 0.56 mmol, 20%). 1H NMR (500 MHz, CDCl 3 ) δ 7.43 (d, J=9.0 Hz, 2H), 7.30 (d, J=9.0 Hz, 2H), 6.93 (d, J=9.0 Hz, 2H), 6.86 (d, J=9.0 Hz, 2H). 
     Methyl 4-(4-bromophenoxy)benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised, from 4-bromo-pehonl (0.42 g, 2.43 mmol) and 4-methoxycarbonyl phenyl boronic acid (0.43 g, 2.43 mmol), according to general procedure D. The title compound was isolated as colourless plate crystals (0.25 g, 0.81 mmol, 33%). 1H NMR (500 MHz, CDCl 3 ) δ 7.94 (d, J=8.9 Hz, 2H), 7.41 (d, J=8.9 Hz, 2H), 6.91 (d, J=8.8 Hz, 2H, 6.87 (d, J=8.9 Hz, 2H), 3.83 (s, 3H); M/Z (ESI+); 307.00 (Found MH + , 306.9961 C 14 H 11 BrO 3  requires 306.9964). 
     5-(4-bromophenoxy)-2H-1,3-benzodioxole 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised, from 4-bromo-pehonl (500 mg, 2.89 mmol) and 3,4-methyleneoxy-phenylboronic acid (719 mg, 4.34 mmol according to general procedure D. The title compound was isolated as a pale yellow oil (196 mg, 0.67 mmol, 23%). δ  1 H NMR (500 MHz, Chloroform-d) δ 7.43 (d, J 8.5 Hz, 2H), 6.86 (d, J 8.5 Hz, 2H), 6.79 (d, J 8.5 Hz, 1H), 6.59 (d, J 2.5 Hz, 1H), 6.51 (dd, J 8.5 &amp; 2.5 Hz, 1H), 6.00 (s, 2H); 
     
       
         
         
             
             
         
       
     
     1.1 General Method E &amp;F 
     A flask charged with the 4-bromo-diarylether (1 equiv.), bispinocolatodiborane (1.1 equiv.), KOAc (3 equiv.) and Pd(dppf)Cl 2  (3 mol %) was flushed with nitrogen. DMF (2.00 mL) was added and the reaction was stirred at 80° C. for 18 hours. After cooling the solution to room temperature, 3-iodotetrahydroquinoline (2 equiv.), PdCl 2 (dppf) (3 mol %) and Na 2 CO 3  (2M, 5 equiv.) were added and the mixture was stirred at 80° C. under nitrogen for a further 24 hours. The solution was cooled to room temperature, the product was extracted with Et 2 O (15.0 mL). The organic layers were combined and washed with H 2 O (15.0 mL), brine and dried over MgSO 4  and concentrated in vacuo. This was followed by purification by silica gel chromatography (ethyl acetate/petroleum ether). 
     2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E&amp;F from 3-iodo-5,6,7,8-tetrahydroquinolin-4(1H)-one (260 mg, 0.9 mmol) and 4-bromo(4-trifluromethoxyphenoxy)phenyl (200 mg, 0.6 mmol). The title compound was isolated as colourless solid (38 mg, 0.09 mmol, 15%).  1 H NMR (500 MHz, DMSO) δ 11.07 (s, 1H), 7.40 (d, J=8.5 Hz, 2H), 7.19 (d, J=8.6 Hz, 2H), 7.13 (d, J=9.0 Hz, 2H), 7.02 (d, J=8.5 Hz, 2H), 2.54 (t, J=6.0 Hz, 2H, H-8), 2.28 (t, J=5.9 Hz, 2H), 2.07 (s, 3H), 1.71 (m, 2H), 1.65 (m, 2H); M/Z (ESI+); 416.15 (Found MH + , 416.1492 C 23 H 20 F 3 NO 3  requires 416.1473). 
     3(4-(4-trifluoromethoxyphenoxy)phenyl)-2,6-dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E&amp;F from 3-iodo-2,6-dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (270 mg, 0.9 mmol) and 4-bromo(4-trifluromethoxyphenoxy)phenyl (200 mg, 0.6 mmol). The title compound was isolated as colourless solid (40 mg, 0.09 mmol, 15%).  1 H NMR (500 MHz, CDCl 3 /MeOD) δ 6.86 (d, J=8.3 Hz, 4H), 6.79-6.64 (m, 4H), 2.43 (dd, J=17.5, 4.9 Hz, 1H), 2.37 (s, 2H), 1.81 (s, 3H), 1.70-1.54 (m, 2H), 1.45 (m, 1H), 1.09 (dt, J=20.7, 10.5 Hz, 1H), 0.76 (d, J=6.6 Hz, 3H); M/Z (ESI+); 452.14 (Found MNa + ; 452.1446 C 24 H 22 F 3 NO 3  requires 452.1444). 
     3(4-(4-trifluoromethoxyphenoxy)phenyl)-2,7-dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E&amp;F from 3-iodo-2,7-dimethyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (120 mg, 0.4 mmol) and 4-bromo(4-trifluromethoxyphenoxy)phenyl (87 mg, 0.27 mmol). The title compound was isolated as colourless solid (30 mg, 0.07 mmol, 26%).  1 H NMR (400 MHz, DMSO) δ 10.90 (s, 1H), 7.41 (d, J=8.5 Hz, 2H), 7.20 (d, J=7.9 Hz, 2H), 7.14 (d, J=8.5 Hz, 2H), 7.03 (d, J=7.9 Hz, 2H), 2.61 (m, 2H), 2.20 (dd, J=16.4, 9.6 Hz, 2H), 2.08 (s, 3H), 1.81 (m, 2H), 1.24 (s, 1H), 1.04 (d, J=5.9 Hz, 3H); M/Z (ESI+); 452.14 (Found MNa + ; 452.1446 C 24 H 22 F 3 NO 3  requires 452.1444). 
     6-Ethyl-3-(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E&amp;F from 3-iodo-2-methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one (300 mg, 0.84 mmol) and 4-bromo-(4-trifluromethoxyphenoxy)phenyl (185 mg, 0.56 mmol). The title compound was afforded as a colourless solid. (20 mg, 0.04 mmol, 7%).  1 H NMR (500 MHz, TFA) δ 7.39 (d, J=7.7 Hz, 4H), 7.34 (d, J=7.1 Hz, 2H), 7.24 (d, J=8.5 Hz, 2H), 3.32 (d, J=14.9 Hz, 2H), 3.21 (dd, J=13.8, 5.6 Hz, 1H), 2.89 (dd, J=18.0, 9.6 Hz, 1H), 2.73 (dd, J=15.3, 6.9 Hz, 1H), 2.57 (s, 3H), 2.52 (d, J=13.5 Hz, 1H), 2.07 (d, J=16.0 Hz, 1H, H-7b); M/Z (ESI+); 484.14 (Found MH +  484.1358, C 24 H 19 F 6 NO 3  requires 484.1342). 
     7-Ethyl-2-methyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E&amp;F from 7-ethyl-2-methylquinolin-4(1H)-one (170 mg, 0.54 mmol) and 4-bromo-(4-trifluromethoxyphenoxy)phenyl (120 mg, 0.36 mmol). The title compound was isolated as a colourless solid (17 mg, 0.04 mmol, 11%).  1 H NMR (500 MHz, CDCl 3 ) δ 11.50 (s, 1H), 7.16 (dd, J=15.3, 8.2 Hz, 4H), 6.94 (dd, J=16.6, 8.3 Hz, 4H), 2.78 (d, J=16.1 Hz, 1H), 2.60 (d, J=21.4 Hz, 1H), 2.39 (s, 1H), 2.13 (dd, J=15.8, 10.8 Hz, 1H), 1.96 (s, 3H), 1.59 (s, 1H), 1.43-1.32 (m, 2H), 1.32-1.18 (m, 2H), 0.94 (t, J=7.2 Hz, 3H); M/Z (ESI+); 444.18 (Found MH + ; 444.1784, C 25 H 24 F 3 NO 3  requires 444.1781). 
     7-trifluromethyl-2-methyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure x from 7-trifluormethyl-2-methylquinolin-4(1H)-one (360 mg, 0.99 mmol) and 4-bromo-(4-trifluromethoxyphenoxy)phenyl (220 mg, 0.66 mmol). The title compound was isolated as a colourless solid (95 mg, 0.20 mmol, 30%). M/Z (ESI+); 484.14 (Found MH+484.1358, C 24 H 19 F 6 NO 3  requires 484.1342). 
     3-[4-(2H-1,3-benzodioxol-5-yloxy)phenyl]-2-methyl-5,6,7,8-tetrahydro-1H-quinolin-4-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 5-(4-bromophenoxy)-2H-1,3-benzodioxole (200 mg, 0.68 mmol) and 3-iodo-5,6,7,8-tetrahydroquinolin-4(1H)-one (288 mg, 1.02 mmol). The title compound was isolated as a pale grey solid (40 mg, 0.11 mmol, 16%). HPLC; 3.28 min (86%); δ  1 H NMR (500 MHz, TFA) δ 7.35 (d, J 8.5 Hz, 2H), 7.31-7.29 (m, 3H), 6.98 (s, 1H), 6.79 (s, 1H), 6.10 (s, 2H), 3.09 (t, J 5.0 Hz, 2H), 2.90 (t, J 5.0 Hz, 2H), 2.52 (s, 3H), 2.11-2.05 (m, 4H); M/Z (ESI); 375.1563, (C 23 H 21 NO 4  requires 375.1471). 
     
       
         
         
             
             
         
       
     
     1.2 General Method E &amp;F 
     A flask charged with the 4-bromo-diarylether (1 equiv.), bispinocolatodiborane (1.1 equiv.), KOAc (3 equiv.) and Pd(dppf)Cl 2  (3 mol %) was flushed with nitrogen. DMF (2.00 mL) was added and the reaction was stirred at 80° C. for 18 hours. After cooling the solution to room temperature, 3-iodotetrahydroquinoline (2 equiv.), PdCl 2 (dppf) (3 mol %) and Na 2 CO 3  (2M, 5 equiv.) were added and the mixture was stirred at 80° C. under nitrogen for a further 24 hours. The solution was cooled to room temperature, the product was extracted with Et 2 O (15.0 mL). The organic layers were combined and washed with H 2 O (15.0 mL), brine and dried over MgSO 4  and concentrated in vacuo. This was followed by purification by silica gel chromatography (ethyl acetate/petroleum ether). 
     4-ethoxy-2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5,6,7,8-tetrahydro quinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 1-Bromo-4-(4-(trifluoromethoxy)phenoxy)benzene (100 mg, 0.30 mmol) according to general procedure E&amp;F, to afford the title compound as a colourless gum/viscous oil (30 mg, 0.07 mmol, 23%).  1 H NMR (500 MHz, Acetone) δ 7.28 (d, J=8.7 Hz, 2H), 7.26 (d, J=9.1 Hz, 2H), 7.09 (d, J=9.1 Hz, 2H), 7.07 (d, J=8.7, 2H), 3.52 (q, J=7.0 Hz, 2H), 2.85 (t, J=6.5 Hz, 2H), 2.78 (t, J=6.2 Hz, 2H), 2.26 (s, 3H), 1.89-1.81 (m, 2H), 1.81-1.72 (m, 2H), 0.93 (t, J=7.0 Hz, 3H); M/Z (ESI+); 444.18 (Found MH + , 444.1792 C 25 H 24 F 3 NO 3  requires 444.1781). 
     Methyl 4-(4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenoxy)benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from methyl 4-(4-bromophenoxy)benzoate (150 mg, 0.49 mmol) according to general procedure E&amp;F. The title compound was isolated as colourless microcrystals (56 mg, 0.13 mmol, 27%).  1 H NMR (500 MHz, CDCl 3 ) δ 8.03 (d, J=8.7 Hz, 2H), 7.29 (d, J=8.4 Hz, 2H), 7.11 (d, J=8.4 Hz, 2H), 7.03 (d, J=8.7 Hz, 2H), 3.90 (s, 3H), 3.51 (q, J=7.0 Hz, 2H), 2.91 (t, J=6.2 Hz, 2H), 2.72 (t, J=6.0 Hz, 2H), 2.32 (s, 3H), 1.91-1.84 (m, 2H), 1.83-1.76 (m, 2H), 1.04 (t, J=7.0 Hz, 3H); M/Z; 418.20 (ESI+); 418.20 (Found MH + , 418.2037 C 26 H 27 NO 4  requires 418.2018). 
     Methyl 4-((5-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)pyridin-2-yl)oxy) benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from methyl 3-((5-bromopyridin-2-yl)oxy)benzoate (100 mg, 0.33 mmol) according to general procedure E&amp;F. The title compound was isolated as a colourless gum/semisolid (30 mg, 0.07 mmol, 21%). 1H NMR (500 MHz, CDCl 3 ) δ 8.13 (d, J=2.3 Hz, 1H, H-6′), 8.10 (d, J=8.7 Hz, 2H), 7.67 (dd, J=8.4, 2.4 Hz, 1H, H-4′), 7.24 (d, J=8.7 Hz, 2H), 7.05 (d, J=8.4 Hz, 1H), 3.91 (s, 3H), 3.53 (q, J=7.0 Hz, 2H), 2.92 (t, J=6.3 Hz, 2H), 2.71 (t, J=6.2 Hz, 2H), 1.06 (t, J=7.0 Hz, 3H); M/Z (ESI+); 419.20 (Found MH + , 419.1993 C 25 H 26 N 2 O 4  requires 419.1970). 
     Methyl 3-(4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenoxy)benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from methyl 3-(4-bromophenoxy)benzoate (150 mg, 0.49 mmol) according to general procedure E&amp;F. The title compound was isolated as colourless crystals (50 mg, 0.12 mmol, 25%).  1 H NMR (500 MHz, CDCl 3 ) δ 7.73 (d, J=7.7 Hz, 1H), 7.65-7.60 (m, 1H), 7.37 (t, J=7.9 Hz, 1H), 7.19 (m, 3H), 7.00 (d, J=8.6 Hz, 2H), 3.83 (s, J=, 3H), 3.45 (q, J=7.0 Hz, 2H), 2.85 (t, J=6.3 Hz, 2H), 2.65 (t, J=6.2 Hz, 2H), 2.26 (s, 3H), 1.88-1.78 (m, 2H), 1.76-1.67 (m, 2H), 0.99 (t, J=7.0 Hz, 3H); M/Z (ESI+); 418.20 (Found MH +  418.2030, C 26 H 27 NO 4  requires 418.2018). 
     Formation of: 3-(4-(4-chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 1-bromo-4-(4-chlorophenoxy)benzene (70 mg, 0.24 mmol) according to general procedure E&amp;F. The title compound was isolated as colourless oil (20 mg, 0.05 mmol, 27%).  1 H NMR (500 MHz, CDCl 3 ) δ 7.25 (d, J=8.9 Hz, 2H), 7.17 (d, J=8.7 Hz, 2H), 6.98 (d, J=8.7 Hz, 2H), 6.93 (d, J=8.9 Hz, 2H), 3.45 (q, J=7.0 Hz, 2H), 2.89 (t, J=6.3 Hz, 2H), 2.65 (t, J=6.1 Hz, 2H), 2.28 (s, 3H), 1.90-1.61 (m, 4H), 0.98 (t, J=7.0 Hz, 3H); M/Z (ESI+); 394.16 (Found MH+394.1575, C 24 H 24 ClNO 2  requires 394.1568). 
     1.3 General Method G 
     To a solution of the 4-ethoxy-3-(diaryl ether)-hydroxyquinolone (1 equiv.) in acetic acid (2 mL mmol −1 ) was added hydrogen bromide (&gt;48% w/v (aq)) (1 mL mmol −1 ). The reaction mixture was then heated to 90° C. and left to reflux for 72 hours. The reaction mixture was neutralised with sodium hydroxide (2 M, 30.0 mL) and precipitate formed. The reaction mixture was then filtered to afford the title compound and purified. 
     Methyl 3-((5-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)pyridin-2-yl)oxy) benzoate 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from methyl 4-((5-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)pyridin-2-yl)oxy) benzoate (30 mg, 0.07 mmol) according to general procedure G. The title compound was isolated as colourless semi solid (13 mg, 0.03 mmol, 45%).  1 H NMR (500 MHz, DMSO) δ 12.83 (s, 1H, NH), 11.03 (s, 1H, CO 2 H), 8.00 (d, J=8.7 Hz, 2H), 7.99 (s, 1H) 7.73 (dd, J=8.4, 2.4 Hz, 1H), 7.24 (d, J=8.7 Hz, 2H), 7.12 (d, J=8.4 Hz, 1H), 2.56 (t, J=5.8 Hz, 2H), 2.30 (t, J=5.8 Hz, 2H), 2.11 (s, 3H), 1.82-1.51 (m, 4H); M/Z (ESI+); 377.15 (Found MH + , 377.1497 C 22 H 20 N 2 O 4  requires 377.1496). 
     4-(4-(2-methyl-4-oxo-1,4,5,6,7,8-hexahydroquinolin-3-yl)phenoxy)benzoic acid 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from methyl 4-(4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenoxy)benzoate (50 mg, 0.17 mmol) according to general procedure G. The title compound was isolated as colourless crystals (33 mg, 0.09 mmol, 48%).  1 H NMR (500 MHz, DMSO) δ 13.79 (s, 1H), 12.80 (s (b), 1H), 7.99 (d, J=8.8 Hz, 2H), 7.36 (d, J=8.7 Hz, 2H), 7.24 (d, J=8.7 Hz, 2H), 7.14 (d, J=8.8 Hz, 2H), 2.92 (t, J=5.1 Hz, 2H), 2.62 (t, J=5.0 Hz, 2H), 2.31 (s, 3H), 1.90-1.76 (m, 4H); M/Z (ESI+); 376.16 (Found MH + , 376.1550, C 23 H 21 NO 4  requires 376.1543). 
     3-(4-(2-methyl-4-oxo-1,4,5,6,7,8-hexahydroquinolin-3-yl)phenoxy)benzoic acid 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3 methyl 3-(4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenoxy)benzoate (50 mg, 0.17 mmol) according to general procedure G. The title compound was isolated as colourless crystals (7 mg, 0.02 mmol, 12%).  1 H NMR (500 MHz, DMSO) δ 13.00 (s, 1H), 11.31 (s, 1H), 7.70 (d, J=7.9 Hz, 1H), 7.52 (t, J=7.9 Hz, 1H), 7.48 (dd, J=2.2, 1.6 Hz, 1H), 7.31 (dd, J=7.9, 1.6 Hz, 1H), 7.21 (d, J=8.6 Hz, 2H), 7.04 (d, J=8.6 Hz, 2H), 2.58 (t, J=5.8 Hz, 2H), 2.32 (t, J=5.8 Hz, 2H), 2.09 (s, 3H), 1.76-1.59 (m, 4H); M/Z (ESI+); 376.15 (Found MH +  376.1547, C 23 H 21 NO 4  requires 376.1543). 
     3-(4-(4-chlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-(4-(4-chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline (20 mg, 0.5 mmol) according to general procedure G. The title compound was isolated as colourless solid (18 mg, 0.05 mmol, 95%).  1 H NMR (500 MHz, DMSO) δ 10.99 (s, 1H), 7.44 (d, J=8.9 Hz, 2H), 7.18 (d, J=8.6 Hz, 2H), 7.05 (d, J=8.9 Hz, 2H), 7.04 (d, J=8.6 Hz, 2H), 2.56 (t, J=5.3 Hz, 2H), 2.29 (t, J=5.3 Hz, 2H), 2.07 (s, 3H), 1.78-1.55 (m, 4H); M/Z (ESI+); 366.13 (Found MH +  366.1262, C 22 H 21 ClNO 2  requires 366.1253). 
     
       
         
         
             
             
         
       
     
     
       
         
         
             
             
         
       
     
     4-ethoxy-3-iodo-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     A suspension of 4(1H), 3-iodo-2-methyl, 5,6,7,8-tetrahydro-quinolinone (2.20 g, 7.61 mmol) and Potassium carbonate (2.10 g, 15.2 mmol) in DMF (20.0 mL) was heated to 50° C. and stirred for 45 minutes. The reaction mixture was removed from the heat and ethyl iodide (0.89 mL, 11.4 mmol) was added dropwise. The reaction mixture was then heated to 50° C. and stirred for a further 18 hours. Formation of a yellow emulsion was observed. The reaction mixture was then quenched with water (40.0 mL). The organic phase was extracted using the polar extraction technique (ethyl acetate, 3×40.0 mL), and the resulting organic layers were combined and dried over MgSO 4  and concentrated in vacuo to afford the title compound as an orange oil. (2.00 g, 6.32 mmol, 83%). δ H NMR (500 MHz, Chloroform-d); δ 3.96 (q, J=7.0 Hz, 2H), 2.84 (t, J=6.3 Hz, 2H), 2.74 (t, J=6.3 Hz, 2H), 2.71 (s, 3H), 1.89-1.82 (m, 2H), 1.78-1.72 (m, 2H), 1.49 (t, J=7.0 Hz, 3H); M/Z (ESI+); 318.04 (Found MH + , 318.0350, C 12 H 17 INO requires 318.0349). 
     
       
         
         
             
             
         
       
     
     4-(4-Ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol 
     
       
         
         
             
             
         
       
     
     To a nitrogen flushed flask charged with 4-ethoxy-3-iodo-2-methyl-5,6,7,8-tetrahydroquinoline (400 mg, 1.26 mmol), 4 hydroxybenzene boronic acid (260 mg, 1.89 mmol) and palladium tetra(triphenylphosphine) (73 mg, 0.06 mmol) was added degassed DMF (10 mL). Potassium carbonate (aq) (3 mL, 2 M) was added and the reaction mixture brought up to 80° C. and stirred for 3 hours. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). The organic phase was then extracted using ethyl acetate (3×20 mL). The organic phases were combined and washed with water (3×20 mL) and then dried with brine (1×10 mL) and MgSO 4 , before concentration in vacuo. The resulting reddish brown solid was then recrystallized in ethyl acetate. To yield the title compound as a colourless solid (220 mg, 0.78 mmol, 61%).  1 H NMR (500 MHz, MeOD) δ 7.07 (d, J=8.6 Hz, 2H), 6.86 (d, J=8.6 Hz, 2H), 3.51 (q, J=7.0 Hz, 2H), 2.83 (t, J=6.3 Hz, 2H), 2.72 (t, J=6.1 Hz, 2H), 2.23 (s, 3H), 1.95-1.72 (m, 4H), 1.00 (t, J=7.0 Hz, 3H); M/Z (ESI+); 284.17 (Found MH +  284.1664, C 18 H 21 NO 2  requires 284.1651). 
     4-ethoxy-2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     A solution of 4-ethoxy, 3-iodo, 2-methyl, 5,6,7,8-tetrahydro, quinolone (1.00 g, 3.16 mmol), 4-phenoxy phenyl boronic acid (1.01 g, 4.73 mmol), Palladium (II) tetra(tri-phenyl-phosphine) (0.18 g, 0.16 mmol) and dipotassium carbonate (2.00 M, 6.40 mL) dissolved in degassed DMF (20.0 mL) was heated to 85° C. and stirred for 12 hours. Observed colour change from yellow to black. The reaction mixture was allowed to cool to room temperature before dilution with ethyl acetate (15.0 mL). The organic layer was extracted using polar extraction technique, before being collected and dried over MgSO 4 . The solution was then concentration in vacuo to afford the title compound as colourless fine needles (0.45 g, 1.25 mmol, 40%). δ H NMR (126 MHz, Chloroform-d); δ 7.35 (t, J=7.6 Hz, 2H), 7.23 (d, J=8.5 Hz, 2H), 7.11 (t, J=7.6 Hz, 1H), 7.05 (d, 4H) 3.42 (q, J=7.0 Hz, 2H), 2.82 (t, J=6.4 Hz, 2H), 2.62 (t, J=6.3 Hz, 2H), 2.23 (s, 3H), 1.80-1.74 (m, 2H), 1.73-1.67 (m, 2H), 1.49 (t, J=7.0 Hz, 3H); M/Z (ESI+); 360.20 (Found MH + , 360.1963, C 24 H 26 NO 2  requires 360.1958). 
     
       
         
         
             
             
         
       
     
     General Method C 
     Copper (II) acetate (1 equiv.), triethylamine (5 equiv.), and pyridine (5 equiv.) was added to a solution of the boronic acid (1.5 equiv.) and phenol (1 equiv.) in dichloromethane (10 mL mmol −1 ) over heat-activated 4 Å molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HCl (0.5 M, 20 mL mmol −1 ) and filtered through a pad of Celite, followed by repeated washing with water (10 mL mmol −1 ). The organic layer was extracted with brine, dried over magnesium sulphate, and concentrated in vacuo. Purification by silica gel chromatography (ethyl acetate/hexane) afforded the title compound. 
     4-Ethoxy-3-(4-(4-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (60 mg, 0.21 mmol) and 4-fluorobenzene boronic acid (45 mg, 0.31 mmol), according to general procedure C as pink micro crystals (70%, 55 mg, 0.15 mmol).  1 H NMR (500 MHz, Chloroform-d) δ 7.14 (d, J=8.6 Hz, 2H), 6.97 (m, 6H), 3.44 (q, J=7.0 Hz, 2H), 2.87 (t, J=6.2 Hz, 2H), 2.64 (t, J=6.1 Hz, 2H), 2.26 (s, 3H), 1.78 (m, 4H), 0.97 (t, J=7.0 Hz, 3H); M/Z (ESI+); 378.19 (Found MH +  378.1877, C 24 H 24 FNO 2  requires). 
     3-(4-(3-Chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (250 mg, 0.88 mmol) and 3-chlorobenzene boronic acid (205 mg, 1.32 mmol), according to general procedure C as a viscous orange oil ( 78 %, 270 mg, 0.68 mmol). 1H NMR (500 MHz, CDCl 3 ) δ 7.28-7.22 (m, 1H), 7.20 (d, J=8.3 Hz, 2H), 7.02 (d, J=8.3 Hz, 2H), 6.81-6.72 (m, 2H), 6.67 (dd, J=10.2, 2.1 Hz, 1H), 3.44 (q, J=7.0 Hz, 2H), 2.86 (t, J=6.2 Hz, 2H), 2.65 (t, J=6.1 Hz, 2H), 2.26 (s, 3H), 1.82 (m, 2H), 1.77-1.69 (m, 2H), 0.98 (t, J=7.0 Hz, 3H); M/Z (ESI+); 394.16 (Found MH + ; 394.1588, C 24 H 24 ClNO 2  requires 394.1574). 
     4-Ethoxy-2-methyl-3-(4-(4-(trifluoromethyl)phenoxy)phenyl)-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (60 mg, 0.21 mmol) and 4-trifluoromethylbenzene boronic acid (62 mg, 0.29 mmol), according to general procedure C as a viscous orange oil (55%, 47 mg, 0.11 mmol). 1H NMR (500 MHz, CDCl 3 ) δ 7.61 (d, J=8.7 Hz, 2H), 7.28 (d, J=8.5 Hz, 2H), 7.15-7.06 (m, 5H), 3.54 (q, J=7.0 Hz, 2H), 2.98 (t, J=6.3 Hz, 2H), 2.72 (t, J=6.2 Hz, 2H), 2.37 (s, 3H), 1.94-1.85 (m, 2H), 1.84-1.77 (m, 2H), 1.06 (t, J=7.0 Hz, 3H), M/Z (ESI+); 428.18 (Found MH +  428.1842, C 25 H 24 F 3 NO 2  requires 428.1832). 
     4-Ethoxy-3-(4-(3-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (250 mg, 0.88 mmol) and 3-fluorobenzene boronic acid (184 mg, 1.32 mmol), according to general procedure G as a yellow oil (57%, 190 mg, 0.50 mmol).  1 H NMR (500 MHz, CDCl 3 ) δ 7.25 (dd, J=15.0, 8.2 Hz, 1H), 7.18 (d, J=8.6 Hz, 2H), 7.04 (d, J=8.6 Hz, 2H), 6.81-6.75 (m, 2H), 6.69 (dt, J=10.1, 2.3 Hz, 1H), 3.49 (q, J=7.0 Hz, 2H), 3.04 (m, 2H), 2.65 (t, J=6.2 Hz, 2H), 2.39 (s, 3H), 1.87-1.79 (m, 2H), 1.79-1.70 (m, 2H), 1.02 (t, J=7.0 Hz, 3H); M/Z (ESI+); 378.19 (Found MH +  378.1877, C 24 H 24 FNO 2  requires). 
     4-Ethoxy-3-(4-(3,4-dichlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (100 mg, 0.34 mmol) and 3,4-dichlorobenzene boronic acid (93 mg, 0.51 mmol), according to general procedure C as an orange oil (49%, 70 mg, 0.16 mmol).  1 H NMR (300 MHz, CDCl 3 ) δ 7.34 (d, J=8.8 Hz, 1H), 7.20 (dd, J=7.1, 1.6 Hz, 2H), 7.06 (d, J=2.8 Hz, 1H), 7.03-6.97 (m, 2H), 6.85 (dd, J=8.8, 2.8 Hz, 1H), 3.46 (q, J=7.0 Hz, 2H), 2.91 (t, J=6.2 Hz, 2H), 2.65 (t, J=6.1 Hz, 2H), 2.29 (s, 3H), 1.90-1.62 (m, 4H), 0.99 (t, J=7.0 Hz, 3H); M/Z (ESI+); 428.12 (Found MH + ; 428.1202, C 24 H 23 Cl 2 NO 2  requires 428.1184). 
     4-Ethoxy-3-(4-(3-chloro-4-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (250 mg, 0.88 mmol) and 3-chloro-4-fluorophenylboronic acid (230 mg, 1.32 mmol), according to general procedure C. The title compound was collected as a pale orange solid (104 mg, 0.25 mmol, 29%).  1 H NMR (400 MHz, CDCl 3 ) δ 7.26 (d, J=8.2 Hz, 2H), 7.17-7.11 (t, J=8.7 Hz, 1H), 7.09 (dd, J=6.1, 2.9 Hz, 1H), 7.04 (d, J=8.3 Hz, 2H), 6.97-6.91 (m, 1H), 3.50 (dd, J=14.0, 7.0 Hz, 1H), 2.91 (t, J=6.2 Hz, 2H), 2.72 (t, J=5.9 Hz, 2H), 2.31 (s, 3H), 1.95-1.84 (m, 2H), 1.81 (m, 2H), 1.04 (t, J=7.0 Hz, 3H); M/Z (ESI); 412.1489, C 24 H 23 ClFNO 2  requires 411.1401. 
     4-Ethoxy-3-(4-(3-trifluoromethoxyphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (200 mg, 0.71 mmol) and 3-trifluoromethoxyphenylboronic acid (218 mg, 1.06 mmol) according to general procedure C. The title compound was collected as a purple/brown oil (132 mg, 0.32 mmol, 42%);  1 H NMR (400 MHz, CDCl 3 ) δ 7.29 (t, J=8.3 Hz, 1H), 7.21 (d, J=8.3 Hz, 2H), 7.03 (d, J=8.2 Hz, 2H), 6.90 (d, J=8.2 Hz, 2H), 6.81 (s, 1H), 3.44 (dd, J=14.0, 7.0 Hz, 2H), 2.84 (t, J=6.2 Hz, 2H), 2.65 (t, J=6.0 Hz, 2H), 2.25 (s, 3H), 1.86-1.78 (m, 2H), 1.74 (dd, J=10.2, 4.6 Hz, 2H), 0.97 (t, J=7.0 Hz, 3H); M/Z (ESI); 444.1786, C 25 H 25 F 3 NO 3  requires 444.1781. 
     4-Ethoxy-3-(4-(3-trifluoromethylphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (300 mg, 1.06 mmol) and 3-trifluoromethylphenyl boronic acid (302 mg, 1.59 mmol) according to general procedure C. The title compound was collected as a yellow oil (198 mg, 0.46 mmol, 44%).  1 H NMR (400 MHz, CDCl 3 ) δ 7.44-7.38 (m, 1H), 7.32 (d, J=7.8 Hz, 1H), 7.17 (s, 2H), 7.12 (d, J=8.3 Hz, 2H), 7.01 (d, J=8.4 Hz, 2H), 3.45 (q, J=7.0 Hz, 2H), 2.85 (t, J=6.0 Hz, 2H), 2.62 (t, J=5.7 Hz, 2H), 2.25 (s, 3H), 1.73 (m, 4H), 1.00 (t, J=7.0 Hz, 3H); M/Z (ESI); 427.1852, C 25 H 24 F 3 NO 2  requires 427.1759. 
     3-[4-(3,5-dichlorophenoxy)phenyl]-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from from 4-(4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinolin-3-yl)phenol (250 mg, 0.88 mmol) and 3,5-dichlorophenylboronic acid (278 mg, 1.32 mmol according to general procedure C. The title compound was collected as a yellow solid (50 mg, 0.12 mmol, 13%). δ  1 H NMR (500 MHz, Chloroform-d) δ 7.34-7.32 (m, 2H), 7.13-7.11 (m, 3H), 6.93 (d, J=1.8 Hz, 2H), 3.54 (q, J=7.0 Hz, 2H), 2.94 (t, J=6.1 Hz, 2H), 2.75 (t, J=6.3 Hz), 2.39 (s, 3H), 1.95-1.81 (m, 4H), 1.08 (t, J=7.0 Hz, 3H); M/Z (ESI); 428.1194, C 24 H 24 Cl 2 NO 2  requires 428.1179. 
     
       
         
         
             
             
         
       
     
     1.4 General Method D 
     To a solution of the 4-ethoxy-3-(diaryl ether)-hydroxyquinoline (1 equiv.) in acetic acid (2 mL mmol −1 ) was added hydrogen bromide (&gt;48% w/v (aq)) (1 mL mmol −1 ). The reaction mixture was then heated to 90° C. and left to reflux for 72 hours. The reaction mixture was neutralised with sodium hydroxide (2 M, 30.0 mL) and precipitate formed. The reaction mixture was then filtered to afford the title compound and purified. 
     Formation of 2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy,3-(4-phenoxy, benzene),2-methy,5,6,7,8-hydroquinolone (0.43 g, 1.20 mmol) following general procedure D to afford the title compound as colourless microcrystals (0.39 g, 1.20 mmol, 99%).  1 H NMR (500 MHz, DMSO-d 6 ); δ 7.38 (t, J=7.9 Hz, 2H, H-3″ &amp; 5″), 7.17 (d, J=8.5 Hz, 2H), 7.14 (t, J=7.4 Hz, 1H), 7.05 (d, J=7.9 Hz, 2H), 6.98 (d, J=8.5 Hz, 2H), 2.56 (t, J=5.9 Hz, 2H), 2.30 (t, J=6.1 Hz, 2H), 2.08 (s, 3H), 1.75-1.68 (m, 2H), 1.68-1.62 (m, 2HM/Z (ESI+); 332.17 (Found MH + , 332.1673, C 22 H 21 NO 2  requires 332.1650). 
     3-(4-(4-Fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy-3-(4-(4-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (45 mg, 0.12 mmol) according to general procedure D. The title compound was isolated as colourless solid (25 mg, 0.07 mmol, 60%).  1 H NMR (500 MHz, DMSO) δ 7.25 (t, J=8.7 Hz, 2H), 7.17 (d, J=8.5 Hz, 2H), 7.11 (dd, J=8.9, 4.5 Hz, 2H), 6.96 (d, J=8.5 Hz, 2H), 2.59-2.53 (m, 2H), 2.30 (t, J=5.2 Hz, 2H), 2.08 (s, 3H), 1.72 (m, 2H), 1.66 (m, 2H); M/Z (ESI+); 350.16 (Found MH +  350.1562, C 22 H 20 FNO 2  requires 350.1550). 
     3-(4-(3-Chlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-(4-(3-chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline (200 mg, 0.51 mmol) according to general procedure D. The title compound was isolated as colourless solid (120 mg, 0.33 mmol, 66%).  1 H NMR (500 MHz, DMSO) δ 11.71 (s, 1H), 7.44 (t, J=8.2 Hz, 1H), 7.25 (d, J=8.6 Hz, 2H), 7.22 (ddd, J=8.0, 1.9, 0.8 Hz, 1H), 7.10 (t, J=2.0 Hz, 1H), 7.09 (d, J=8.6 Hz, 2H), 7.03 (ddd, J=8.2, 2.3, 0.6, 1H), 2.65 (t, J=5.9 Hz, 2H), 2.39 (t, J=5.2 Hz, 2H), 2.14 (s, 3H), 1.84-1.59 (m, 4H); M/Z (ESI+); 366.13 (Found MH +  366.1262, C 22 H 20 ClNO 2  requires 366.1255). 
     2-Methyl-3-(4-(4-(trifluoromethyl)phenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy-2-methyl-3-(4-(4-(trifluoromethyl)phenoxy)phenyl)-5,6,7,8-tetrahydroquinoline (47 mg, 0.12 mmol) according to general procedure D. The title compound was isolated as colourless solid (25 mg, 0.07 mmol, 60%).  1 H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 7.77 (d, J=8.6 Hz, 2H), 7.26 (d, J=8.6 Hz, 2H), 7.19 (d, J=8.6 Hz, 2H), 7.12 (d, J=8.6 Hz, 2H), 2.59 (t, J=5.8 Hz, 2H), 2.33 (t, J=6.4 Hz, 2H), 2.12 (s, 3H), 1.73 (m, 2H), 1.70-1.64 (m, 2H); M/Z (ESI+); 400.15 (Found MH + ; 400.1528, C 23 H 20 F 3 NO 2  requires 400.1519). 
     3-(4-(3-Fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy-3-(4-(3-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (170 mg, 0.45 mmol) according to general procedure D. The title compound was isolated as colourless solid (110 mg, 0.31 mmol, 70%).  1 H NMR (500 MHz, DMSO) δ 7.47 (dt, J=8.6, 7.1 Hz, 1H), 7.31 (d, J=8.7 Hz, 2H), 7.17 (d, J=8.7 Hz, 2H), 7.02 (tdd, J=8.5, 2.3, 0.7 Hz, 1H), 6.97-6.88 (m, 2H), 2.83 (t, J=6.1 Hz, 2H), 2.54 (t, J=5.8 Hz, 2H), 2.25 (s, 3H), 1.87-1.69 (m, 4H); M/Z (ESI+); 350.16 (Found MH + ; 350.1569, C 22 H 21 FNO 2  requires 350.1556). 
     3-(4-(3,4-Dichlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-Ethoxy-3-(4-(3-trifluoromethoxyphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (100 mg, 0.23 mmol) according to general procedure D. The title compound was isolated as colourless solid (72 mg, 0.16 mmol, 76%).  1 H NMR (501 MHz, DMSO) δ 11.27 (s, 1H, NH), 7.51 (t, J=8.3 Hz, 1H), 7.22 (d, J=8.5 Hz, 2H), 7.12 (d, J=7.6 Hz, 1H), 7.07 (d, J=8.5 Hz, 2H), 7.03 (dd, J=8.6, 1.7 Hz, 1H), 7.00 (s, 1H), 2.58 (t, J=5.2 Hz, 2H), 2.32 (t, J=6.2 Hz, 2H), 2.09 (s, 3H), 1.76-1.69 (m, 2H), 1.69-1.61 (m, 2H); M/Z (ESI+); 416.15 (Found MH + ; 416.1469, C 23 H 21 F 3 NO 3  requires 416.1468). 
     3-(4-(3,4-Dichlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-Ethoxy-3-(4-(3-trifluoromethylphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (193 mg, 0.45 mmol) according to general procedure D. The title compound was isolated as colourless solid (174 mg, 0.44 mmol, 96%). 1 H NMR (501 MHz, DMSO) δ 11.15 (s, 1H), 7.63 (t, J=8.6 Hz, 1H), 7.48 (d, J=8.2 Hz, 1H), 7.30 (s, 2H), 7.22 (d, J=8.4 Hz, 2H), 7.07 (d, J=8.4 Hz, 2H), 2.56 (t, J=3.3 Hz, 2H), 2.30 (t, J=5.3 Hz, 2H), 2.08 (s, 3H), 1.71 (dd, J=6.0, 4.6 Hz, 2H), 1.68-1.60 (m, 2H); M/Z (ESI+); 400.15 (Found MH + ; 400.1519 requires C 23 H 21 F 3 NO 2  requires 400.1519). 
     3-(4-(3,4-Dichlorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy-3-(4-(3,4-dichloro phenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (60 mg, 0.15 mmol) according to general procedure D. The title compound was isolated as colourless solid (35 mg, 0.08 mmol, 59%).  1 H NMR (500 MHz, DMSO) δ 10.95 (s, 1H), 7.66 (d, J=8.5 Hz, 1H), 7.31 (s, 1H), 7.23 (d, J=8.2 Hz, 2H), 7.08 (d, J=7.6 Hz, 2H), 7.04 (d, J=8.9 Hz, 1H), 2.55 (m, 2H), 2.30 (m, Hz, 2H), 2.09 (s, 3H), 1.72 (m, 2H), 1.66 (m, 2H); M/Z (ESI+); 400.09 (Found MH + ; 400.0881, C 22 H 20 Cl 2 NO 2  requires 400.0866). 
     3-[4-(3-chloro-4-fluorophenoxy)phenyl]-2-methyl-5,6,7,8-tetrahydro-1H-quinolin-4-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-Ethoxy-3-(4-(3-chloro-4-fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinoline (90 mg, 2.18 mmol) The title compound was isolated as a pale grey precipitate (55 mg, 0.14 mmol, 66%). 1H NMR (500 MHz, TFA) δ 7.39 (d, J 8.6 Hz, 2H), 7.32 (d, J 8.5 Hz, 2H), 7.27-7.24 (m, 2H), 7.12-7.09 (m, 1H), 3.10 (t, J 5.8 Hz, 2H), 2.91 (t, J 5.9 Hz, 2H), 2.54 (s, 3H), 2.15-2.03 (m, 4H); M/Z (ESI); 384.1167, (C 22 H 20 ClFNO 2  requires 384.1161). 
     3-[4-(3,5-dichlorophenoxy)phenyl]-2-methyl-5,6,7,8-tetrahydro-1H-quinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-[4-(3,5-dichlorophenoxy)phenyl]-4-ethoxy-2-methyl-5,6,7,8-tetrahydroquinoline (40 mg, 0.93 mmol) according to general procedure D. The title compound was isolated as colourless solid (31 mg, 0.08 mmol, 83%). δ  1 H NMR (500 MHz, TFA) δ 7.44 (d, J=8.5 Hz, 2H), 7.39 (d, J=8.0 Hz, 2H), 7.30 (s, 1H), 7.10 (s, 2H), 3.12 (t, J=5.5 Hz, 2H), 2.93 (t, J=5.5 Hz, 2H), 2.57 (s, 3H), 2.09-2.00 (m, 4H); M/Z (ESI); 400.0874, C 22 H 20 Cl 2 NO 2  requires 400.0866. 
     
       
         
         
             
             
         
       
     
     General Method A 
     2,2-Dimethyl-1,3-dioxane-4,6-dione (1.5 equiv.) was dissolved in trimethylorthoacetate (2 equiv.) and heated to 115° C. for 2 hrs. The reaction was cooled to allow the addition of the aniline (1 equiv.) before being heated to 115° C. for a further 2 hrs. The reaction mixture was then allowed to cool and was concentrated in vacuo, remaining solvent was washed off with cold methanol. The precipitate was then dissolved in minimum volume of Dowtherm A and refluxed at 250° C. for 1.5 hours. The reaction mixture was allowed to cool and the precipitate filtered followed by washing with hexane to afford the title compound. 
     2-Methyl-1,7-napthyrid-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised using 3-amino pyridine (3.0 g, 32 mmol) following general procedure A. To give the title compound as colourless solid (489 mg, 3.1 mmol, 10%). 1H NMR (500 MHz, CDCl 3 ) δ 8.52 (s, 1H, H-8), 7.72 (d, J=8.0 Hz, 1H, H-5), 7.59-7.31 (m, 1H, H-6), 6.18 (s, 1H, H-3), 2.28 (s, 3H, Me). M/Z (ESI+); (Found MH + ; requires). 
     General Method B 
     2-Methyl-napthyrid-4(1H)-one (1 equiv.) and N-Iodosuccinamide (1.2 equiv.) were dissolved in acetonitrile (5 mL mmol −1 ) and stirred and heated at 80° C. for 3 hours. The reaction mixture was then allowed to cool and the mixture filtered, the precipitate was then washed with water (15 mL) to afford the title compound as a colourless solid. 
     3-Iodo-2-methyl-1,7-napthyrid-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised using 2-Methyl-1,7-napthyrid-4(1H)-one (480 mg, 3.0 mmol) following general procedure B. To give the title compound as colourless solid (740 mg, 2.6 mmol, 86%).  1 H NMR (500 MHz, CDCl 3 ) δ 8.36-7.91 (m, 1H), 7.49 (dd, J=8.4, 1.1 Hz, 1H), 7.18 (dd, J=8.6, 4.2 Hz, 1H), 2.27 (s, 3H). M/Z (ESI+); (Found MH + ; requires). 
     General Method C 
     A suspension of the 4(1H), 3-Iodo-2-methyl-napthyrid-4(1H)-one (1 equiv.) and potassium carbonate (2 equiv.) in DMF (20.0 mL) was heated to 50° C. and stirred for 45 minutes. The reaction mixture was removed from the heat and ethyl iodide (1.5 equiv.) was added dropwise. The reaction mixture was then heated and kept at 50° C. with stirring for a further 18 hrs. Formation of a yellow emulsion was observed. The reaction mixture was then quenched with water (40.0 mL). The organic phase was extracted using the polar extraction technique (ethyl acetate, 3×40.0 mL), and the resulting organic layers were combined and dried over MgSO 4  and concentrated in vacuo to afford the title compound. 
     4-Ethoxy-3-iodo-2-methyl-1,7-napthyridine 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised using, 3-Iodo-2-methyl-napthyrid-4(1H)-one (720 mg, 2.5 mmol) following general procedure C. To give the title compound as brown gum (244 mg, 0.8 mmol, 33%).  1 H NMR (500 MHz, CDCl 3 ) δ 8.87 (dd, J=4.0, 1.5 Hz, 1H), 8.31 (dd, J=8.5, 1.6 Hz, 1H), 7.63 (dd, J=8.5, 4.1 Hz, 1H), 4.84 (q, J=7.0 Hz, 2H), 3.00 (s, 3H), 1.59 (t, J=7.0 Hz, 3); M/Z (ESI+); (Found MH + ; requires). 
     General Method F 
     To a nitrogen flushed flask charged with the 4-Ethoxy-3-iodo-2-methyl-napthyridine (400 mg, 1.26 mmol), 4-hydroxybenzene boronic acid (260 mg, 1.89 mmol) and palladium tetra(triphenylphosphine) (73 mg, 0.06 mmol) was added degassed DMF (10 mL). Potassium carbonate (3 mL, 2 M (aq) ) was added and the reaction mixture brought up to 80° C. and stirred for 3 hours. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). The organic phase was then extracted using ethyl acetate (3×20 mL). The organic phases were combined and washed with water (3×20 mL) and then dried with brine (1×10 mL) and MgSO 4 , before concentration in vacuo. The resulting solid was then recrystallized in ethyl acetate to afford the title compound. 
     4-Ethoxy-3-phenol-2-methyl-1,7-napthyridine 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised using, 4-Ethoxy-3-iodo-2-methyl-1,7-napthyridine (230 mg, 0.73 mmol) following general procedure F. To give the title compound an orange powder (80 mg, 0.8 mmol, 28%). 1H NMR (400 MHz, MeOD) δ 8.78 (dd, J=4.1, 1.4 Hz, 1H), 8.24 (dd, J=8.6, 1.4 Hz, 1H), 7.64 (dd, J=8.6, 4.2 Hz, 1H), 7.08 (d, J=8.5 Hz, 2H), 6.84 (d, J=8.5 Hz, 2H), 4.12 (q, J=7.0 Hz, 2H), 2.39 (s, 3H), 1.05 (t, J=7.0 Hz, 3H); M/Z (ESI+); (Found MH + ; requires). 
     General Method G 
     Copper (II) acetate (1 equiv.), triethylamine (5 equiv.), and pyridine (5 equiv.) was added to a solution of the boronic acid (1.5 equiv.) and phenol (1 equiv.) in dichloromethane (10 mL mmol −1 ) over heat-activated 4 Å molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HCl (0.5 M, 20 mL mmol −1 ) and filtered through a pad of Celite, followed by repeated washing with water (10 mL mmol −1 ). The organic layer was extracted with brine, dried over magnesium sulphate, and concentrated in vacuo. Purification by silica gel chromatography (ethyl acetate/hexane) afforded the title compound. 
     4-Ethyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methyl-1,7-napthyridone 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised using 4-Ethoxy-3-iodo-2-methyl-1,7-napthyridine (70 mg, 0.25 mmol) and 4-trifluoromethoxybenzenboronic acid (79 mg, 0.38 mmol) following general procedure G. To give the title compound as a red crystalline solid (34 mg, 0.08 mmol, 20%). 1H NMR (400 MHz, CDCl 3 ) δ 8.90 (dd, J=4.0, 1.3 Hz, 1H), 8.33 (dd, J=8.5, 1.3 Hz, 1H), 7.61 (dd, J=8.5, 4.1 Hz, 1H), 7.31 (d, J=8.5 Hz, 2H), 7.24 (d, J=8.7 Hz, 2H), 7.13 (d, J=8.7 Hz, 2H), 7.10 (d, J=9.1 Hz, 2H), 4.43 (q, J=7.0 Hz, 2H), 2.54 (s, 3H), 1.19 (t, J=7.0 Hz, 3H); M/Z (ESI+); (Found MH + ; requires). 
     General Method J 
     To a solution of the 4-Ethyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methylnapthyridone (1 equiv.) in acetic acid (2 mL mmol −1 ) was added hydrogen bromide (&gt;48% w/v (aq)) (1 mL mmol −1 ). The reaction mixture was then heated to 90° C. and left to reflux for 72 hours. The reaction mixture was neutralised with sodium hydroxide (2 M, 30.0 mL) and precipitate formed. The reaction mixture was then filtered to afford the title compound. 
     3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methyl-1,7-napthyrid-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-Ethyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methyl-1,7-napthyridone (31 mg, 0.07 mmol). To give the title compound as a colourless solid (13 mg, 0.03 mmol, 45%).  1 H NMR (400 MHz, CDCl 3 ) δ 8.44 (d, J=3.6 Hz, 1H), 7.75 (d, J=8.2 Hz, 1H), 7.36 (dd, J=8.3, 4.1 Hz, 1H), 7.02 (d, J=8.6 Hz, 2H), 6.96 (d, J=8.5 Hz, 2H), 6.83 (d, J=9.2 Hz, 4H), 2.09 (s, 3H); M/Z (ESI+); 413.11 (Found MH + ; 413.1104 C 22 H 15 F 3 N 2 O 3  requires 413.1107). 
     
       
         
         
             
             
         
       
     
     3-phenol-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4(1H)-3-iodo-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (500 mg, 1.73 mmol) and 4-hydroxyphenylboronic acid (318 mg, 2.30 mmol) and palladium tetra(triphenylphosphine) (73 mg, 0.06 mmol) was added degassed DMF (10 mL). Potassium carbonate (aq) (3 mL, 2 M) was added and the reaction mixture brought up to 80° C. and stirred for 3 hours. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). Organics were extracted with ethyl acetate (3×10 mL). The aqueous layer was neutralised using hydrochloric acid (2 M), causing the title compound, a grey precipitate to crash out which was collected by vacuum filtration (150 mg, 0.58 mmol, 44%).  1 H NMR (400 MHz, MeOD) δ 6.91 (d, J=8.6 Hz, 2H), 6.71 (d, J=8.6 Hz, 2H), 2.57 (t, J=6.0 Hz), 2.39 (t, J=5.6 Hz, 2H), 2.03 (s, 3H), 1.77-1.61 (m, 4H); M/Z (ESI); 255.1341 (C 16 H 17 NO 2  requires 255.1259). 
     3-{4-[(2,6-dichloropyridin-4-yl)oxy]phenyl}-2-methyl-5,6,7,8-tetrahydro-1H-quinolin-4-one 
     
       
         
         
             
             
         
       
     
     3-phenol-2-methyl-5,6,7,8-tetrahydroquinolin-4(1H)-one (120 mg, 0.47 mmol) and potassium carbonate (78 mg, 0.56 mmol) were dissolved in DMF (3 mL) and the reaction mixture was stirred for 15 mins. Following this, 2,4,6-Trichloropyridine (86 mg, 0.47 mmol) was added and the mixture was heated to 100° C. and stirred for 18 hours under an inert atmosphere. The reaction mixture was allowed to cool to room temperature and was diluted with water (5 ml). The resulting pale grey precipitate was collected by vacuum filtration, washed with water (5 ml) and dried (118 mg, 0.29 mmol, 63%). δ  1 H NMR (500 MHz, TFA) δ 7.66 (d, J 8.5 Hz, 2H), 7.56 (d, J 8.5 Hz, 2H), 7.44 (s, 2H), 3.10 (t, J 5.0 Hz, 2H), 2.90 (t, J 5.0 Hz, 2H), 2.55 (s, 3H), 2.10-2.08 (m, 4H); M/Z (ESI); 400.0826, (C 21 H 18 Cl 2 N 2 O 2  requires 400.0745). 
     
       
         
         
             
             
         
       
     
     4-Ethoxy-3-(6-chloropyrdin-3-yl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     To a nitrogen flushed flask charged with 4-ethoxy-3-iodo-2-methyl-5,6,7,8-tetrahydroquinoline (1.5 g, 4.7 mmol), 2-chloropyridine-5-boronic acid (1.12 g, 7.1 mmol) and palladium tetra(triphenylphosphine) (271 mg, 0.24 mmol) was added degassed DMF (20 mL). Potassium carbonate (3 mL, 2 M (aq) ) was added and the reaction mixture brought up to 80° C. and stirred for 3 hours. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). The organic phase was then extracted using ethyl acetate (3×20 mL). The organic phases were combined and washed with water (3×20 mL) and then dried with brine (1×10 mL) and MgSO 4 , before concentration in vacuo. The resulting residue was purified by column chromatography (Pet:EtOAc), to yield the title compound as a yellow platelets (330 mg, 1.09 mmol, 23%). HPLC; 2.17 min (100% ref area);  1 H NMR (500 MHz, CDCl 3 ) δ 8.33 (d, J=2.4 Hz, 1H), 7.60 (dd, J=8.2, 2.4 Hz, 1H), 7.44-7.42 (d, J=8.2, 1H), 3.53 (q, J=7.0 Hz, 2H), 2.98 (t, J=6.2 Hz, 2H), 2.72 (t, J=6.2 Hz, 2H), 2.35 (s, 3H), 1.93-1.85 (m, 2H), 1.84-1.76 (m, 2H), 1.06 (t, J=7.0 Hz, 3H); M/Z (ESI+); 303.13 (Found MH + ; 303.1266, C 17 H 19 ClN 2 O requires 303.1259). 
     4-Ethoxy-3-(6-(4-trifluoromethoxyphenoxy)pyridin-3-yl)-2-methyl-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     4-Ethoxy-3-(6-chloropyrdin-3-yl)-2-methyl-5,6,7,8-tetrahydroquinoline (250 mg, 0.82 mmol), 4-trifluoromethoxyphenol (178 mg, 1.0 mmol) and potassium carbonate (276 mg, 1.7 mmol) were dissolved in DMF and refluxed at 110° C. for 24 hrs. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). The organic phase was then extracted using ethyl acetate (3×20 mL). The organic phases were combined and washed with water (3×20 mL) and then dried with brine (1×10 mL) and MgSO 4 , before concentration in vacuo. The resulting residue was purified by reverse phase column chromatography (H 2 O:acetonitrile), to yield the title compound as a yellow oil (75 mg, 0.17 mmol, 20%). 1H NMR (400 MHz, CDCl 3 ) δ 8.03 (d, J=2.2 Hz, 1H), 7.58 (dd, J=8.4, 2.2 Hz, 1H), 7.29-7.07 (m, 4H), 6.95 (d, J=8.4 Hz, 1H), 3.46 (q, J=7.0 Hz, 2H), 2.85 (t, J=6.3 Hz, 2H), 2.64 (t, J=6.1 Hz, 2H), 2.25 (s, 3H), 1.81 (dt, J=12.2, 6.3 Hz, 2H), 1.77-1.68 (m, 2H), 0.99 (t, J=7.0 Hz, 3H); M/Z (ESI+); 445.18 (Found MH + ; 445.1759, C 24 H 23 F 3 N 2 O 3  requires 445.1739). 
     3-(6-(4-Trifluoromethoxyphenoxy)pyridin-3-yl)-2-methyl-5,6,7,8-tetrahydroquinolin-(4)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 4-ethoxy-3-(6-(4-trifluoromethoxyphenoxy)pyridin-3-yl)-2-methyl-5,6,7,8-tetrahydroquinoline (70 mg, 0.15 mmol) according to general procedure J. The title compound was isolated as colourless solid (13 mg, 0.03 mmol, 20%).  1 H NMR (400 MHz, DMSO) δ 11.07 (s, 1H), 7.94 (d, J=2.2 Hz, 1H), 7.70 (dd, J=8.4, 2.4 Hz, 1H), 7.43 (d, J=8.7 Hz, 2H), 7.29 (d, J=9.0 Hz, 2H), 7.09 (d, J=8.4 Hz, 1H), 2.56 (t, J=5.1 Hz, 2H), 2.30 (t, J=5.9 Hz, H), 2.10 (s, 3H), 1.79-1.57 (m, 4H); M/Z (ESI+); 417.14 (Found MH + ; 417.1432, C 22 H 19 F 3 N 2 O 3  requires 417.1421). 
     
       
         
         
             
             
         
       
       
         
         
             
             
         
       
     
     General Method B 
     The 4-hydroxylquinolone (1 equiv.) was dissolved in acetic acid (10.0 mL) under inert conditions. platinum dioxide (5% weight equiv.) was added and a hydrogen balloon was attached. The reaction was left to proceed for 12 hours. The resulting suspension was filtered through a pad of Celite and washed with ethyl acetate (10.0 mL). The filtrate was concentrated in vacuo to afford a yellow/brown oil. Purification by column chromatography (10% methanol in chloroform) afforded the title compound. 
     2-(Methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure B from 2-(methoxycarboxylate)quinolin-4(1H)-one (500 mg, 2.5 mmol). The title compound was isolated as colourless solid (470 mg, 2.4 mmol, %).  1 H NMR (500 MHz, CDCl 3 ) δ 8.89 (s, 1H), 7.07 (s, 1H), 3.95 (s, 3H), 2.74 (t, J=6.1 Hz, 2H), 2.56 (t, J=6.2 Hz, 2H), 1.82 (dt, J=8.0, 6.1 Hz, 1H), 1.79-1.69 (m, 1H); M/Z (ESI+); 208.10 (Found MH + ; 208.0977, C 11 H 13 NO 3  requires 208.0974). 
     1.5 General Method C 
     The tetrahydroquinolin-4(1H)-one (1 equiv.) and N-Iodosuccinamide (1.2 equiv.) were dissolved in acetonitrile (5 mL mmol −1 ) and stirred and heated at 80° C. for 3 hours. The reaction mixture was then allowed to cool and the mixture filtered, the precipitate was then washed with water (15 mL) to afford the title compound as a colourless solid 
     3-Iodo-2-(methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure C from 2-(methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(1H)-one (450 mg, 2.20 mmol). The title compound was isolated as colourless solid (612 mg, 1.8 mmol, 84%).  1 H NMR (400 MHz, DMSO) δ 11.93 (s, 1H), 3.91 (s, 3H), 2.58 (s, 2H), 2.34 (t, 2H), 1.90-1.45 (m, 4H); M/Z (ESI+); 333.99 (Found MH + ; 333.9935, C 11 H 12 INO 3  requires; 333.9935). 
     General Method D 
     A suspension of the 4(1H), 3-iodo-tetrahydroquinolinone (1 equiv.) and potassium carbonate (2 equiv.) in DMF (20.0 mL) was heated to 50° C. and stirred for 45 minutes. The reaction mixture was removed from the heat and ethyl iodide (1.5 equiv.) was added dropwise. The reaction mixture was then heated and kept at 50° C. with stirring for a further 18 hrs. Formation of a yellow emulsion was observed. The reaction mixture was then quenched with water (40.0 mL). The organic phase was extracted using the polar extraction technique (ethyl acetate, 3×40.0 mL), and the resulting organic layers were combined and dried over MgSO 4  and concentrated in vacuo to afford the title compound. 
     4-Ethoxy-3-iodo-2-(methoxycarboxylate)-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure D from 3-iodo-2-(methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(1H)-one (500 mg, 1.5 mmol). The title compound was isolated as colourless crystals (450 mg, 1.25 mmol, 83%).  1 H NMR (300 MHz, CDCl 3 ) δ 3.94 (q, J=7.0 Hz, 2H), 3.90 (s, 3H), 2.84 (t, J=6.4 Hz, 2H), 2.73 (t, J=6.2 Hz, 2H), 1.87-1.64 (m, 4H), 1.43 (t, J=7.0 Hz, 3H); M/Z (ESI+); 362.03 (Found MH + ; 362.0256, C 13 H 16 INO 3  requires 362.0248). 
     1.6 General Method E 
     To a nitrogen flushed flask charged with the 4-ethoxy-3-iodo-tetrahydroquinoline (400 mg, 1.26 mmol), 4-hydroxybenzene boronic acid (260 mg, 1.89 mmol) and palladium tetra(triphenylphosphine) (73 mg, 0.06 mmol) was added degassed DMF (10 mL). Potassium carbonate (3 mL, 2 M (aq) ) was added and the reaction mixture brought up to 80° C. and stirred for 3 hours. The reaction mixture was then cooled to room temperature and diluted with water (10 mL). The organic phase was then extracted using ethyl acetate (3×20 mL). The organic phases were combined and washed with water (3×20 mL) and then dried with brine (1×10 mL) and MgSO 4 , before concentration in vacuo. The resulting solid was then recrystallized in ethyl acetate to afford the title compound. 
     4-(4-Ethoxy--(methoxycarboxylate)-5,6,7,8-tetrahydroquinolin-3-yl)phenol 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure E from 4-ethoxy-3-iodo-2-(methoxycarboxylate)-5,6,7,8-tetrahydro quinoline (400 mg, 1.11 mmol). The title compound was isolated as a solid (200 mg, 0.61 mmol, 55%).  1 H NMR (500 MHz, CDCl 3 ) δ 7.11 (d, J=8.6 Hz, 2H), 6.77 (d, J=8.6 Hz, 2H), 3.60 (s, 3H), 3.43 (q, J=7.0 Hz, 2H), 2.91 (t, J=6.4 Hz, 2H), 2.71 (t, J=6.3 Hz, 2H), 1.82 (m, 2H), 1.78-1.69 (m, 2H), 0.98 (t, J=7.0 Hz, 3H); M/Z (ESI+); 328.16 (Found MH + ; 328.1551, C 19 H 21 NO 4  requires; 328.1543). 
     General Method F 
     Copper (II) acetate (1 equiv.), triethylamine (5 equiv.), and pyridine (5 equiv.) was added to a solution of the boronic acid (1.5 equiv.) and phenol (1 equiv.) in dichloromethane (10 mL mmol −1 ) over heat-activated 4 Å molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HCl (0.5 M, 20 mL mmol −1 ) and filtered through a pad of Celite, followed by repeated washing with water (10 mL mmol −1 ). The organic layer was extracted with brine, dried over magnesium sulphate, and concentrated in vacuo. Purification by silica gel chromatography (ethyl acetate/hexane) afforded the title compound. 
     4-Ethoxy-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-(methoxycarboxylate)-5,6,7,8-tetrahydroquinoline 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure F from 4-(4-ethoxy--(methoxycarboxylate)-5,6,7,8-tetrahydroquinolin-3-yl)phenol (180 mg, 0.55 mmol). The title compound was isolated as a yellow oil (210 mg, 0.43 mmol, 78%).  1 H NMR (500 MHz, CDCl 3 ) δ 7.32 (d, J=8.6 Hz, 2H), 7.22 (d, J=8.6 Hz, 2H), 7.05 (dd, J=8.8, 3.0 Hz, 4H), 3.73 (s, 3H), 3.55 (q, J=7.0 Hz, 2H), 3.05 (t, J=4.7 Hz, 2H), 2.80 (t, J=6.2 Hz, 2H), 1.99-1.88 (m, 2H), 1.88-1.79 (m, 2H), 1.09 (t, J=7.0 Hz, 3H). 
     General Method G 
     To a solution of the 4-ethoxy-3-(diaryl ether)-hydroxyquinoline (1 equiv.) in acetic acid (2 mL mmol −1 ) was added hydrogen bromide (&gt;48% w/v (aq)) (1 mL mmol −1 ). The reaction mixture was then heated to 90° C. and left to reflux for 72 hours. The reaction mixture was neutralised with sodium hydroxide (2 M, 30.0 mL) and precipitate formed. The reaction mixture was then filtered to afford the title compound. 
     3(4-(4-Trifluoromethoxyphenoxy)phenyl)-2-(carboxylate)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised following general procedure G from 4-ethoxy-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-(methoxycarboxylate)-5,6,7,8-tetrahydroquinoline (200 mg, 0.42 mmol). The title compound was isolated as a colourless solid (80 mg, 0.18 mmol, 43%).  1 H NMR (400 MHz, DMSO) δ 7.41 (d, J=8.8 Hz, 2H), 7.21 (d, J=8.3 Hz, 2H), 7.12 (d, J=8.8 Hz, 2H), 7.01 (d, J=8.3 Hz, 2H), 2.64 (t, J=5.6 Hz, 2H), 2.35 (t, J=5.6 Hz, 2H), 1.94-1.33 (m, 4H); M/Z (ESI+); 446.12 (Found MH + ; 446.1207, C 23 H 18 F 3 NO 5  requires 446.1210). 
     3(4-(4-Trifluoromethoxyphenoxy)phenyl)-2-(methylhydroxy)-5,6,7,8-tetrahydroquinolin-4(1H)-one 
     
       
         
         
             
             
         
       
     
     3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-(carboxylate)-5,6,7,8-tetrahydroquinolin-4(1H)-one (80 mg, 0.17 mmol) was dissolved in methanol (5 mL) with the addition of HCl (1 mL, conc.) heated to 80° C. for 24 hours. The reaction mixture was diluted with water (10 mL) and the organics extracted with EtOAc (3×10 mL) before being dried and concentrated in vacuo. The crude material was then dissolved in dry THF under inert atmosphere and cooled to 0° C. Diisobutylaluminium hydride was then added slowly with stirring. After two hours the reaction pH was lowered to 3 through addition of HCl (2M). Dilution of the solution with water caused precipitation. The title compound was isolated as via filtration as a pale yellow solid (38 mg, 0.09 mmol, 55%). 1H NMR (400 MHz, DMSO) δ 11.06 (s, 1H), 7.41 (d, J=8.8 Hz, 2H), 7.25 (d, J=8.6 Hz, 2H), 7.15 (d, J=9.1 Hz, 2H), 7.05 (d, J=8.6 Hz, 2H), 5.53 (s, 1H), 4.25 (s, 2H), 2.67 (t, J=5.6 Hz, 2H), 2.35 (t, J=6.2 Hz, 2H), 1.82-1.56 (m, 4H); M/Z (ESI+); 432.14 (Found MH+; 432.1445, C 23 H 20 F 3 NO 4  requires 432.1423). 
     
       
         
         
             
             
         
       
     
     1,2-dimethyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4-one 
     
       
         
         
             
             
         
       
     
     2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5,6,7,8-tetrahydroquinolin-4(1H)-one (60 mg, 0.14 mmol) was dissolved in DMF (0.1 mL) under Nitrogen. Sodium Hydride (4 mg, 0.17 mmol) was added and the reaction heated to 90° C. for 30 minutes. Methyl iodide (80 mg, 0.56 mmol) was added and the reaction continued for a further 2 hours. Reaction mixture was allowed to cool and organics extracted with ethyl acetate, followed by drying with brine and magnesium sulphate. Organics were concentrated in vacuo and purified by column chromatography (DCM). To give the title compound as a colourless solid (20 mg, 0.04 mmol, 35%).  1 H NMR (400 MHz, DMSO) δ 7.41 (d, J=8.6 Hz, 2H), 7.19-7.08 (m, 4H), 7.06 (d, J=8.5 Hz, 2H), 3.53 (s, 3H), 2.71 (t, J=6.2 Hz, 2H), 2.38 (t, J=6.0 Hz, 2H), 2.19 (s, 3H), 1.75 (d, J=5.7 Hz, 2H), 1.66-1.56 (m, 2H). 
     
       
         
         
             
             
         
       
     
     1,2,3,4,5,6,7,8-Octahydroquinazoline-2,4,dione 
     
       
         
         
             
             
         
       
     
     Urea (0.48 g, 8.0 mmol) and ethyl-2-oxocyclohexancarbonylate (1.0 g, 6.0 mmol) were dissolved in ethanol (10 mL). Sodium methoxide (3 mL, 12.0 mmol) was added and the reaction mixture refluxed at 80° C. for 15 hours. The reaction mixture was allowed to cool and the resulting precipitate was washed with diethyl ether (2×10 mL) to afford the title compound as a white solid. (526 mg 3.17 mmol, 53%).  1 H NMR (501 MHz, DMSO) δ 10.72 (s, 1H), 8.50 (s, 1H), 2.28 (t, J=6.2 Hz, 2H), 2.12 (t, J=6.2 Hz, 2H), 1.69-1.60 (m, 2H), 1.59-1.51 (m, 2H); M/Z (ESI+); 167.08 (Found MH + ; 167.0815, C 8 H 10 N 2 O 2  requires 167.0815). 
     3-(4-Phenoxyphenyl)-1,2,3,4,5,6,7,8-octahydroquinazoline-2,4,dione 
     
       
         
         
             
             
         
       
     
     1,2,3,4,5,6,7,8-Octahydroquinazoline-2,4,dione (300 mg, 1.8 mmol), 4phenoxyphenyl boronic acid (600 mg, 2.7 mmol) and copper acetate (330 mg, 1.8 mmol) were dissolved in ethanol (20 mL). Triethylamine (1.2 mL, 9.0 mmol), and pyridine (0.66 mL, 9.0 mmol) were added immediately and the reaction stirred overnight. The reaction was filtered through celite neutralised with HCl (0.5 M, 60 mL) to give crude solid, this was then recrystallized in DCM to afford product as colourless needles (60 mg, 0.18 mmol, 10%).  1 H NMR (500 MHz, DMSO) δ 11.04 (s, 1H), 7.45 (t, J=7.1 Hz, 2H), 7.20 (d, J=7.5 Hz, 3H), 7.09 (d, J=7.8 Hz, 2H), 7.04 (d, J=7.9 Hz, 2H), 2.39 (s, 2H), 2.22 (s, 2H), 1.68 (m, 4H); M/Z (ESI+); 335.14 (Found MH + ; 335.1394, C 20 H 18 N 2 O 3  requires 335.1390). 
     
       
         
         
             
             
         
       
     
     General Procedure B 
     Toluene (2.00 mL) was added to a flask flushed with nitrogen and charged with 1-Bromo-4-(4-trifluoromethoxy)phenoxy)benzene (0.30 g, 0.90 mmol), ethyl acetoacetate (0.252 mL, 0.99 mmol), palladium acetate (10.1 mg, 0.045 mmol), (2-Biphenyl)di-tert-butylphosphine (26.8 mg, 0.09 mmol) and potassium phosphate (0.252 g, 1.2 mmol). The reaction mixture was then heated to 90° C. for 16 hours. The reaction mixture was cooled to room temperature followed by dilution in DCM (15.0 mL) and filtration through a pad of Celite. The reaction mixture was then concentrated in vacuo and passed through a silica plug. The resulting oil containing crude ethyl 3-oxo-2--4-(4-(trifluoromethoxy)phenoxy)phenyl)butanoate (1 equiv.) was dissolved in acetic acid (2.00 ml). 3-amino-tria-/pyrazole (1 equiv.) was added to the solution. The solution was heated to 120° C. and refluxed for 16 hours. The reaction mixture was then allowed to cool to room temperature. Addition of H 2 O (2.00 ml) caused precipitation of a white solid. Precipitate was filtered and washed with H 2 O (2×10.0 mL). The solid was then recrystallized in appropriate solvent to give the title compound. 
     2,5-dimethyl-6-(4-(4-(trifluoromethoxy)phenoxy)phenyl)pyrazolo[1,5-a]pyrimidin-7(4H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-amino-5 methyl-pyrazole (30.0 mg, 0.31 mmol) according to general procedure B (recrystallized in EtOAc) to afford the title compound as colourless platelets (47.0 mg, 0.11 mmol, 36%). δ H NMR (500 MHz, Chloroform-d); δ 7.27 (d, J=8.6 Hz, 2H), 7.16 (d, J=8.7 Hz, 2H), 6.99 (d, J=8.9 Hz, 2H), 6.95 (d, J=8.6 Hz, 2H), 5.80 (s, 1H), 2.34 (s, 3H), 2.21 (s, 3H) M/Z (ESI); 419.12 (Found MH +  416.1221, C 21 H 16 F 3 N 3 O 3  requires 416.1217). 
     5-methyl-2-(methylthio)-6-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-[1,2,4]triazolo [1,5-a]pyrimidin-7(4H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-amino-5-methio-1,2,4triazole (30.0 mg, 0.31 mmol) according to general procedure B to afford the title compound as colourless flake crystals (recrystallized EtOAc) (54.0 mg, 0.12 mmol, 39%). δ H NMR (500 MHz, Chloroform-d); δ 7.30 (d, J=8.6 Hz, 2H), 7.22 (d, J=8.7 Hz, 2H), 7.09 (d, J=8.7 Hz, 2H), 7.07 (d, J=8.6 Hz, 2H), 2.74 (s, 3H), 2.49 (s, 2H); M/Z (ESI); 449.09 (Found MH +  449.0893, C 20 H 15 F 3 N 4 O 3 S requires 449.0893). 
     5-methyl-7-oxo-6-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-amino-4-carbonitrile-1,2,pyrazole (45 mg, 0.42 mmol) according to general procedure B to afford the title compound as white flake crystals (recrystallized EtOAc), (43 mg, 0.10 mmol, 23%);  1 H NMR (500 MHz, DMSO) δ 8.49 (s, 1H), 7.51 (d, J=8.9 Hz, 2H), 7.44 (d, J=8.6 Hz, 2H), 7.28 (d, J=8.9, Hz, 2H), 7.20 (d, J=8.6 Hz, 2H), 2.32 (s, 3H). M/Z (ESI+); 427.10 (Found MH +  427.1018, C 21 H 13 F 3 N 4 O 3  requires 427.1012). 
     5-methyl-2-phenyl-6-(4-(4-(trifluoromethoxy)phenoxy)phenyl)pyrazolo[1,5-a]pyrimidin-7(4H)-one 
     
       
         
         
             
             
         
       
     
     The title compound was synthesised from 3-amino-4-carbonitrile-1,2,pyrazole (0.067 g, 0.42 mmol) according to general procedure B (recrystallized in DMSO) to afford the title compound as a grey micro crystals (0.15 g, 0.31 mmol, 74%).  1 H NMR (500 MHz, DMSO) δ 12.47 (s, 1H, NH), 8.01 (d, J=6.8 Hz, 2H, H-2* &amp; 6*), 7.53-7.40 (m, 5H, H-3*, 4*, 5*,2′ &amp; 6′), 7.38 (d, J=8.7 Hz, 2H, H-2″ &amp; 6″), 7.20 (d, J=9.1 Hz, 2H, H-3′ &amp; 5′), 7.11 (d, J=8.7 Hz, 2H, H-3″ &amp; 5″), 6.62 (s, 1H, H-3), 2.22 (s, 3H, Me); M/Z (ESI+); 478.1378 (Found MH+, C 26 H 18 F 3 N 3 O 3  requires 478.1373). 
     In Vitro Challenge Assay for  Toxoplasma  Tachyzoites Protocol adapted from Fomovska, et. al. (Fomovska A, Huang Q, El Bissati K, Mui E J, Witola W H, Cheng G, et al. Novel N-Benzoyl-2-Hydroxybenzamide Disrupts Unique Parasite Secretory Pathway. Antimicrob Agents Chemother [Internet]. 2012 May [cited 2015 Jul. 8]; 56(5):2666-82; Fomovska A, Wood R D, Mui E, Dubey J P, Ferreira L R, Hickman M R, et al. Salicylanilide inhibitors of  Toxoplasma gondii . J Med Chem. 2012 Oct. 11; 55(19):8375-91). Human foreskin fibroblasts (HFF) were cultured on a flat, clear-bottomed, black 96-well plate to 90% to 100% confluence. IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C (1×, [+] glutamine, [+] 25 mM HEPES, [−] Phenol red, 10% FBS)[gibco, Denmark]). Type I RH parasites expressing Yellow Fluorescent Protein (RH—YFP) were lysed from host cells by double passage through a 27-gauge needle. Parasites were counted and diluted to 32,000/mL in IMDM-C. Fibroblast cultures were infected with 3200 tachyzoites of the Type I RH strain expressing Yellow Fluorescent Protein (RH—YFP) and returned to incubator at 37° C. for 1-2 hours to allow for infection (Gubbels M-J, Li C, Striepen B. High-Throughput Growth Assay for  Toxoplasma gondii  Using Yellow Fluorescent Protein. Antimicrob Agents Chemother [Internet]. 2003 January [cited 2015 Jul. 8]; 47(1):309-16). Various concentrations of the compounds were made using IMDM-C, and 20 μl were added to each designated well, with triplicates for each condition. Controls included pyrimethamine/sulfadiazine (current standard of treatment), 0.1% DMSO only, fibroblast only, and an untreated YFP gradient with 2 fold dilutions of the parasite. Cells were incubated at 37° C. for 72 hours. Plates were read using a fluorimeter (Synergy H4 Hybrid Reader, BioTek) to ascertain the amount of yellow fluorescent protein, in relative fluorescence units (RFU), as a measure of parasite burden after treatment. Data was collected using Gen5 software. IC50 was calculated by graphical analysis in Excel. 
     In Vitro Challenge Assay for Bradyzoites 
     HFF cells were grown in IMDM (1×, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS, [gibco, Denmark]) on removable, sterile glass disks in the bottom of a clear, flat-bottomed 24-well plate. Cultures were infected with 3×104 parasites (EGS strain) per well, in 0.5 mL media and plate was returned to incubator at 37° C. overnight. The following day, the media was removed and clear IMDM and compounds were added to making various concentrations of the drug, to a total volume of 0.5 mL. 2 wells were filled with media only, as a control. Plates were returned to the 37° C. incubator for 72 hours, and checked once every 24 hours. If tachyzoites were visible in the control before 72 hours, the cells were fixed and stained. Cells were fixed using 4% paraformaldehyde and stained with Fluorescein-labeled  Dolichos biflorus  Agglutinin, DAPI, and BAG1. Disks were removed and mounted onto glass slides and visualized using microscopy (Nikon T17). Slides were scanned using a CRi Pannoramic Scan Whole Slide Scanner and viewed using Panoramic Viewer Software. Effects of the compounds were quantified by counting cysts in the controls and treated cells. Cysts and persisting organisms were counted in a representative field of view and then multiplied by a factor determined by the total area of the disk in order to estimate the number of cysts and organisms in each condition. Data was collected using Gen5 software. IC50 was calculated by graphical analysis in Excel. 
     
       
         
           
               
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 Brady 
                 Pf D6 
               
               
                 ID 
                 Structure 
                 Tachy IC 50  μM 
                 IC 50  μM 
                 IC 50  μM 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 MJM136 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1.0-10.0 
                 &gt;10 
                 0.2 
               
               
                   
               
               
                 MJM141 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1.0-10.0 
                 1.0-10.0  
                 0.16 
               
               
                   
               
               
                 JAG006 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;1 
                 N.D. 
                 0.29 
               
               
                   
               
               
                 JAG013 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;1 
                 N.D. 
                 1.31 
               
               
                   
               
               
                 JAG014 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;1 
                 N.D. 
                 0.71 
               
               
                   
               
               
                 JAG015 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;1 
                 N.D. 
                 &gt;20 
               
               
                   
               
               
                 MJM170 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.03 
                 1.0-10.0 
                 0.01 
               
               
                   
               
               
                 JAG21 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.09 
                 N.D. 
                 0.01435 
               
               
                   
               
               
                 JAG039 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 7.6 
                 N.D. 
                 9.595 
               
               
                   
               
               
                 JAG046 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;10 
                 N.D. 
                 6.716 
               
               
                   
               
               
                 JAG047 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;10 
                 N.D. 
                 3.746 
               
               
                   
               
               
                 JAG50 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.055 
                 N.D. 
                 0.04664 
               
               
                   
               
               
                 JAG58 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.04-0.08 
                 N.D. 
                 Awaiting Testing 
               
               
                   
               
               
                 JAG63 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.1-0.3 
                 N.D. 
                 Awaiting Testing 
               
               
                   
               
               
                 JAG062 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.016 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG069 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.02 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG023 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS006/ JAG143 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.06-0.08 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS012/ JAG144 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.3 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS021/ JAG145 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.08 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS034/ JAG148 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.1-0.5 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS022 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.02-0.04 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG084 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.04-0.08 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG091 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG092 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG095 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;10 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG099 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.32 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 AS032 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.1-0.3 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG100 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 &gt;10 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG106 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 ~1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG107 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG121 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG129 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.1 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG162 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 0.5 
                 N.D. 
                 N.D. 
               
               
                   
               
               
                 JAG094 
                 
                   
                     
                     
                         
                         
                     
                   
                 
                 1 
                 N.D. 
                 N.D. 
               
               
                   
               
            
           
         
       
     
     Biological Activity Studies 
     Malaria In Vitro Studies: 
     D6 is a drug sensitive strain from Sierra Leone, C235 is a multi-drug resistant stain from Thailand, W2 is a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. These assays were performed using standard protocols. 
     Compound Activity Against  Plasmodium  falciparum 
     Compound activity against  P. falciparum , a causative agent of malaria, was tested using the Malaria SYBR Green I—Based Fluorescence (MSF) Assay. This; microtiter plate drug sensitivity assay uses the presence of malarial DNA as a measure of parasitic proliferation in the presence of antimalarial drugs or experimental compounds based on modifications of previously described methods known in the art. As the intercalation of SYBR Green I dye and its resulting fluorescence is relative to parasite growth, a test compound that inhibits the growth of the parasite will result in a lower fluorescence. Selected compounds were examined for activity against four strains of  P. falciparum : D6 (CDC/Sierra Leone), a drugsensitive strain readily killed by chloroquine, TM91-C235, a multi-drug resistant strain resistant to chloroquine, W2, a chloroquine resistant strain from Thailand, and C2B has resistance to a variety of drugs including atovaquone. 
     
       
         
           
               
               
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                   
                 SYBR 
                   
               
               
                   
                   
                 SYBR 
                   
                 Green 
                 SYBR 
               
               
                   
                   
                 Green D6 
                 SYBR 
                 C235 IC50 
                 TM91C235 
               
               
                 ID 
                 Parasite strains 
                 IC50 (uM) 
                 D6 R 2   
                 (uM) 
                 R 2   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 MJM129 
                 D6, C235, W2, C2B 
                 0.03 
                 0.94 
                 0.07 
                 0.94 
               
               
                 MJM136 
                 D6, C235, W2, C2B 
                 0.20 
                 0.99 
                 0.58 
                 0.98 
               
               
                 MJM141 
                 D6, C235, W2, C2B 
                 0.16 
                 0.96 
                 0.57 
                 0.95 
               
               
                 MJM170 
                 D6, C235, W2, C2B 
                 0.01 
                 0.98 
                 0.03 
                 0.99 
               
               
                 JAG006 
                 D6, C235, W2, C2B 
                 0.29 
                 0.90 
                 0.88 
                 0.92 
               
               
                 JAG013 
                 D6, C235, W2, C2B 
                 1.31 
                 0.98 
                 2.60 
                 0.96 
               
               
                 JAG014 
                 D6, C235, W2, C2B 
                 0.71 
                 0.94 
                 1.35 
                 0.99 
               
               
                 JAG015 
                 D6, C235, W2, C2B 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 JM10 
                 D6, C235, W2, C2B 
                 0.88 
                 0.94 
                 4.48 
                 0.97 
               
               
                 JAG021 
                 D6, C235, W2, C2B 
                 0.01435 
                 0.9572 
                 0.06164 
                 0.9706 
               
               
                 JAG047 
                 D6, C235, W2, C2B 
                 3.746 
                 0.9738 
                 12.56 
                 0.9218 
               
               
                 JAG046 
                 D6, C235, W2, C2B 
                 6.716 
                 0.9844 
                 &gt;20 
                 N/A 
               
               
                 JAG039 
                 D6, C235, W2, C2B 
                 9.595 
                 0.9532 
                 &gt;20 
                 N/A 
               
               
                 JAG050 
                 D6, C235, W2, C2B 
                 0.04664 
                 0.9138 
                 0.06913 
                 0.9562 
               
               
                 RG38 
                 D6, C235, W2, C2B 
                 2.884 
                 0.8936 
                 13.66 
                 0.8338 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
             
               
                   
               
               
                   
                   
                 SYBR 
                   
                 SYBR 
                   
               
               
                   
                   
                 Green W2 
                 SYBR W2 
                 Green C2B 
                 SYBR C2B 
               
               
                 ID 
                 Parasite strains 
                 IC50 (uM) 
                 R 2   
                 IC50 (uM) 
                 R 2   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 MJM129 
                 D6, C235, W2, C2B 
                 0.08 
                 0.93 
                 0.01 
                 0.94 
               
               
                 MJM136 
                 D6, C235, W2, C2B 
                 0.55 
                 0.98 
                 0.38 
                 0.99 
               
               
                 MJM141 
                 D6, C235, W2, C2B 
                 0.63 
                 0.88 
                 0.48 
                 0.95 
               
               
                 MJM170 
                 D6, C235, W2, C2B 
                 0.03 
                 0.99 
                 0.01 
                 0.99 
               
               
                 JAG006 
                 D6, C235, W2, C2B 
                 2.46 
                 0.92 
                 1.66 
                 0.94 
               
               
                 JAG013 
                 D6, C235, W2, C2B 
                 2.35 
                 0.96 
                 1.39 
                 0.94 
               
               
                 JAG014 
                 D6, C235, W2, C2B 
                 1.27 
                 0.99 
                 0.92 
                 0.98 
               
               
                 JAG015 
                 D6, C235, W2, C2B 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 JM10 
                 D6, C235, W2, C2B 
                 5.36 
                 0.90 
                 6.75 
                 0.81 
               
               
                 JAG021 
                 D6, C235, W2, C2B 
                 0.05518 
                 0.9727 
                 0.04042 
                 0.9847 
               
               
                 JAG047 
                 D6, C235, W2, C2B 
                 9.072 
                 0.9358 
                 7.781 
                 0.9575 
               
               
                 JAG046 
                 D6, C235, W2, C2B 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 JAG039 
                 D6, C235, W2, C2B 
                 &gt;20 
                 N/A 
                 &gt;20 
                 N/A 
               
               
                 JAG050 
                 D6, C235, W2, C2B 
                 0.03136 
                 0.9693 
                 0.03635 
                 0.9427 
               
               
                 RG38 
                 D6, C235, W2, C2B 
                 9.245 
                 0.7954 
                 &gt;20 
                 N/A 
               
               
                   
               
            
           
         
       
     
     Example 5: Effect of Active Forms of  T. gondii  on Transcriptomes, Proteomes and Mechanisms Whereby this Occurs and Reflection of the Same Type of Damage to Neuronal Cells in Circulating Biomarkers from Children 
     Since we found signature pathways reflecting influence of the bradyzoite stage (characteristic of the chronic  Toxoplasma gondii  infection) in primary human neuronal stem cells in tissue culture on pathways of neurodevelopment, neuroplasticity, and neurotoxicity, we asked whether the active form of the parasite would also affect those pathways. It did. We found alterations in pathways similar to those shown with EGS bradyzoites in transcriptomics and proteomics ( FIGS.  14 A- 14 D  with explanatory figure legends and methods). These abnormalities suggested that there might be circulating biomarkers reflecting such damage to neuronal cells in patients. In that context we then asked whether serum biomarkers from ill children would reflect neuronal damage and neurodegeneration. 
     Methods. 
     Biomarkers: Serum collection was from children in the National Collaborative Congenital ToxoplasmosisStudy (NCCCTS). Children have serum drawn at each visit. Sera characterized were obtained at a visit when new seizures were noted for ill children. These sera were analyzed with nano proteomic and miR analyses as described earlier by Hood, Wang et al. This was done using a panel of markers known to be abnormal in patients with Alzheimer&#39;s and other neurodegenerative diseases. This was done to determine whether the same biomarkers present in serum or plasma from persons with these neurodegenerative disease might be present in sera from the ill children. The children are described more fully in the figure legend. 
     Murine study of Apolipoprotein A1: Wildtype mice on a C 57 B16/J background, mice in which the Apolipoprotein A1 gene was knocked out (Apo A1−/−) were utilized in this experiment. They were immunized with an attenuated strain of the RH strain of  Toxoplasma  in which ribosomal proteins small subunit 13 was placed under the control of a tetracycline repressor by placing 4 tet 0 elements in the promoter and a tetracycline regulatable repressor with YFP was stably transfected. This immunized the mice and subsequently the mice were challenged with the Me49 strain  T. gondii  and cysts were counted or luminescence in brain measured. 
     EGS and Canonical Type 1,2,3 transcriptomics details and Type 1, 2, 3 proteomics, analysis of alternatively spliced genes, and immunoflurescense studies: Details of the specific genes with altered transcription caused by EGS in Example 1 are discussed above. Trascriptomics were carried out as described in Example 1. iTRAQ data from  T. gondii  infected cell cultures. Protein quantified, extracted, subjected to mass spectroscopy, and sequence analysis from each flask, ˜180-190 ug proteins were extracted and 50 ug were used for 8-plex iTRAQ. A raw table listing relative ratios for all peptide identified in 8 samples was created. The ratio should be 0.125 (1.000/8) if one peptide/protein evenly distributes in 8 samples. Ratios of peptides from the same proteins are then calculated to protein ratios. A “Ratio to Channel 0” then included a total of 4,367 proteins identified with iTRAQ ratio. The protein ratios crossed 8 samples (4 conditions in duplicates) and were raw data from mass spec and converted to ratios against Channel 0, i.e. Control sample. They are then normalized and ratios made. “Prot with high score” has 3,359 proteins identified by more than 1 peptide and with ProteinProphet probability &gt;0.8 (=FDR&lt;1%). Among these 3,3359 proteins with high confidence, 10 proteins up &gt;2-fold in either of the 3 infected cells vs. controls, while 28 proteins down &gt;2-fold were identified. Occurrence of differences in alternative splicing between infected and uninfected cells was done with rMATS. Method for IFA are as described in Example 1. The antibodies are to SAG1, P50-NFkB. 
     Results: 
     Human serum biomarkers in ill congenitally infected children reflect  T. gondii  infection and neuronal damage. Three pairs of children were studied. In each demographically-matched pair, one child had severe disease and the other had mild or no clinical illness. Each child had serum stored from evaluations at the same ages. The second pair are dizygotic, discordant twins. Each of the three ill children had new myoclonic-“infantile” spasms, or hypsarrhythmic seizures. For two, this was associated with a rise in or high  T. gondii  specific IgG antibody titers ( FIG.  14 A ). IgG was not measured for the third ill child. A panel of nanoproteomics and miR sequencing was performed on serum obtained at the time of this new illness. The two ill children diagnosed more recently had T2 weighted abnormalities on brain MRIs similar to active inflammatory and parasitic caused brain disease seen in a murine model. Ill children compared with their paired healthy controls had alterations in miRs and increases in serum proteins associated with neurodegeneration, inflammation, a misfolded protein response and protein misfolding. Elevated proteins included clusterin, and oxytocin ( FIGS.  14 A- 14 D ). PGLYRP2 (N-acetylmuramoyl-L-alanine amidase) and Apolipoprotein B1 were depressed. miR-17-92, which  T. gondi  RH strain markedly increases in HFF cultures, also was increased in sera of the ill children, as was miR-124 ( FIGS.  14 B- 14 C ). miR-124 is associated with neurodegeneration. This indicates active brain destruction by the parasite or the response to it. These circulating proteins and miRs are clinically useful biomarkers to identify active toxoplasmic brain (and possibly retinal) disease. 
     To determine whether the presence of one of these biomarkers could be confirmed, a murine model was used. In this example of biomarkers in a murine experiment recapitulating the data of biomarkers in the serum of the ill children, APOA1 knockout and wild type mice were infected with  Toxoplasma . The wild type and uninfected mice had less radiance from luciferase parasites and fewer cysts, and less immunologic reaction to the lower parasite burden in brain (data not shown). This demonstrates that the circulating ApoA1 diminishing in the boys who were ill as a biomarker. This provides evidence that these biomarkers that were abnormal in the children had counterparts in murine models. 
     To determine whether similar pathways as were abnormal in EGS Example 1 were perturbed by the canonical U.S./European types of parasites and mechanisms whereby this might occur, transcriptomics, proteomics, analysis of alternatively spliced genes and immunofluorescent were also preformed. Experimental data showed similar perturbation of pathways by canonical U.S./European type parasites that infected the children with the biomarkers through similar transcriptomics analyses demonstrating biological effect of Type I, II, III parasites on localization of NFkB, STAT 3 and STAT 6 in primary human neuronal stem cells. These abnormalities are caused by the canonical U.S. and European types of parasites growing as tachyzoites in the human primary neuronal stem cells and monocytic cells. These finding along with those demonstrated by the Omic studies of EGS (Example 1) suggest a mechanism whereby circulating biomarkers reflecting damage to neuronal cells in patients can occur. Placed in this context, we hypothesize that serum biomarkers from ill children reflect neuronal damage and neurodegeneration, as confirmed by our murine models, and findings seen in tissue culture and/or in patients. 
     Discussion 
     The signature pathways we noted in studies of human primary neuronal stem cells which reflected abnormalities and gene products associated with neurodegenerative disease and the mechanisms whereby  T. gondii  can cause such pathology prompted study of biomarkers in a small number of ill versus well children. Biomarkers of active brain  T. gondii  infection in humans were found. The serum biomarkers shown in  FIGS.  14 A- 14 D  are increased (e.g., clusterin, oxytocin, amyloid, and mir 17-92 and mir 124) or diminished, including PGLYRP2 (N-acetylmuramoyl-L-alanine amidase) and Apolipooprotein-A1 which are indicative of infection. These are consistent with the transcriptome demonstrating signature pathways in GO slim and KEGG analyses with effect on ribosomes, alternative splicing and neurodegenerative diseases, including Alzheimer&#39;s disease, Huntingtons disease, and Parkinson&#39;s disease by encysted EGS, and for example pathways of response to oxidative stress, regulation of apotosis, and alternative splicing of toll receptors that were abnormal in the same cells infected by the canonical US/European parasites (active tachyzoites) that the children had. Other manifestations of active disease in the brain diminished with treatment and are not abnormal in the dizygotic healthy twin of one child or demographically matched well children. This is consistent with these biomarkers being selected to be assayed with MiR sequencing and proteomics based on their differences in diseases of neurodegeneration. These ill children had developed new seizures, elevations in antibody titer, elevated cerebrospinal fluid protein in one child, and abnormal T2 weighted alterations in T2 weighted brain magnetic resonance imaging. The biomarkers that were characteristic of neurodegeneration in the ill children and when diminished were associated with greater severity of disease in a murine model will be useful to monitor disease and response to treatment of disease due to this parasite. Restoration to normal values being indicative of favorable response to treatment and presence may also mark recrudescence of disease. ApoA1 may also be a useful treatment.