Apicomplexan Parasitic Diseases

Cross Reference

This application claims priority to U.S. Provisional Patent Applications 62/270264 filed December 21, 2015, and 62/306385 filed March 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

R01 AI071319(NIAID) and R01 AI027530 (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):

(I)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof,

wherein

ring A combines with Y ¹ and Y ₂ to form a C3- ₇ Cycloalkenyl or heteroaryl ring, wherein the C:,- ₇ cycloalkenyl or heteroaryl is optionally substituted by

halogen, Ci _-3 alkyl, Ci- ₃ alkoxy, Ci- ₃ haloalkyl, -0-Ci- ₃ haloalkyl, -S-Ci- 3haloalkyl, -C(0)OR, cyano or phenyl;

YMs C or N;

Y ² is C orN;

X ¹ is C(R ^xl ) or N,

wherein R ^xl is hydrogen, halogen, Ci _-3 alkoxy or Ci _-3 haloalkyl; X ² is C(R ^x2 ) or N,

wherein R ^x2 is hydrogen, halogen,

X ³ is 0, N(R), S or C _1-3 alkyl;

X ⁴ is C orN;

X ⁵ is C orN;

R ¹ is hydrogen or C _1-3 alkyl;

R ² is hydrogen, C _1-3 alkyl, d _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

n is 0, 1, 2, 3 or 4; each R is independently halogen, Ci. ₃ alkyl, Ci- ₃ alkoxy, Ci- ₃ haloalkyl, -O-Ci.

₃ haloalkyl, -S-Ci _-3 haloalkyl, -C(0)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 Ci- 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=>I modification at residue 570 ("AP2 IV-4 Μ570Γ) 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 of the up-regulated genes listed in Figure 1 or Figure 2.

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 of the apicomplexan parasite genes in Figures 3-5.

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 listed in Figures 3-5, 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 listed in Figure 1-2 , 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 Al (apoAl), 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 ApoAl.

Description of the Figures

Figure 1. Host transcriptomics data during EGS infections of human HFF, MM6 or NSC cells. Differential gene expression analysis of human fibroblasts infected with T. gondii EGS strain after 2 hs, 18 hs, and 48 hs, monomac 6 cells infected with T. gondii EGS for 18 hs or neuronal stem cells infected with T. gondii EGS strain for 18 hours.

Figure 2. Host miRNA transcriptomics data during EGS infections of MM6 or NSC cells. Differential expression analysis of human miRNA genes from MM6 or NSC cells infected with T. gondii EGS strain for 18 hours.

Figure 3. EGS transcriptomics data during MM6 infections. Differential expression analysis of T. gondii genes from MM6 cells infected with T. gondii EGS strain for 18 hours compared to T. gondii gene expression from MM6 cells infected with GT1, ME49 or VEG strains for 18 hours

Figure 4. EGS expression during NSC infections. Differential expression analysis of

T. gondii genes from neuronal stem cells infected with T. gondii EGS strain for 18 hours compared to T. gondii gene expression from neuronal stem cells infected with either GT1, ME49 or VEG strain for 18 hours.

Figure 5. EGS transcriptomics data during HFF infections. Differential T. gondii gene expressing analysis of human HFF cells infected with T. gondii EGS strain for 2 hs, 18 hs or 48 hs compared to the average T. gondii gene expression of human MM6 and neuronal stem cells infected with either GT1, ME49 or VEG strains of T. gondii for 18 hours

Figure 6 EGS morphology and effect on host cell transcriptomes a. EGS in human MM6 cells and NSC form cysts. Left NSC with EGS. Right MM6 with EGS. Note green dolichos cyst walls and BAGl(red) in NSC. DAPI stained nuclei(blue). b, c , d. 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 (b) and Venn diagram are used to show general comparison of DEGs identified between the two cell lines (c). 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 (b-d). Functional enrichment analysis was performed for gene ontology (GO) biological process and KEGG pathways (d). P-values derived from analysis were -loglO 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. e. 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.

Figure 7. Differential Gene Expression (DGE) analyses and effects of inhibition of cytochrome bcl. 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; LogFC, logarithm of the fold change in gene expression. CST1, SAG-related sequence SRS44 ^s114 ; LDH2, lactate dehydrogenase 2 ^s115 ; LDH1, lactate dehydrogenase I ^s115 ; EN02, enolase 2; ENOl, enolase I ^s116 ; SAG1, SAG-related sequence SRS29B; BAG1, bradyzoite antigen BAG1 . b. DGE analysis of genes encoding AP2 family of transcription factor during the same infection experiments as described in (m). Red and green arrows

SI 17 denote AP2 genes found to be over- or under-expressed during bradyzoite development "*", q-value < 0.05. c. T. gondii cytochrome family genes differentially expressed during same experimental infections as described in (m). "*", q-value < 0.05. d. 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 μΜ (p<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 uM 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.

Figure 8. 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 b. Saccharomyces cerevisiae cy tochrome bc _\ X-ray structure (PDB ID: 1KB9) ⁵ The complex contains 11 subunits and 3 respiratory subunits (cytochrome b, cytochrome cl and Rieske protein). The cytochrome b subunit provides both quinone binding sites (Q ₀ and Q highlighted as grey and pink surfaces respectively.

Figure 9. ELQ inhibitors provide a new scaffold and approach yielding compounds that are potent inhibitors of tachyzoites and cysts in vitro, a-e 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. 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). b,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, d. EGS transfected with stage specific reporters for fluors, red tachyzoite SAG1, Green bradyzoite LDH2.

Figure 10 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, a: 25mg/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<0.004) . For the standard curve in the inset, RFU increase with increasing concentrations of fluorescent tachyzoites (R ² = .99). b. MJM 170 25 mg/kg daily reduces Type 2 parasites, 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 da s: cyst count of wet prep of brain homogenate. d. Zebra fish can be used to visualize fluorescent tachyzoites and cysts in more chronic infections.

Figure 11. MJM 170 targets apicomplexan cytochrome bc Qi : modelling, yeast surrogate assays, target validation, co-crystallography and nanoM inhibition of P.falciparum and T.gondii a. Modeling: MJM170 (yellow) modelled within cytochrome b Qi site (grey) highlighting residues (green) involved in binding, b. Mutations for yeast, P. falciparum, predicted for T.gondii and bovine enzyme. Relevant mutations are indicated by colored dots in Qi 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 Qi domain of P.

falciparum, c. Cytochrome b mutants and sequence accession numbers, d. MJM 170 inhibits wild-type but not mutant yeast. Compounds MJM 170 and ELQ 271 with wild ty pe and mutant yeast validate predictions that M221 K/Q would create a steric clash and resistance, 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 <50nM 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, f. MJM170 binds within Qi site of bovine cytochrome bc _\ as shown by X-ray crystallography. f(i). An omit Fo-Fc electron density map (green) at 5σ allows unambiguous positioning of MJM170 (magenta) within the Qi site with the tetrahydroquinolone group near heme DH (white) and diphenyl ether directed out of the channel. f(ii) -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 bjj and Phe220 with the carbonyl group positioned in a polar region surrounded by Ser35 and Asp228. g. A stereo picture of the 2Fo-Fc electron density map. Electron density at 1σ level around cytochrome b a-helixes 118-128 and 183-199 close to MJM180 compound in X-ray structure of cytochrome&ci. Inset: Crystal of mammalian cytochrome bcl complex.

Figure 12. MJM170 potently inhibits P.falciparum mitochondrial electron transport important for synthesis of pyrimidines, is modestly synergistic with atovaquone, additive with cycloguanil and antagonistic with Qi inhibitor, a. MJM170 is highly potent (Dd2, black curve, EC50 = 29.5nM) without cross-resistance in previously reported cytochrome b drug-resistant mutant parasite lines including ubiquinone reduction site mutants (Dd2 ^G33A and Dd2 ^G3~v _: 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 . EC50 values were calculated using whole- cell SYBR Green assay and listed as mean ± standard deviation of three biological replicates, each with triplicate measurements, b., c. Isobolograms with MJM170 plus atovaquone or cycloguanil or Qi inhibitor BRD6323: 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 inhibitor}' 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 < 1.0, addivity as FIC = 1.0, and antagonism as FIC > 1.0. 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 bulk}' inhibitor of cytochrome be, 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. Figure 13 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.

Figure 14 The results of a cytotoxicity assay. 10 μΜ solution of compound was compared to the DMSO control closest to 0.1% DMSO (0% DMSO) and the 50 μΜ solution was compared to the DMSO control closest to 0.5% DMSO (0.625% DMSO). The differences were not found to be statistically significant.

Figure 15. Effects of compounds against EGS. a-c) Graphs comparing the effects of JAG050 and JAG021 on EGS. Images from scanned slides. Three different forms were observed: cysts, pseudocysts, and small organisms, pictured in (d), untreated control, magnified, e) untreated control f) JAG050 10 μΜ and g) JAG021 1 μΜ. Cells were stained with DAPI (blue) to stain nuclei, BAG1 (red), a bradyzoite antigen, and dolichos (green), which stains cyst walls. White arrow marks cyst.

Figure 16. Binding assays show selectivity with binding to the bovine enzyme which is not as robust as has been seen with other cytbc inhibitors

Figure 17. 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 2.5mg/kg and 3 doses protect at 0.5mg/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.

Figure 18. Tafenoquine and JAG21 are both needed to contain RPS 13Δ. One additional mouse in the tafenoquine and JAG21 died outside the time on this graph others remained healthy.

Figure 19. Serum biomarkers from boys with active brain disease due to

Toxoplasma reflect infection and neurodegeneration. 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 b-e. 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.

Figure 20. List of up-regulated or down-regulated genes involved in specific host cell pathways or indications.

Figure 21 List of exemplary proteins important for apicomplexan parasite bradyzoite development and/or survival in the host.

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, CA), "Guide to Protein Purification" m. Methods in Enzymology (M.P. Deutshcer, ed., (1990) Academic Press, Inc.); PGR Protocols: A Guide to Methods and Applications (Innis, et al.

1990. Academic Press, San Diego, CA), Culture of Animal Cells: A Manual of Basic Technique, 2 ^nd Ed. (R.I. Freshney. 1987. Liss, Inc. New York, NY), 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, TX).

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 (Gin; Q), glycine (Gly; G), histidine (His; H), isoleucine (He; 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=>I modification at residue 570 ("AP2 IV-4 Μ570Γ) 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 ency sted parasite turns on host cell pathways important for altering ribosomal function, mis-splicing of transcripts, oxidative pathways, and, those pathways found to be altered in Alzheimer's and Parkinson'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

GGNRPHYHVAKQEWRVRYYMNGKPJCMRTYSAKFYGYETAHTMAEDFAHYVDKH

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: MAAPAPSAEARPAKRRCFPLPRETPVSSEDETRKTLQHDTLGCLPRSSSGQPE LAAASAASQVGHLSSAALLQLVQTQSAGGVPQAVLRNLFSSIHRNPKPLPANALAAT PNSSLYASLTSLSSAAALPGAGPAYSQAPSPASADLLQSEQFGSAAK PSPNEASPILA LLGEAARAATTPRTVPALSAVCPAASSGVSLPSASDTLALAQSSLSSSTGCASDVKAS RPEEHPAFASGTANRQSLLQALLLSTAPLAFSGPSLSSASTTLPASSGAVSSRNAGAY QFERLLQAEAAKVKALLPNATSKSMSQSSVPQRDLTRKTSLFPDPRGLSADDASRRY NTRGANSGGAGLRRGTGVHATTEQSGALDAGERTRPFGAGEDESAQGKPDSRGRQ RPG

ALDASNILGLLAAFQPSQAPAIRDLSAPSHLSAAATGALPLTASFTASALASSQCLP A

GTPASSSASPPFSEVLSTTEESSTTKETDASASTLLAFLQKYSAVSGLGGASDFLGQ LQ

GKSSLPPLSLAEPSSALPSSFLGGSDGGΉDTRNGNGEKTTPPIHLFQSAFRIPSPS QQN

LLDALLASSCTTATSRSDGSGNLGCPVVDERNAKLAGPAHPLPCSFPQISSSSGEPG R

KTGGRVHRQGTSQSGGRVRSGKNGGSAAPPRQSSSENVPSTPTVSSHEAPHRAGFPS

QTPYELSASPSHQLDLLRLGAFLGGAGKQDASVHSDETGTLSGEPSHRSCSLSRGLT Q

ESVLQLSDTTSTSREGEPNEPSQGCVNVAASLPAFGPQPSSGAAKAREGRRGAGGAG

AAPPVPLRADVTLGGNRPHYHVAKQEWRVRYYMNGKRKMRTYSAKrYGYETA

HTMAEDFAHYVDKHEALPDSMMMTAMMLQAQANSAASSGOTVPLARGIRASSAS

AGAGGHVSKSATKGSVAASSEGSTSMGSDATRSQEGEAAELCPLAAGLSRPLASMH

SAAGNAVAQGRQESKEEAPGGQAWFGEPGKFRASSEAALCGSGSSAEGRDGHESEV

LWATLGKVHDASQGKKIKPEKPLTVARGRLALGAEDKSQNLGVDLGDSGGAQGLP

GVRQPRQMKNSEECSLRDSDKGMALSKRFGFLPSQTPSCDSMTLPFPGGFDALSLSS

ALSSCASLPVAHEGN FQ GHTGDIVALASQSGTQRPASVVLSRDANVSGSSPSHPT

WQREGAAVSGRADEFSSLSVTPSTVPLSSFTMEDIKGEEGDPSRRFALVGESMK VS

APEVQALFPTSSIANAELLPVDFLHSNSCSADKLESSIPRGLAGN PSMTATAVAATA

VSHQIFDTITLFGEFLREFAKEKVNEFHEYGLEASPLTVEASPEVSLFGKATFGRCP VA

GGSTPAGISKMSGETLSGLSASELSLVSARTNTTTGEEQFALARGLFPGDSEGDRDE K

KPQLSQQELLVLSHALVNLTSSTYVLMHTLKASLSKSTEAVQLHQPLLEAASEAKAT

DEAKTREEQESSECDHEYPPGSSLEATTGALPFRLSPALSASSKDLPSLSASASLES VT

PFAGLPLEEGTLSASVGLASSDDEHDTSLLFKTEAAKKRSLFSTAADGDESRTYNDG

LGQPMEEEIRSCVSTSCGEAVATTTLSAIGPGTGASGALLDSESRESLGEKPGAALR A

GAHTPAPSRAPTPSRTFSFTSSSTATSAALLCDSNVVHEKLSAQGKDSEAGERKGDS E

KEEEVEMWKEEDEEVQRCTGSAETDSTEATRGEEAWRRGKQSEKKPSVITTALNLL

ETHRHLALTISQLKRPVAQQLRFILPIAAPQLLPCILPPASFQGTGESGDGKAEAEA KG

SSSLGQVLETALGHGTRLAPSASAMVPPRKDEAASAVPEAKTLTGLANAGVTREAA SRTLEAEQVSRKRSREEVVDSETAGDEGDMENVPETRDGTTRPGSRQYDTSPSNDGT KPPATAKSRVIRDQAALERLLLAPFQDTPTCSCTDRPCPCDRQQVADMIYLFYAVPA RQQAESSKEGSTQRLQFAARDTNERKDARTGEETQGGETEAKEVIRDPEERGVCEGS SSQNAHTQFDAETASSSMSSDPRADKESNAQDAHMAD TSFVSDLPQPSGEFAPSLL SETSLDVAMADSRGTPSEIHGFFTRSDEQKRASFSSSSLLAAGHAVASFSSSLAGVVS GAGERRECAGPSLGDLSTIGLLSLSYPAMLAFILPLQSLLHTVSGMILTLHKKLIHRFIC AHLRLVLDDDMRRPAGGALKSRGAHGDTEAAEAQVERRRREHEREETTNLAIGYRE GNAEAANTFPLVDTVSSLLSPGSLRQENSEVERRDNDEERLELITGIARESPKPSEKDS VSPFLSTAPCPGTEAESSDCSASSACSGTPTEGTEGGETGDIASFLSPSGEVKQTIMLA

(SEQ ID NO: 2)

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.

November 22, 2010; dx.doi.org/10.1371/journal.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 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 BAGl encoding gene promoter or a functional equivalent thereof. The BAGl 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 BAGl promoter is a promoter from any strain of T. gondii that promotes expression of BAGl 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 BAGl 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 GO arrested parasite (such as RPS 13 delta) and is used to identify companion compounds for tetrahydroquinolones (THQ) that eliminate the GO arrested stage of an apicomplexan parasite, such as Ί. 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 GO state, Gl 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 anhydrotetracy cline 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 Gl 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 RPS 13 delta in mice, and involves the observations that when RPS13 delta is administered to wild type mice without tetracycline the RPS 13 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 -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, RPS 13 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, RPS 13 delta can be used to test compounds in vitro against this GO 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 GO arrested hypnozoite-like phase of the apicomplexan infections the active tachyzoite, the slowly growing bradyzoite, and the GO 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 (Figure 6). 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 (Figure 6). The number of genes significantly up or down regulated in MM6 and NSC cells compared to uninfected controls are depicted in Figure 6. 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 (Figure 6e. 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 in Figure 1 (protein encoding genes) or Figure 2 (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 from Figures 20-21, 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'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, C1R, 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's, Huntington's disease, Alzheimer'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

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'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, NDUFAl, VDAC3, NDUFV2, COX6A1, UQCRB

hsa05016 Huntington'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, NDUFAl, VDAC3, SOD2, NDUFV2, COX6A1, UQCRB hsa05010 Alzheimer'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, NDUFAl, 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 infecton, comprising treating a subject with an apicomplexan parasite infection an amount effective to inhibit activity or expression from the apicoimplexan parasite of one or more proteins listed in Figure 21.

In another embodiment, the invention provides methods for identifying a compound to treat an apicomplexan infection, comprising identify ing a compound that inhibits activity or expression of one or more proteins listed in Figure 21 from an apicoimplexan parasite present in an infected host cell.

The proteins listed in Figure 21 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 (Figure 7b-c). 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 (Figure 7 a-c). 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 in Figures 3-5 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 the markers listed in Figures 3-5, 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 the markers listed in Figure 1-2 , 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 improv es 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 the markers listed in Figures 1-5 (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's brain or other neurologic tissue.

In another aspect, the present disclosure provides compounds having the structure of Formula (I):

wherein

ring A combines with Y and Y ₂ to form a C3- ₇ cycloalkenyl or heteroaryl ring,

wherein the C3- ₇ cycloalkenyl or heteroaryl is optionally substituted by

halogen, C _1-3 alkyl, Ci^alkoxy, Ci^haloalkyl, -0-Ci- ₃ haloalkyl, -S-Ci_ 3haloalkyl, -C(0)OR, cyano or phenyl;

Y s C or N;

Y ² is C or N;

X ¹ is C(R ^xl ) or N,

wherein R ^xl is hydrogen, halogen, C _h alky 1, Ci- ₃ alkoxy or

C(R ^x2 ) or N,

wherein R ^x is hydrogen, halogen, C _h alky 1, Ci- ₃ alkoxy or

X ³ is O, N(R), S or Ci _-3 alkyl;

X ⁴ is C or N; X ⁵ is C or N;

R ¹ is hydrogen or C _h alky!;

R ² is hydrogen, Ci_ ₃ alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

n is 0, 1, 2, 3 or 4;

each R ³ is independently halogen, Ci^alkyl, C^alkoxy, Ci^haloalkyl, -O-Ci-

₃ haloalkyl, -S-Ci _-3 haloalkyl, -C(0)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

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 (la):

(la)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof,

wherein

ring A combines with Y ¹ and Y ₂ to form a C3- ₇ cycloalkenyl or heteroaryl ring, wherein the C:,- ₇ cycloalkenyl or heteroaryl is optionally substituted by halogen, Ci _-3 alkyl, -0-Ci- ₃ haloalkyl, -S-Ci.

₃ haloalkyl, -C(0)OR, cyano or phenyl;

Y ¹ is C or N;

Y ² is C or N;

X ¹ is C(R ^xl ) or N,

wherein R ^xl is hydrogen, halogen, Ci^alkyl, C _1-3 alkoxy or Ci- ₃ haloalkyl; X ² is C(R ^x2 ) or N,

wherein R ^x2 is hydrogen, halogen, Ci^alkyl, C _1-3 alkoxy or Ci^haloalkyl; X ³ is 0, N(R), S or Ci- ₃ alkyl;

R ¹ is hydrogen or Ci^alkyl; R is hydrogen, C _1-3 alkyl or -C(0)OR;

n is 0, 1, 2, 3 or 4;

each R ³ is independently halogen, Ci- ₃ alkyl, Ci- ₃ alkoxy, Ci _-3 haloalkyl, -O-Ci.

₃ haloalkyl, -S-Ci _-3 haloalkyl, -C(0)OR or SF ₅ ; and

each R is independently hydrogen or Ci _-3 alkyl.

In some embodiments the compounds are of Formula (lb):

(lb).

embodiments, the compounds are of Formula (Ic):

(Ic).

In some embodiments, the com ounds are of Formula (II):

(Π)

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 (Ila):

(Ila).

embodiments, the compounds are of Formula (IIa-1):

(IIa-1)

wherein

R ³ is hydrogen, halogen, Ci^alkyl or Ci^haloalkyl.

In some embodiments the compounds are of Formula (III):

(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 (Ilia):

(Ilia)

wherein

Y ³ is C(R ⁵ ) or N; and

R ⁴ and R ⁵ are independently hydrogen, halogen, Ci- ₃ alkoxy, Ci- ₃ haloalkyl,

-0-Ci- ₃ haloalkyl, -S-Ci- ₃ haloalkyl, -C(0)OR, cyano or phenyl.

In some embodiments the compounds are of Formula (Illb):

(Illb).

In some embodiments, the compounds are of R ⁴ is hydrogen or Ci- ₃ alkyl. In some embodiments the compounds are of Formula (IIIb-1):

(IIIb-1).

embodiments, the compounds are of Formula (IIIc):

(IIIc).

In some embodiments,

R ⁴ is hydrogen or phenyl; and

R ⁵ is hydrogen or cyano.

In some embodiments the compounds are of Formula (IIIc-1):

(IIIc-1).

embodiments the com ounds are of Formula (IV):

(IV)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof,

wherein

ring A combines with Y ¹ and Y ₂ to form a C3- ₇ cycloalkenyl or heteroaryl ring, wherein the C:,- ₇ cycloalkenyl or heteroaryl is optionally substituted by halogen, Ci _-3 alkyl, -0-Ci- ₃ haloalkyl, -S-Ci_ 3haloalkyl, -C(0)OR, cyano or phenyl;

Y s C or N;

Y ² is C or N;

X ¹ is C(R ^xl ) or N,

wherein R ^xl is hydrogen, halogen, Ci. ₃ alkyl, Ci- ₃ alkoxy or Ci- ₃ haloalkyl; X ² is C(R ^x2 ) or N,

wherein R ^x2 is hydrogen, halogen, Ci. ₃ alkyl, Ci- ₃ alkoxy or Ci _-3 haloalkyl; X ³ is 0, N(R), S or C _1-3 alkyl;

X ⁵ is C or N;

R ¹ is hydrogen or Ci- ₃ alkyl;

R ² is hydrogen, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

n is 0, 1, 2, 3 or 4;

each R ³ is independently halogen, Ci^alkyl, C^alkoxy, Ci^haloalkyl, -O-Ci-

₃ haloalkyL -S-Ci _-3 haloalkyl, -C(0)OR or SF ₅ ; and

each R is independently hydrogen or Ci _-3 alkyl.

In some embodiments, the com ounds are of Formula (IV a):

(IVa)

wherein

ring A combines with the carbon atoms with which it is attached to form a C ₃ - 7cycloalkenyl.

In some embodiments, the com ounds are of Formula (IVb):

(IVb). In some embodiments, Y ¹ is C. In other embodiments, Y ¹ is N.

2 2

In some embodiments, Y is C. In other embodiments, Y is N.

In some embodiments, Y ¹ is C. In other embodiments, Y ¹ is N.

In some embodiments, X ¹ is C(R ^xl ) wherein R ^xl is hydrogen, halogen, C^alkyl, C . :,alkoxy or Ci^haloalkyl. In other embodiments, X ¹ is N.

In some embodiments, X ¹ is C(R ^xl ) wherein R ^xl is selected from any of groups (la)-

(lx):

(la) hydroge Ci- ₃ alkoxy or

(lb) halogen, or

(lc) hydrogen;

(Id) halogen or

(le) halogen or

(If) Ci.salkyl;

(lg) hydrogen, methyl or ethyl;

(lh) methyl or ethyl;

(li) methyl;

(ij) ethyl;

(lk) propyl;

(U) hydrogen, methyl or propyl;

(lm) methyl or propyl;

(In) hydrogen, ethyl or propyl;

(lo) ethyl or propyl;

(lp) Ci- ₃ haloalkyl;

(lq) Ci- ₃ fluoralkyl;

(lr) fluoromethyl

(Is) difluoromethyl

(It) trifluoromethyl

(lu) fluoromethyl

(lv) fluoropropyl

(lw) -CH ₂ OH;

(lx) -CH ₂ OR;

In some embodiments, X ² is CO** ² ) wherein R ^x2 is hydrogen, halogen, C^alkyl, C _\ . ₃ alkoxy or C^haloalkyl. In other embodiments, X ² is N. In some embodiments, X ² is Ci ² ) wherein R ^x2 is selected from any of groups (2a)-

(2a) hydrogen, halogen, Ci- ₃ alkyl, Ci- ₃ alkoxy or

(2b) halogen, C _1-3 alkyl, Ci^alkoxy or Ci^haloalkyl;

(2c) hydrogen;

(2d) halogen or C^haloalkyl;

(2e) halogen or

(21) Ci- 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) Ci- ₃ haloalkyl;

(2q) C^fluoralkyl;

(2r) fluoromethyl

(2s) difluoromethyl

(2t) trifluoromethyl

(2u) fluoromethyl

(2v) fluoropropyl

(2w) -CH ₂ OH;

(2x) -CH ₂ OR;

In some embodiments, X is selected from any of groups (3a)-(3p):

(3a) 0, N(R), S or C _1-3 alkyl;

(3b) 0, N(R) or S;

(3c) O or N(R);

(3d) 0;

(3e) N(R);

(31) S or Ci _-3 alkyl;

(3g) 0, N(R), or Ci. ₃ alkyl; (3h) 0 or d-salkyl;

(3i) N(R), S or Cwalkyl;

(3j) N(R) or Ci _-3 alkyl;

(3k) 0 or Ci _-3 alkyl;

(31) Ci.galkyl;

(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 Ci _-3 alkyl;

(4b) hydrogen;

(4c) d. ₃ alkyl;

(4d) hydrogen, methyl or ethyl;

(4e) methyl or ethyl;

(41) methyl;

(4g) ethyl;

(4h) propyl;

(4i) hydrogen, methyl or propyl;

(4j) methyl or propyl;

(4k) hydrogen, ethyl or propyl;

(41) ethyl or propyl;

In some embodiments, R ² is selected from any of groups (5a)-(5gg): (5a) hydrogen, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR; (5b) Ci. ₃ alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

(5c) hydrogen, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

(5d) hydrogen, C _1-3 alkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

(5e) hydrogen, Ci _-3 alkyl, d _-3 haloalkyl, -CH ₂ OR or -C(0)OR;

(51) hydrogen, C _1-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, or -C(0)OR;

(5g) hydrogen, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, or -CH ₂ OR;

(5h) hydrogen or Ci _-3 alkyl;

(5i) hydrogen; (5j) Ci. ₃ alkyl;

(5k) hydrogen, methyl or ethyl;

(51) 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) Ci. ₃ haloalkyl, -CH ₂ OH, -CH ₂ OR or -C(0)OR;

(5u) Ci-3haloalkyl;

(5v) Ci. ₃ fluoralkyl;

(5w) fluoromethyl

(5x) difluoromethyl

(5y) trifluoromethyl

(5z) fluoromethyl

(5aa) fluoropropyl

(5bb) -CH ₂ OH;

(5cc) -CH ₂ OR;

(5dd) -C(0)OR;

(5ee) -C(0)OH;

(5ff) -C(0)OMe;

(5gg) -C(0)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 O or l .

(6e) n is 1 or 2.

(6f) n is 2 or 3.

(6g) n is 1.

(6h) n is 2.

(6i) n is 3. (6j) n is 4.

(6k) n is O.

In some embodiments, R ³ is selected from any of groups (7a)-(7cc):

(7a) each R ³ is independently halogen, C _1-3 alkyl, Ci^alkoxy, C _1-3 haloalkyl, -O-Ci-

₃ haloalkyl, -S-Ci- ₃ haloalkyl, -C(0)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 Ci. ₃ alkyl, Ci- ₃ alkoxy, Ci- ₃ haloalkyl, -O-Ci.

₃ haloalkyl, -S-Ci _-3 haloalkyL -C(0)OR or SF ₅ ;

(7c) each R ³ is independently halogen, Ci- ₃ alkoxy, Ci. ₃ haloalkyl, -0-Ci _-3 haloalkyl,

-S-Ci _-3 haloalkyl, -C(0)OR or SF ₅ ;

(7d) each R ³ is independently halogen, Ci- ₃ alkyl, Ci. ₃ haloalkyl, -0-Ci- ₃ haloalkyl,

-S-Ci _-3 haloalkyl, -C(0)OR or SF ₅ ;

(7e) each R is independently halogen, -0-Ci. ₃ haloalkyl, -S-Ci_

₃ haloalkyl, -C(0)OR or SF ₅ ;

(If) each R ³ is independently halogen, C _1-3 alkyl, Ci^alkoxy, -O-Ci^haloalkyl, -S-

Ci. ₃ haloalkyl, -C(0)OR or SF ₅ ;

(7g) each R ³ is independently Ci^alkyl, Ci- ₃ alkoxy, -0-Ci- ₃ haloalkyl, -S-Ci_

₃ haloalkyl, -C(0)OR or SF ₅ ;

(7h) each R ³ is independently -0-Ci _-3 haloalkyl, -S-Ci. ₃ haloalkyl, -C(0)OR or SF ₅ ; (7i) each R ³ is independently halogen, Ci. ₃ alkoxy, Ci _-3 haloalkyl, -O-Ci.

₃ haloalkyl, -S-Ci _-3 haloalkyl, -C(0)OR or SF ₅ ;

(7j) each R ³ is independently halogen, Ci _-3 haloalkyl, -0-Ci. ₃ haloalkyl, -C(0)OR, or two R groups, together with the carbons to which they are attached, form a

1,3-dioxolane;

(7k) each R ³ is independently halogen, Cihaloalkyl, -O-Cihaloalkyl, -C(0)OR, or two R ³ groups, together with the carbons to which they are attached, form a 1,3-dioxolane;

(71) each R ³ is independently fluoro, chloro, Ci^haloalkyl, -O-Ci^haloalkyl,

-C(0)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, -0-Ci _-3 haloalkyl,

-C(0)OR, or two R ³ groups, together with the carbons to which they are attached, form a 1,3-dioxolane; (7n) each R is independently fluoro, chloro, trifluoromethyl, -OCF3, -C(0)OR, or two R groups, together with the carbons to which they are attached, form a 1,3-dioxolane;

(7o) each R ³ is independently fluoro. chloro, trifluoromethyl, -OCF3, -C(0)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, -OCF3, -C(0)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, -OCF3, -C(0)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, -OCF3, or two R ³ groups, together with the carbons to which they are attached, form a 1,3- dioxolane;

(7s) each R is independently fluoro, chloro, trifluoromethyl or -OCF3;

(7t) each R ³ is independently fluoro, chloro, trifluoromethyl, -OCF3 or -C(0)OH;

(7u) each R ³ is independently fluoro, chloro, trifluoromethyl or -OCF3;

(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(0)OH;

(7cc) two R 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)-(81):

(8a) hydrogen or C^aUcyl;

(8b) hydrogen;

(8c) Ci. 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;

(81) ethyl or propyl;

In some embodiments, the compound is of Formula (I), (la), (lb) or (Ic), and X ¹ , X ² , X ³ , R ¹ , R ² , R ³ and n are selected from any combination of groups (la)-(81).

In some embodiments, the compound is of Formula (II), (Ila) 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 (la)-(81).

In some embodiments, the compound is of Formula (III), (Ilia), (Illb), (IIIb-1), (IIIc) or (IIIc-1), and X ¹ , X ² , X R ¹ , R ² , R ³ and n are selected from any combination of groups (la)-(81).

In some embodiments, the compound is of Formula (IV), (IV a) or (IVb) and X ¹ , X ² ,

3 1 2 3

X R , R , R ^J and n are selected from any combination of groups (la)-(81).

In some embodiments, the compound is:

No. ID Structure Name

l.Q-tt pc s stems l)qui

ne

ne

in-

5A.fiis fl p> ridonc s>s1ems No. ID Structure Name enyl)- 7(4H)-

nyl)py -one

nyl)py -one

-

5-methyl-7-oxo-6-(4-(4- (trifluoromethoxy)phenoxy)phenyl)- 4,7-dihydropyrazolo[l,5-a]pyrimidine- 3-carbonitrile

5-methyl-2-phenyl-6-(4-(4-

JAG015 (trifluoromethoxy)phenoxy)phenyl)py razolo[l,5-a]pyrimidin-7(4H)-one

I cli iihvdi oqiiiiioloties ( 1 HQ)

7 MJM170 2-methyl-3-(4-phenoxyphenyl)- 5,6,7,8-tetrahydroquinolin-4(lH)-one ID Structure Name

JAG21

e

JAG039

JAG046

JAG047

JAG50

JAG58

JAG63

e JAG062

No. ID Structure Name

16 JAG067

l,2-dimethyl-3-(4-(4-

17 JAG023 f ^" if :f (trifluoromethoxy)phenoxy)phenyl)- 5,6,7,8-tetrahydroquinolin-4(lH)-one ,2- 18 JAG077 in-

19 AS006 l)- one

20 AS0012 )- one )-2-

21 AS021 n-

22 AS022 l- one

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound is:

aci

4(lH)-one ID Name

7-Trifluromethyl-2-methyl-3(4-(4-

JAG162 trifluoromethoxyphenoxy)phenyl)-5,6,7,8- tetrahydroquinolin-4(lH)-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 inMedicinal 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):

(I-P)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

nng A, Y ¹ , Y ² , X ¹ , X ² , X ³ , X ⁴ , X ⁵ , R, R ³ and n are as described above;

R ² is hydrogen, d _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR', -C(0)R', -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is

independently hydrogen or C^alkyl. In some embodiments the prodrug is a compound of Formula (Ia-p):

(Ia-p)

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

nng 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, Ci_ ₃ alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^" , -C(0)R ^" , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or C _h alky!.

In some embodiments the prodrug is a compound of Formula (Ib-p):

(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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR -C(0)R -C(0)NR' ₂ or -OP(0)(OR')OR\ wherein each R' is independently hydrogen or C _h alky!.

In some embodiments, the rodrug is a compound of Formula (Ic-p):

(Ic-p)

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

ring A, Y ¹ , Y ² , R and R ^~ are as described above; and P is -C(0)OR\ -C(0)R\ -C(0)NR' ₂ or -OP(0)(OR')OR\ wherein each R' is independently hydrogen or Ci- ₃ alkyl.

In some embodiments, the rodrug is a compound of Formula (II-p):

(II-p)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

1 2 3 2 3

ring A, X , X , X , R, R , R and n are as described above;

R ² is hydrogen, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR -C(0)R -C(0)NR' ₂ or -OP(0)(OR')OR\ wherein each R' is independently hydrogen or C _1-3 alkyl.

In some embodiments the prodrug is a compound of Formula (Ila-p):

(Ila-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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^: , -C(0)R ^: , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or Ci _-3 alkyl.

In some embodiments, the rodrug is a compound of Formula (IIa-1-p):

(IIa-1-p) or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

R, R and n are as described above:

R ² is hydrogen, Ci_ ₃ alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^" , -C(0)R ^" , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or C^alkyl.

In some embodiments the prodrug is a compound of Formula (IIa-2-p):

(IIa-2-p)

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

P is -C(0)OR\ -C(0)R\ -C(0)NR ₂ or -OP(0)(OR')OR\ wherein each R'

independently hydrogen or Ci- ₃ alkyl.

In some embodiment he prodrug is a compound of Formula (IIa-3-p):

(IIa-3-p)

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

P is -C(0)OR ^" , -C(0)R', -C(0)NR ^" ₂ or -OP(0)(OR')OR', wherein each R'

independently hydrogen or C^alkyl.

In some embodiments, the rodrug is a compound of Formula (III-p):

(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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR -C(0)R -C(0)NR' ₂ or -OP(0)(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):

(IIIa-p)

or a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein

Y ³ , X ¹ , X ² , X ³ , R, R ² , R ³ , R ⁴ and n are as described above;

R ² is hydrogen, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^: , -C(0)R ^: , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or Ci _-3 alkyl.

In some embodiments the prodrug is a compound of Formula (IIIb-p):

(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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR -C(0)R -C(0)NR' ₂ or -OP(0)(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):

(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, Ci_ ₃ alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^" , -C(0)R ^" , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or C _h alky!.

In some embodiments the prodrug is a compound of Formula (IIIc-p):

(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, d _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^: , -C(0)R ^: , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or C _h alky!.

In some embodiments the prodrug is a compound of Formula (IIIc-l-p):

(IIIc-l-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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR -C(0)R -C(0)NR' ₂ or -OP(0)(OR')OR\ wherein each R' is independently hydrogen or C _1-3 alkyl.

In some embodiments, the rodrug is a compound of Formula (IV-p):

(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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^: , -C(0)R ^: , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or Ci _-3 alkyl.

In some embodiments, the rodrug is a compound of Formula (IVa-p):

(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, Ci _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^" , -C(0)R ^" , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is independently hydrogen or C _1-3 alkyl. In some embodiments, the rodrug is a compound of Formula (IVb-p):

(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, d _-3 alkyl, Ci _-3 haloalkyl, -CH ₂ OH, -CH ₂ OR, -C(0)OR or -CH ₂ OP; and

P is -C(0)OR ^" , -C(0)R ^" , -C(0)NR' ₂ or -OP(0)(OR')OR', wherein each R' is

independently hydrogen or C _h alky!.

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), (Illb-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 (la)-(81).

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-l-p),

(IV-p), (Iva-p) or (IVb-p), X ¹ , X X R , R R ^J and n are selected from any combination of groups (la)-(81), and P is -C(0) 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-l-p),

(IV-p), (Iva-p) or (IVb-p), X ¹ , X X R , R , R ^J and n are selected from any combination of groups (la)-(81), and P is -C(0)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-l-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 (la)-(81), and P is -C(0)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-l-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 (la)-(81), and P is -OP(0)(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's brain and/or the subject'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's brain and/or the subject'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/Figure 8 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'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, norbomenyl and bicyclo[2.2.2]oct-2-enyl. Fused bicy clic 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 -CI, -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-l-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-l-yl, thienopyridinyl, 4,5,6,7- tetrahydrobenzo[c][l,2,5]oxadiazolyl, and 6,7-dihydrobenzo[c] [l,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 -NO2 group.

The term "oxo" as used herein means a =0 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 Al (apoAl), 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 ApoAl 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 ApoAl 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 ApoAl . As shown in the examples that follow, a reduction in apoAl closely correlates with active T. gondii infection. The apoAl may be administered as a protein therapeutic, or may be administered in an expression construct (such as a recombinant viral vector, etc.) that expresses apoAl (i.e. : gene therapy).

In one embodiment, the subject to be treated has a decreased level of serum ApoAl compared to control.

UniProtKB - P02647 (APOA1 HUMAN)

M AAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK VQPYLDDFQK WQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ GLLPVLESFK VSFLSALEEY T KLNTQ (SEQ ID NO: 4).

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-(lH)-quinolone scaffolds that target the cytochrome bci complex Qi site, of which, a substituted 5,6,7, 8-tetrahydroquinolin-4-one inhibits active infection (IC50, 30 nM) and cysts (IC50, 4 μΜ) in vitro, and in vivo (25 mg/kg), and drug resistant Plasmodium falciparum (IC50, <30 nM), with clinically relevant synergy. Mutant yeast and co-cry stall ographic studies demonstrate binding to the bc _} complex (¾ 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 ⁰ , especially eye and brain ^{1 0} and cause fatalities ^S1"20 . Primary infections may be asymptomatic, or cause fever, headache, malaise, lymphadenopathy, and rarely

meningoencephalitis, myocarditis, or pericarditis ⁹ ' ^{1 U2} . Retinochoroiditis and retinal scars develop in up to 30% of infected persons ^ ⁷ ' ¹³ , and epilepsy may occur ^{6 14} . In immune- compromised and congenitally infected persons, active infection frequently is harmful ⁰ . 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, 11} .

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"24 . 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 y ear. 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 ²⁴³ , 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 . Further, cytochrome bc _} expression is markedly increased in encysted EGS bradyzoites suggesting cytochrome bci might be a viable drug target for this life stage. This mitochondrial membrane bound protein complex cytochome bc _\ , 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-(lH)- quinolone scaffolds that target the Qj site of cytochrome bcl 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' 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 TgCatBrl, TgCatBrl 8 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=>I (570) and a disordered area beginning at 821,

GGNRPHYHV AKQEWRVRY YMNGKRKMRTYS AKF Y

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' 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 (Figure 5) 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 day s 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 2x10 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 MM 6 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 (Figure 6a) 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 (Figure 6). 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 (Figure 6). The number of genes significantly up or down regulated in MM6 and NSC cells compared to uninfected controls are depicted in Figure 6.

Overexpressed genes differ from those of GT1, ME49 and VEG tachyzoite-infected human NSC cells (Figure 7a), 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 (Figure 6e; Figure 2). 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 (Figure 7b-c). 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 (Figure 7 a-c). Identifying novel and efficacious compounds against T. sondii cytochrome bc

Iincreased expression of cytochromes in EGS (Figure 7c) made it pertinent to synthesize and test an endochin-like quinolone (ELQ) 271, which was previously reported to inhibit T. gondii cytochrome bc _} Qj site and reduce, but not eliminate, brain cyst numbers in mice ² '. ELQ271 also inhibited EGS in vitro (Figure 7d 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 _} had a modest effect on tachyzoite replication and a small effect on size and number of EGS cysts (Figure 7d 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 _} ) inhibitors of P. falciparum cytochrome at nanomolar concentrations ²⁷ . ELQs are part of the 4-(lH)-quinolone class of cytochrome bci inhibitor

36,42,40,45,49,52,53,54,56-62 ^ ( _{Dogget et} ^ _13tn international Toxoplasmosis Meeting Abstract. Gettysburg Pennsylvania, 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 bcl, 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 _} with improved solubility (Figure 8) compared to known quinolone-based inhibitors. Noting the previous work of GS on the preclinical development of Clopidol derivatives which led to terminating studies secondary to toxicity in the rat models, as another serious deficiency ⁶ ' and the incorporation of the diphenyl ether group onto the central 4-(lH)-quinolone core as reported by Riscoe et al. ²⁷ , we focused on the central core ring system. Doggett, Riscoe et al's ²⁷ ELQ 271 (Figure 8) was reported to be ineffective against yeast with a mutation in the Qi site. Nonetheless, it recently was shown that ELQs can bind both Qi and Q ₀ depending on subtle chemical changes ^51~3 . As a result of our initial efforts, a 5,6,7,8-tetrahydroquinolone (MJM170, 2) displayed promising results. (Figure 8; Table 2). We chose ELQ271 for comparison because it had the greatest activity at the lowest dose (5mg/kg) in the mouse model of Doggett despite the higher cytotoxicity toward human fibroblasts in the in vitro toxicity studies. ²¹

MJM170 is a potent inhibitor of T. gondii tachyzoites (RH-YFP strain, IC ₅₀ 0.03 μΜ) and bradyzoites (EGS strain, IC50 4 μΜ), equipotent to ELQ271 (Table 2, Figure 9).

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 > 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

Structure

Mol. Wt. 411.4 331.4 T. gondii

Tachyzoite IC ₅₀ 0.03 0.03

μ

T. gondii

Bradyzoite IC50 1 4

μΜ

P. falciparum 0.03 (D6) 0.09 [TM91C235] 0.10 0.01 [D6] 0.03 (TM91C235] 0.03 IC50 μΜ ³ fW2) 0.13 (C2B) (W2) 0.01 (C2B)

HFF Toxicity CC50

20 20

μΜ

Kinetic Solubility

0.15 1.97

PBS ρΗ 7. μΜ"

FaSSIF Solubility

3.4 9.8

pH 6.5 μΜ ^b

Human

microsomal

171.9 146.3

stability T ₂

mins ^b

Mouse

microsomal

> 200 21.0

stability T1/2

mins ^b

MDCK-MDR1

PappA-B N.D. 32.1

x lO ⁶ cm/s ^b

MDCK-MDR1

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 zebraflslt assay. MJM 170 was highly efficacious against RH (Figure 10a) and Prugniaud (Figure 10b) strain tachyzoites in mice at 25mg/kg without toxicity for 5 days (p<0.00), and modestly reduced numbers of Me49 strain cysts established >2months earlier when treated with 12.5-25mg mg/kg for 17 days (p<0.002) (Figure 10c). 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 (Figure lOd).

Cytochrome bc _} Qj is the binding site of MJM170 which is potent against

Plasmodium falciparum and yeast. Tetrahydroquinolone binds to the Qi site of cytochrome bcj: Studies to determine whether cytochrome bcj Qi is the molecular target of MJM170 initially included studies of resistance of yeast and P. falciparum with known cytochrome b Qi mutations predicted to cause a steric clash with MJM170 (Figure 11). Recently, we reported co-crystal structures of GSK's cytochrome bc _} inhibitors bound to bovine cytochrome bc _} at the Qi site ^" demonstrating that these pyridone inhibitors and other structurally related inhibitors bind to an alternative site to atovaquone on cytochrome bc _} . This structure allowed us to model MJM170 within the Qi site using the Maestro Suite from Schrodinger. This molecular modelling predicted steric clashes in mutant yeast and P.

falciparum cytochrome bc with MJM170 (Figure 11a).

Co-crystallization of MJM170 with bovine cytochrome bcj 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 (Figure lid). There was no steric clash for P. falciparum- model based upon this crystal stucture, consistent with in vitro assays (Figures 11 e,f). MJM170 was co-crystallized with bovine cytochrome bc _\ and the resulting good quality electron density maps allowed for unambiguous placement of MJM170 within the Qi site (Figure 111). The planar region of the quinolone group is held between heme bjj 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 Phel8

(Figure llf). An example of a stereo electron density involving Ilel l8-Metl29 and Phel 83- Phe 199 is shown in Figure llg).

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 (Figure lid), and documented that the Qi 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 _} 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 ₀ site on cytochrome bci. A yeast M221Q substitution within the Qi site displayed resistance to ELQ inhibition further confirming that this to be the target site ¹¹ . MJM170 and ELQ271 were effective against S. cerevisiae wild type parental AD 1-9 strain at lmM, 100, 5 and 1 μΜ 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 Qi site predicted to yield a steric clash upon inhibitor binding were resistant to MJM170 (Figure lid)

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 _} Qi mutant (Figure 12). 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 (Figure 12a).

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 triazines 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 Qi inhibitor for P. falciparum (Figure 12b). 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 ency sted 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 unbeatable life cycle stage, and biologic consequences of such persistent infection. RNAseq and iniR 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 unbeatable 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, ency sted 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 ency sted bradyzoites in vitro.

Recent cry stallographic studies with the bovine cytochrome bc _\ complex allowed us to rationally design a novel compound to target the Qi site of cytochrome b. Our novel compound was designed to address issues with poor solubility of existing quinolone/pyridone Qi inhibitors. One of these compounds MJM170, a substituted 5,6,7,8-tetrahydroquinolin-4- one inhibits active infection (IC50 30 nM) and cysts (IC50 4 μΜ) 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 hav e 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 <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 _\ confirm the mechanism of action/target for MJM170. The co-crystal structure of MJM170 in complex with bovine cytochrome bc _\ reveals a clear binding mode within the Qi site. Using homology models of the apicomplexan Qi 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 _\ . The larger binding pocket of the apicomplexan versus the mammalian bc _\ 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'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 & 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 Integrativ e Biology of the Cell IACUC and all experimental protocols were approved by the IRB committees, and the Centre national de la 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; GTl. All other than EGS are T.gondii tachyzoites . These parasites are passaged in HFF.

Isolation ofDNA andRNA. 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 RTN scores were > 8.

Gene sequencing, genomics, RNA andMiR 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 lOObp 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 GTl (SRR516419), VEG (SRR516406) and TgCatBrl (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 vl3.0 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 2h, 18h or 48h was treated with miPvNeasy Mini Kit columns (Qiagen) following manufacturer instructions to separate mRNA and miRNA fractions. Afterwards, lllumina barcoded sequencing libraries were constructed with TruSeq RNA Sample Preparation Kits v2 (lllumina) for mRNA and miRNA TruSeq Small RNA Library Preparation Kit (lllumina) for miRNA. Libraries were sequenced as lOObp single reads with lllumina HiSeq 2000 apparatus in pulls of 6 or 9 samples per lane for mRNA (yield ~3Gbp per sample) and miRNA (yield ~2Gbp 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 log2 -fold-change > 1.5 (i.e. fold-change > 2 and < 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 TgCatBrl. 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'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 JP, Ferreira LR. 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 >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, l.OOg, 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%); R _{ 0.14 (10% MeOH-DCM); δ _Η (300 MHz, CDC1 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); 8 _C (125 MHz, CDC1 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) Buty lamine (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, 1.02g, 6.28 mmol, 1.00 eq) in DMF (10.0 ml). To this heterogeneous mixture was added I ₂ (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 0 and dried (Na ₂ S0 ₄ ) to give the desired product as a colourless solid (1.76g, 6.09 mmol, quantative yield); δ _Η (300 MHz, DMSO-</ 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 x 30 ml), brine (3 x 30 ml), dried (Na ₂ S0 ₄ ) and concentrated to give a pale yellow oil (1.09 g, 3.44 mmol, 61%); R _f 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 _Η (500 MHz, CDC1 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 & CH ₃ ), 2.84 (2H, t, J 6.5, CH ₂ ), 3.97 (2H, q, J 7.0, OCH ₂ ); 6 _C (125 MHz, CDC1 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 (OCFt 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-tetrahydroquin oline (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 C0 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 0 (25 ml). Combined organics were washed with H 0 (3 x 30 ml), then brine (3 x 30 ml), dried (Na ₂ S0 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%); R _f 0.31 (3: 1 Pet-EtOAc); HPLC (RT = 3.08 mins); δ _Η (300 MHz, CDC1 ₃ ) 1.04 (3H, t, J 7.0, ethoxy CH ₃ ), 1.76-1.93 (4H, m, 2xCH 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); b _c (125 MHz, CDCI 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: MFt ⁺ , 360.1973.

C ₂₄ H ₂₆ N0 ₂ requires MH, 360.1964). Synthesis of 2-methyl-3-(4-phenoxyphenyl)-4-ethoxy-5,6,7,8-tetrahydroquin oline (MJM170, 4) ⁴⁹ Aqueous hydrobromic acid (>48%) (1.00 ml) was added to a solution of 2- methyl-3-(4-phenoxyphenyl)-4-ethoxy-5,6,7.8-tetrahydroquinol ine (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 0 to give the desired product as an off-white solid (0.155 g, 0.467 mmol, 74%); HPLC (RT = 2.56 mins); δ _Η (500 MHz, DMSO-</ ₆ ) 1.66-1.72 (4H, m, 2xCH 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); 8 _C (125 MHz, DMSO-<¾) 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); mJz (ES) (Found: MH ⁺ , 332.1654. C ₂₂ H ₂₂ N0 ₂ requires ME, 332.1645).

ADME studies of inhibitors: Compounds that were highly effective in vitro (IC50 <1 μΜ) were tested for ADME profiling ^843"58 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-MDRl 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 μΐ 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 μΐ 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 μΜ 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 (lx, [+] 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 (lx, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C(lx, [+] 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 μΐ 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 μΜ. Data was collected using Gen5 software and analyzed with Excel.

Type II parasites. 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 (lx, [+] 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 3xl0 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 Do chos Biflorus Agglutinin, DAPI, and anti-BAGl, and anti-SAGl. 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's t- test. P<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 zebra fish):

Initial screening with tachyzoites using I VIS, 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 Figure 6.

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 ^Sl9 .

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 infectivily 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&E) or

immunoperoxidase stained. All sections were examined and assessed without knowledge of the group from which they originated ⁸³⁹ .

Testing of cytochrome b Qi 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 strains ^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 respirator ' deficient mutants within the center N of cytochrome h in S accharomy ces cerevi si ae.

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 ₆ oo 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 (ImM, 500 μΜ, 100 μΜ, and 10 μΜ) 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 Qi and DHODH mutants and drug combinations or 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 0 ⁺ serum and 0.25% AlbuMAX® II (Life Technologies 11021-045).

In vitro drug sensitivity and EC so 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. EC50 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. EC50 values were calculated as above, and FICs were calculated for each drug combination as described ⁸⁷⁶ . Synergy was defined as an FIC < 1.0, additivity as FIC = 1.0, and antagonism as FIC > 1.0. Molecular Modelling/Chemogenomics. X-ray structures of the cytochrome bc _\ complex are available from the Protein DataBank ⁸ "'. An Homology model of the T. gondii cytochrome bc _\ 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 ⁵⁸² & eHiTs ⁵⁸³ (SymBioSis), Maestro & Glide ⁵⁸⁴ (Schrodinger), AutoDock (Scripps Institute), ROCS/EON ⁸⁸⁵ & VIDA ⁵⁸⁶ (OpenEye) and the Marvin/JChem suites (ChemAxon).

X-ray crystallography: Cytochrome bci was purified usig standard technqiues. 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. bci 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/mm. 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. bci and separate remaining contaminants. The cyt. bc _} 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 iMosflm 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 Qj site of cyt. bci using Coot. Cycles of alternating Refmac5 and manual modelling resulted in a completed model. Data collection and refinement statistics are summarised In table 1 A. 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'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.

References for Example 1

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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 <125 nM) and bradyzoites (IC 90 500 nM), and drug resistant Plasmodium falciparum in vitro (IC 90 <50nM), not toxic to human HepG cells (>17 μΜ). 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 (3mg/kg single dose) to protect against a GO arrested parasite that could persist in interferon Y knockout mice similar to the effect of tafenoquine for malaria hypnozoites. There was cure with oral dosing, 0.625mg/kg, 3 oral doses of JAG21, and cure with a single dose of 2.5mg/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 cy tochrome 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 bom 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 congenita! infection globally, causing 12 million disability adjusted li e 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 1.25mg 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 GO/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 (lx, [+] 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 (lx, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C (lx, [+] 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 μΐ 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.

An initial screening assay of 10 μΜ, Ι μΜ, 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 μΜ. If compounds did appear to be effective at 1 μΜ, another experiment was conducted to assess effect at 1 uM, 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 μΜ and 50 μΜ. Compounds were diluted in IMDM-C, and 20 μΐ 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 μΐ 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 fiuorimeter 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 (lx, [+] 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 3x10 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 μΐ, 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 fiuorimeter and analyzed graphically in Prism (GraphPad Software).

Toxoplasma in vivo

IVIS. Mice were infected lntrapentoneally with 20x10 ³ Toxoplasma gondii (Pru strain expressing luciferase) tachyzoites. Treatment commenced 2 hours later with JAG21 (5mg/kg) which was dissolved in DMSO and administered intraperitoneally in a total volume of 0.05ml. 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 inj ection with 150 mg/kg of D-luciferin potassium salt solution.

Brain cysts: Mice were infected intraperitoneally with 20x 10 ^J Treatment commenced 2 hours later with JAG21 (5 mg/kg) which was dissolved in DMSO and administered intraperitoneally in a total volume of 0.05ml. 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 3mg/kg tafenoquine was administered once on day -1. Cysts in brain were quantitated after concluding treatment

RPS13 Δ. This GO arrested parasite persists in tissue culture for prolonged times in the absence of tetracycline. The design of this experiment is shown in Figure 18. 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

21 3

Methods for enzyme assays ^" : 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 μΐ 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 μΐ of 96% ethanol (acidified with 10 mM HC1). 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 & Jensen 2005) ²³ . Cultures contained a 2% suspension of 0+ 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 μΜ gentamicin sulphate. Cultures were grown under a gaseous headspace of 4 % O2 and 3% CO2 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 HP0 ₄ , 8.0 mM Na ₂ HP0 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 K2HPO4, 50 mM KH2PO4, 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 _\ native assay

Plasmodium falciparum bc _\ complex cytochrome c reductase (Pfoci) 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 μΐ,. Potassium cyanide (10 μΜ), oxidised cytochrome c (30 μΜ), 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 μΜ. DMSO (0.1% v/v) and atovaquone (1 μΜ), a known malarial cytochrome bc _\ complex inhibitor, were used as negative and positive controls respectively. The reaction was initiated by the addition of 50 μΜ 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-I/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 μ&'ιηΐ 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, CT, 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) hydroxy ethyl 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, MA, USA) IVIS instrument at 24, 48 and 72 hr post-sporozoite infection. Additionally, using a flow cytometry system (FC500 MPL, Beckman Coulter, Miami, FL, USA), blood-stage infections were measured. For the IVIS calibration in each test, positive and negative controls were used. D-Luciferin potassium salt, (Xenogen, California 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 lsofiurane. 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 bcl 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 HP0 ₄ ; 2 mM succinic acid; 0.5 mM EDTA) was added at a ration of 2.6L buffer per 1 L of muscle tissue. The solution was then homogenised. The resulting homogenate was adjustered 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.

Solubilization 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 bcl: 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 hydroxy apatite 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 bci, 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- equihbrated 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 bci fractions were then collected and concentrated to 30 mg/m.

Bovine Enzyme crystallography: Compounds designed using structure-based analyses of cytochrome b co-cry stalized 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:.10 mM stock solutions were made with 100% Dimethyl Sulfoxide (DMSO) [Sigma Aldrich] and working concentrations were made with IMDM-C (lx, [+] glutamine, [+] 25 mM HEPES, [-] Phenol red, 10% FBS)[gibco, Denmark]).

Statistical Analysis: A Pearson test was used to confirm a correlation betw een 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 μΜ, and were tested at lower concentrations. A representative graph of this data is shown in Figure 13. JAG050 and JAG021 were identified as lead compounds because the IC50 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 μΜ and 50 μΜ. Results of this experiment are in Figure 14 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>0.05). This suggests that these compounds are not toxic at 10 μΜ or 50 μΜ 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 = 98.

Table 3. Cytotoxicity to human foreskin fibroblasts was therefore assessed for all compounds at 10 μΜ and 50 μΜ. Graph is representative of replicate experiment.

Observation Control JAG050 10 μΜ JAG050 1 μΜ JAG021 10 μΜ JAG021 1 μΜ

1 1 in- < »1* SSi -9 J 2 |«:|

Pseudocysts 3884 1 21 2269 2638 2955 mall «i »smi>>m>> » :-4

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 (Figure 15d). 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 μΜ and 10 μΜ for both compounds (p <0.05, p<0.005, Figure 15a-c).

ADME properties ofTHQs. 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 μΜ respectively, were higher than MJM170 ( 2 μΜ) and ELQ-271 (0.2 μΜ). JAG021 was the most metabolically stable compound in human liver microsomes (>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 >10 xlO ⁶ cm/s) and low efflux (efflux ratio <1.5). i Compound ; Solubility (pH j Human liver i Mouse liver

! ⁷ · ⁴ )* j microsomes* i microsomes*

; ELQ271 ; 0.15 uM j 171.93 min ; 448.13 min j MJM170 : 1.97 μΜ 146.33 min i 20.97 min

I JAG021 I 7.07 uM ; oo I 101.09 min

; JAG050 ; 16.41 uM j 99.04 min i 68.55 min

Table 4. Chart compares properties of solubility and half-life of JAG050 and JAG021 to parent compounds ELQ 271 and MJM170. The test system was 100 mM Phosphate Buffer (pH 7.4). : <10 μΜ is low solubility, 10 - 80 μΜ is moderate solubility and >80 μΜ is high solubility. A < 30 minutes indicates susceptibility to metabolism, between 30 and 120 minutes indicates moderate metabolism and >120 minutes indicates stability in the liver.

Enzyme assays: Enzyme reduction of cytochrome c by the parasite extract is mediated by P. falciparum bc _\ complex cytochrome c reductase (Pft>c ). All three compounds (1 μΜ) 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 Pfic _\ . Additional data demonstrating effect on bovine and plasmodium falciparum enzyme are shown in Table 5. There is selectivity for the malaria enzyme.

: 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' Cytbcl but not fully, indicating that it will be less toxic for bovine/human cyt be (Figure 16)

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 μΜ treatment group for both compounds. However, these differences were not found to be statistically significant (p >0.05).

Effective of JAG21 on Toxoplasma gondii . JAG21 at 5 mg/kg eliminates T. gondii tachyzoites seen in luminescence studies (Figure 17).

JAG21 against GO 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 RPS13A minus tetracycline (Figure 18). 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 40-65nM 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 SYBR Green Green

Compound SYBR SYBR SYBR

D6 C235 TM91C23 W2 C2B

ID D6 R ² W2 R ² C2B R ²

IC50 IC50 5 R ² IC50 IC50

(uM) (uM) (uM) (uM)

JAG006 0.29 0.90 0.88 0.92 2.46 0.92 1.66 0.94

JAGN21 0.01435 0,9572 0.06164 0.9706 0.05518 0.972^ 0.04042 0,9X4?

JAG050 0.04664 0.9138 0.06913 0.9562 0.03136 0.9693 0.03635 0.9427

JAG039 9.595 0.9532 >20 N/A >20 N/A >20 N/A

RG38 2.884 0.8936 13.66 0.8338 9.245 0.7954 >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. (Figure 17)

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

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5. Wallon M, Garweg JG, Abrahamowicz M, Comu C, Vinault S, Quantin C, et al. Ophthalmic outcomes of congenital toxoplasmosis followed until adolescence. Pediatrics.

2014 Mar;133(3):e601-8.

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CONGENITAL TOXOPLASMIC CHORIORETINITIS: Pediatr Infect Dis J [Internet]. 2006 Mar [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 0, 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 Sep;21(3):656-8.

10. Phan L, asza K, Jalbrzikowski J, Noble AG, 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 Sep; 146(3).

11. Vercesi AE, Rodngues CO, Uyemura SA, Zhong L, Moreno SNJ. 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 AA, Nasr M, Araujo FG. Two 2-hydroxy-3-alkyl-l,4-naphthoquinones with in vitro and in vivo activities against Toxoplasma gondii. Antimicrob Agents Chemother. 1998 Sep;42(9):2284-9.

13. Doggett JS, Nilsen A, Forquer I, Wegmann KW, Jones-Brando L, Yolken RH, et al. Endochin-like quinolones are highly efficacious against acute and latent experimental toxoplasmosis. Proc Natl Acad Sci U S A. 2012 Sep 25;109(39): 15936-41.

14. Capper MJ, O'Neill PM, Fisher N, Strange RW, Moss D, Ward SA, et al.

Antimalarial 4(lH)-pyridones bind to the Qi site of cytochrome bcl. Proc Natl Acad Sci U S A. 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 Jan [cited 2015 Jul 8];47(1):309-16.

16. Vidigal PVT, Santos DVV, Castro FC, Couto JC de F, Vitor RW de A, Brasileiro Filho G. Prenatal toxoplasmosis diagnosis from amniotic fluid by PCR. Rev Soc Bras Med Trop [Internet]. 2002 Feb [cited 2015 Jul 8];35(1): 1-6.

17. Silva LA, Brandao GP, Pinheiro BV, Vitor RWA. Immunosuppression with cyclophosphamide favors reinfection with recombinant Toxoplasma gondii strains. Parasite J Societe Fr Parasitol [Internet]. 2012 Aug [cited 2015 Jul 8];19(3):249-57.

18. Fomovska A, Huang Q, El Bissati K, Mui EJ, Witola WH, 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 RD, Mui E, Dubey JP, Ferreira LR, Hickman MR, 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. & 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 thm 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 μπι 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. ¾ NMR spectra were obtained with a Bruker DRX400, Varian VXR400 or VXR300. H NMR spectra were reported in parts per million (δ) relative to TMS (0.0), DMSO-d6 (2.50) or CD ₃ OD (4.80) as an internal reference. All ^l U NMR spectra were taken in CDC13 unless otherwise indicated.

H

a) i) Meldrums acid, triethylorthoacetate, 110 °C, ii) Aniline, 110 °C, iii) Dowtherm A, 250 °C, b) Pt0 ₂ , H ₂ , AcOH, c) NIS, Acetonitrile, 80 °C, d) Cu(OAc) ₂ , Pyridine, TEA, DCM, e) Pd(dppf)CI ₂ Bispinocolatodiborane, KOAc, DMF, 80 °C. t) Pd(dppf)CI ₂ , Na ₂ C0 ₃ , DMF, 80 °C.

a)i) Meldrums acid, triethylorthoacetate, 110 °C, ii) Aniline, 110 °C, iii) Dowtherm A, 250 °C

General method A

2,2-Dimethyl-l,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(lH)-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 %).1H 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, CnH ₈ F ₃ NO requires 228.0630).

7-ethyl-2-methylquinolin-4(lH)-one 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 %) ^l H NMR (500 MHz, CDC1 ₃ ) 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( 1 H)-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%).^ NMR (400 MHz, CDC1 ₃ ) 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(lH)-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 seperation 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 niL) 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-tetrahvdroquinolin-4(lH)-one. A solution of 4-hydroxyl 2-methyl-quinilone (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 Ci ₀ Hi ₃ NO requires 164.1075).

2-Methyl-6-(trifluoromethyl)-5.6.7.8-tetrahydroquinolin-4 (lH)-one The title compound was synthesised following general procedure B from 2- methyl-6-(trifluoromethyl)quinolin-4(lH)-one (466 mg, 2.0 mmol), The title compound was isolated as colourless solid (230 mg, 0.99 mmol, 49%). *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, CnH ₁₂ F ₃ NO requires 232.0949).

2.6-Dimethyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one The title compound was synthesised following general procedure B from 2,6- dimethyl-quinolin-4(lH)-one ( 1.0 g, 5.78 mmol), The title compound was isolated as a colourless solid (780 mg, 4.30 mmol, 76 %). *H NMR (400 MHz, CDC1 ₃ ) δ 12.26 (s, IH), 6.09 (s, IH), 2.88 - 2.64 (m, 3H), 2.30 (s, 3H), 1.98 (dd, J= 16.9, 10.1 Hz, IH), 1.87 (d, J = 12.4 Hz, IH), 1.77 (m, IH), 1.39 (ddd, J = 23.9, 11.1, 6.0 Hz, IH), 1.08 (d, J= 6.5 Hz, 3H); M/Z (ESI+); 178.13 (Found MH ⁺ ; 178.1280, C11H15NO requires 177.1154).

2.7-Dimethyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one The title compound was synthesised following general procedure B from 2,7- Dimethyl-quinolin-4(lH)-one (350 mg, 2.0 mmol). The title compound was isolated as a colourless solid (311 mg, 1.75 mmol, 88 %).¾ NMR (500 MHz, MeOD) δ 6.31 (s, IH), 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, CnHisNO requires 177.1154).

7-ethyl-2-methyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one The title compound was synthesised following general procedure B from 7- ethyl-2-methylquinolin-4(lH)-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, CDC13) δ 12.20 (s, IH), 6.09 (s, IH), 2.88 - 2.66 (m, 2H), 2.46 - 2.19 (m, 5H, 2-Me), 1.95 (d, J = 13.0 Hz, IH), 1.63 (s, IH), 1.38 (td, J = 13.9, 6.9 Hz, 2H), 1.33 - 1.22 (m, IH) 0.94 (t, J= 7.4, 3H); M/Z (ESI+); 192.14 (Found MH ⁺ ; 192.1378 C12H17NO requires 192.1383).

7-trifluormethyl-2-methyl-5,6,7,8-tetrahvdroquinolin-4(lH )-one The title compound was synthesised following general procedure B from a mixture of 7-trifluormethyl-2-methy lquinolin-4(lH)-one & 5-trifluormethyl-2- methylquinolin-4(lH)-one (1.5 g). The title compound was isolated as a colourless solid (495 mg, 2.14 mmol). *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, CnH^NO requires 232.0949).

c) NIS, Acetonitrile, 80 °C

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(lH)-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 ^χ 10 mL water) afforded the title compound.

4( \H), 3-iodo-2-methyl-5.6.7.8-tetrahydroquinolin-4( lH)-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(lH)-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 ^χ 10 mL water) to afford the title compound (39) as colourless microcrystals (1.45 g, 5.02 mmol, 86 %). *H 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 Hi ₂ INO requires 290.0036).

3-Iodo-2-methyl-6-(trifluoromethyl)-5.6.7.8-tetrahvdroqui nolin-4(lH)-one The title compound was synthesised following general procedure C from 2- methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-4(lH)- one (230 mg, 1.0 mmol). The title compound was isolated as colourless solid (300 mg, 0.84 mmol, 84%). *H NMR (400 MHz, DMSO) 5 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, CiiHnF ₃ rNO requires 357.9910).

3-Iodo-2.6-dimethyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one

The title compound was synthesised following general procedure C from 2,6- dimethyl-5,6,7,8-tetrahydro quinolin-4(lH)-one (750 mg, 4.24 mmol). The title compound was isolated as colourless solid (740 mg, 2.44 mmol, 58 %). *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 _n Hi ₄ INO requires 304.0193). 3-Iodo-7-ethyl-2-methyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one The title compound was synthesised following general procedure C from 7- ethyl-2-methyl-5,6,7,8-tetrahydroquinolin-4(lH)-one (110 mg, 0.57 mmol). The title compound was isolated as colourless solid (180 mg, 0.57 mmol, 99 %). *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, C12H16INO requires 318.0349).

3-Iodo-7-trifluormethyl -2-methyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one The title compound was synthesised following general procedure C from 7- trifluormethyl-2-methylquinolin-4(lH)-one (480 mg, 2.10 mmol). The title compound was isolated as a colourless solid (688 mg, 1.92 mmol, 91 %). *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, CnHnF O requires 357.9910).

d) Cu(OAc) ₂ , Pyridine, TEA, DCM,

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 A molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HC1 (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. l-Bromo-4-(4-(trifluoromethoxy)phenoxy)benzene.

^Br XXX ^0CF3 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 as 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%). ^J H NMR (500 MHz, CDC1 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

Ci ₄ HnBr0 ₃ requires; 306.9964). l-bromo-4-(4-chlorophenoxy)benzene 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%). *H NMR (500 MHz, CDC1 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

0 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%). *H NMR (500 MHz, CDC1 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 Ci ₄ HnBr0 ₃ requires 306.9964).

5-(4-bromophenoxy)-2H-1.3-benzodioxole

Br^^^ ^{\/^} o 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 1H 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 & 2.5 Hz, 1H), 6.00 (s, 2H);

e) Pd(dppf)CI _2, Bispinocolatodiborane, KOAc, DMF, 80 °C. f) Pd(dppf)CI ₂ , Na ₂ C0 ₃ , DMF, 80 °C.

1.1 General method E &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 CC>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^O (15.0 mL). The organic layers were combined and washed with H ₂ 0 (15.0 mL), brine and dried over MgSC>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-tetrahvdroquinolin-4(lH)-one

The title compound was synthesised following general procedure

E&F from 3-iodo-5,6,7,8-tetrahydroquinolin-4(lH)-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 %). ^ 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 C23H20F3NO3 requires 416.1473).

3(4-(4-trifluoromethoxyphenoxy)phenyl)-2.6-dimethyl-5.6.7 .8-tetrahvdroquinolin-4(lH)-one

The title compound was synthesised following general procedure E&F from 3-iodo-2,6-dimethy l-5,6,7,8-tetrahydroquinolin-4(lH)-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 %). *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

C24H22F3NO3 requires 452.1444).

3(4-(4-trifluoromethoxyphenoxy)phenyl)-2.7-dimethyl-5.6.7 .8-tetrahvdroquinolin-4(lH)-one

The title compound was synthesised following general procedure E&F from 3-iodo-2,7-dimethyl-5,6,7,8-tetrahydroquinolin-4(lH)-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 %).¾ 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 C24H22F3NO3 requires 452.1444).

6-Ethyl-3-(4-(4-trifluoromethoxyphenoxy)phenyl)-2-methyl- 5.6.7.8-tetrahvdroquinolin- 4(THVone The title compound was synthesised following general procedure E&F from 3-iodo-2-methyl-6-(trifluoromethyl)-5,6,7,8-tetrahydroquinol in-4(lH)- 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 %). *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 Hi9F ₆ N0 ₃ requires

484.1342). 7-Ethyl-2-methyl-3(4-(4-trifluoromethoxyphenoxy)phenyl)-5.6. 7.8-tetrahydroquinolin-

4(lH)-one

The title compound was synthesised following general procedure E&F from 7-ethyl-2-methylquinolin-4(lH)-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 %). *H NMR (500 MHz, CDCI3) 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, C25H24F3NO3 requires 444.1781). 7-trifluromethyl-2-methyl-3(4-(4-trifluoromethoxyphenoxy)phe nyl)-5.6J,8- tetrahvdroquinolin-4(lH)-one

The title compound was synthesised following general procedure x from 7-trifluormethyl-2-methylquinolin-4(lH)-one (360 mg, 0.99 mmol) and 4- bromo-(4-tnfluromethoxyphenoxy)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 Hi9F ₆ N0 ₃ requires 484.1342). 3-[4-(2H-l J-benzodioxol-5-yloxy)phenyll-2-methyl-5.6 .8-tetrahydro-lH-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(lH)-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 1H NMR (500 MHz, TFA) δ 7.35 (d, J 8.5 Hz, 2H), 7.31-7.29 (m, 3H), 6.98 (s, IH), 6.79 (s, IH), 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 ₂ iN0 ₄ requires 375.1471).

e) Pd(d HBr, AcOH 120 °C. 1.2 General method E &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.), PdC^dppf) (3 mol%) and Na ₂ C0 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 0 (15.0 mL). The organic layers were combined and washed with H ₂ 0 (15.0 mL), brine and dried over MgSO 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-tetrahvdro quinoline The title compound_was synthesised from l-Bromo-4-(4-

(trifluoromethoxy)phenoxy)benzene (100 mg, 0.30 mmol) according to general procedure E&F, to afford the title compound as a colourless gum/viscous oil (30 mg, 0.07 mmol, 23%). *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 C25H24F3NO3 requires 444.1781).

Methyl 4-(4-(4-ethoxy-2-methyl-5.6.7.8-tetrahydroquinolin-3-yl)phen oxy)benzoate as synthesised from methyl 4-(4- bromophenoxy)benzoate (150 mg, 0.49 mmol) according to general procedure E&F. The title compound was isolated as colourless microcrystals (56 mg, 0.13 mmol, 27%). *H NMR (500 MHz, CDCI3) 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 C26H27NO4 requires 418.2018).

Methyl 4-((5-(4-ethoxy-2-methyl-5.6.7.8-tetrahvdroquinolin-3-yl)pyr idin-2-yl)oxy) benzoate

title compound_was synthesised from methyl 3-((5- bromopyridin-2-yl)oxy)benzoate (100 mg, 0.33 mmol) according to general procedure E&F. The title compound_was isolated as a colourless gum/semisolid (30 mg, 0.07 mmol, 21%). 1H NMR (500 MHz, CDC1 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 C25H26N2O4 requires 419.1970).

Methyl 3-(4-(4-ethoxy-2-methyl-5.6J.8-tetrahvdroquinolin-3-yl)pheno xy)benzoate The title compound was synthesised from methyl 3-(4- bromophenoxy)benzoate (150 mg, 0.49 mmol) according to general procedure Ε&Γ. The title compound.was isolated as colourless crystals (50 mg, 0.12 mmol, 25%). ^ MR (500 MHz, CDC1 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, C26H27NO4 requires 418.2018).

Formation of: 3-(4-(4-chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5.6.7.8-tetr ahvdroquinoline

The title compound was synthesised from l-bromo-4-(4- chlorophenoxy)benzene (70 mg, 0.24 mmol) according to general procedure Ε&Γ. The title compound was isolated as colourless oil (20 mg, 0.05 mmol, 27%). *H NMR (500 MHz, CDCI3) 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, C24H24CINO2 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 (>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 etrahvdroquinolin-3-yl)pyridin-2-yl)oxy) benzoate

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%). *H NMR (500 MHz, DMSO) δ 12.83 (s, IH, NH), 11.03 (s, IH, C0 ₂ H), 8.00 (d, J = 8.7 Hz, 2H), 7.99 (s, IH) 7.73 (dd, J= 8.4, 2.4 Hz, IH), 7.24 (d, J= 8.7 Hz, 2H), 7.12 (d, J= 8.4 Hz, IH), 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 C22H20N2O4 requires 377.1496).

4-(4-(2-methyl-4-oxo-l,4,5,6J.8-hexahvdroquinolin-3-yl)ph enoxy)benzoic acid

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%). ^! H NMR (500 MHz, DMSO) δ 13.79 (s, IH), 12.80 (s (b), IH), 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, C23H ₂₁ N0 ₄ requires 376.1543). 3-(4-(2-methyl-4-oxo-1.4.5.6.7.8-hexahvdroquinolin-3-yl)phen oxy)benzoic acid

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%). ^J H NMR (500 MHz, DMSO) δ 13.00 (s, IH), 11.31 (s, IH), 7.70 (d, J= 7.9 Hz, lH), 7.52 (t, J = 7.9 Hz, IH), 7.48 (dd, J = 2.2, 1.6 Hz, 1H), 7.31 (dd, J= 7.9, 1.6 Hz, IH), 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, C23H21NO4 requires 376.1543).

3- (4-(4-chlorophenoxy)phenyl)-2-methyl-5.6.7.8-tetrahvdroquino lin-4(lH)-one title compound was synthesised from 3-(4-(4- chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroqu inoline (20 mg, 0.5 mmol) according to general procedure G. The title compound was isolated as colourless solid (18 mg, 0.05 mmol, 95 %). *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 CINO ₂ requires 366.1253).

3&4-CI, 3-CI 4-F, 3&5- Cl

a) Etl, K ₂ C0 ₃ D F, 80 °C, b) 4-Hydroxyphenyl boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ , D F, 80 °C, c) Phenyl boronic acid, Cu(OAc) ₂ , Pyridine, TEA, DCM, d) HBr (40% aq), Acetic acid, 120 °C.

a) Etl, K ₂ C0 ₃ DMF, 80 °C 4-ethoxy-3-iodo-2-methyl-5.6.7.8-tetrahvdroquinoline. 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 x 40.0 mL), and the resulting organic layers were combined and dried over MgS0 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 Hi ₇ INO requires 318.0349).

b) 4-Hydroxyphenyl boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ , DMF, 80 °C, 4-(4-Ethoxy-2-methyl-5.6.7.8-tetrahvdroquinolin-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 x 20 mL). The organic phases were combined and washed with water (3 x 20 mL) and then dried with brine (1 x 10 mL) and MgS04, before concentration in vacuo. The resulting redish brown solid was then recrystallized in ethyl acetate. To yield the title compound as a colourless solid (220 mg, 0.78 mmol, 61%). *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, Ci ₈ H ₂ iN0 ₂ requires 284.1651).

4-ethoxy-2-methyl-3-(4-phenoxyphenyl)-5.6.7.8-tetrahydroq uinoline. 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 MgSC . 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, C24H26NO2 requires 360.1958).

c) Phenyl boronic acid, Cu(OAc) ₂ , Pyridine, TEA, DCM 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 mmor ¹ ) over heat-activated 4 A molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HC1 (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-t etrahvdroquinoline 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). ^l U 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, C24H24FNO2 requires). 3-(4-(3-Chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5.6.7.8-tetr ahvdroquinoline

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). *H NMR (500 MHz, CDCI3) 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, C24H24CINO2 requires 394.1574).

4-Ethoxy-2-methyl-3-(4-(4-(trifluoromethyl)phenoxy)phenyl )-5.6.7.8-tetrahydroquinoline

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). ^J H NMR (500 MHz, CDC1 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, C25H24F3NO2 requires 428.1832).

4-Ethoxy-3-(4-(3-fluorophenoxy)phenyl)-2-methyl-5.6.7.8-t etrahvdroquinoline

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-flurobenzene boronic acid (184 mg, 1.32 mmol), according to general procedure G as a yellow oil (57%, 190 mg, 0.50 mmol). H NMR (500 MHz, CDC1 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, C24H24FNO2 requires).

4-Ethoxy-3-(4-(3^-dichlorophenoxy)phenyl)-2-methyl-5.6J.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). 1H NMR (300 MHz, CDCI3) 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, C24H23CI2NO2 requires 428.1184). 4-Ethoxy-3-(4-(3-chloro-4-fluorophenoxy)phenyl)-2-methyl-5.6 .7.8-tetrahvdroquinoline

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 %). ![ NMR (400 MHz, CDCI3) 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, C24H23CIFNO2 requires 411.1401.

4-Ethoxy-3-(4-(3-trifluoromethoxyphenoxy)phenyl)-2-methyl -5.6.7.8-tetrahvdroquinoline 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 %); *H NMR (400 MHz, CDC1 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, C25H25F3NO3 requires 444.1781.

4-Ethoxy-3-(4-(3-tnfluoromethylphenoxy)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 %). *H NMR (400 MHz, CDC1 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, C25H24F3NO2 requires 427.1759.

3-[4-(3.5-dichlorophenoxy)phenyll-4-ethoxy-2-methyl-5.6.7 .8-tetrahvdroquinoline 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 ¾ 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, C24H24CI2NO2 requires 428.1179.

d) HBr (40% aq), Acetic acid, 120 °C.

1.4 General method D

To a solution of the 4-ethoxy-3-(diaryl ether)-hydroxyquinolone (1 equiv.) in acetic acid (2 niL ηιηιοΓ ¹ ) was added hydrogen bromide (>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(lH )-one

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 %). *H NMR (500 MHz, DMSO-d ₆ ); δ 7.38 (t, J = 7.9 Hz, 2H, H-3" & 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, C22H ₂₁ N0 ₂ requires 332.1650).

3-(4-(4-Fluorophenoxy)phenyl)-2-methyl-5.6.7.8-tetrahydro quinolin-4(lH)-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%). ^! 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, C22H20FNO2 requires 350.1550). 3-(4-(3-Chlorophenoxy)phenyl)-2-metfayl-5.6J.8-tetrahygroqui nolin-4(lH)-one

The title compound was synthesised from 3-(4-(3- chlorophenoxy)phenyl)-4-ethoxy-2-methyl-5,6,7,8-tetrahydroqu inoline (200 mg, 0.51 mmol) according to general procedure D. The title compound was isolated as colourless solid (120 mg, 0.33 mmol, 66%). ^! H NMR (500 MHz, DMSO) 5 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 ₂ oClN0 ₂ requires 366.1255). 2-Methyl-3-(4-(4-(trifluoromethyl)phenoxy)phenyl)-5.6.7.8-te trahvdroquinolin-4(lH)-one

The title compound was synthesised from 4-ethoxy-2-methyl-3-(4-

(4-(trifluoromethyl)phenoxy)phenyl)-5,6,7,8-tetrahydroqui noline (47 mg, 0.12 mmol) according to general procedure D. The title compound was isolated as colourless solid (25 mg, 0.07 mmol, 60%). ^! 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, C23H20F3NO2 requires 400.1519).

3-(4-(3-Fluorophenoxy)phenyl)-2-methyl-5.6.7.8-tetrahvdro quinolin-4(lH)-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%). ^! 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, C22H21FNO2 requires 350.1556).

3-(4-(3.4-Dichlorophenoxy)phenyl)-2-methyl-5.6J.8-tetrahv droquinolin-4(lH)-one

The title compound was synthesised from 4-Ethoxy-3-(4-(3- trifluoromethoxyphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroq uinoline (100 mg, 0.23 mmol) according to general procedure D. The title compound was isolated as colourless solid (72 mg, 0.16 mmol, 76 %). *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, C23H21F3NO3 requires 416.1468).

3-(4-(3.4-Dichlorophenoxy)phenyl)-2-methyl-5.6.7.8-tetrah vdroquinolin-4(lH)-one

The title compound was synthesised from 4-Ethoxy-3-(4-(3- trifluoromethylphenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroqu inoline (193 mg, 0.45 mmol) according to general procedure D. The title compound was isolated as colourless solid (174 mg, 0.44 mmol, 96 %).¾ 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 C23H21F3NO2 requires 400.1519).

3-(4-(3.4-Dichlorophenoxy)phenyl)-2-methyl-5.6.7.8-tetrah vdroquinolin-4(lH)-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 %). *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, C22H20CI2NO2 requires 400.0866).

3-[4-(3-chloro-4-fluorophenoxy)phenyll-2-methyl-5.6J.8-te trahvdro-lH-quinolin-4-one

title compound was synthesised from 4-Ethoxy-3-(4-(3-chloro-4- fluorophenoxy)phenyl)-2-methyl-5,6,7,8-tetrahydroquinohne (90 mg, 2.18 mmol) The title compound was isolated as a pale grey precipitate (55 mg, 0.14 mmol, 66 %). !! 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, (C22H20CIFNO2 requires 384.1161).

3-[4-(3.5-dichlorophenoxy)phenyll-2-methyl-5.6.7.8-tetrah vdro-lH-quinolin-4(lH)-one

The title compound was synthesised from 3-[4-(3,5- dichlorophenoxy)phenyl]-4-ethoxy-2-methyl-5,6,7,8-tetrahydro quinoline (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 *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, C22H20CI2NO2 requires 400.0866.

a) i) Meldrums acid, triethylorthoacetate, 110 °C, ii) Aniline, 110 °C, iii) Dowtherm A, 250 °C, b) NIS, Acetonitrile, 80 °C, c) Etl, K ₂ C0 _3i DMF, 80 °C, d) 4-Hydroxyphenyl boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ , DMF, 80 °C, e) Phenyl boronic acid, Cu(OAc) ₂ , Pyridine, TEA, DCM, f) HBr (40% aq), Acetic acid, 120 °C.

General method A

2,2-Dimethyl-l,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-l .7-napthynd-4( lHVone 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%). ^J H NMR (500 MHz, CDC1 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-Methy l-napthyrid-4(lH)-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(lH)-one The title compound was synthesised using 2-Methyl-l,7-napthyrid-4(lH)-one (480 mg, 3.0 mmol) following general procedure B. To give the title compound as colourless solid (740 mg, 2.6 mmol, 86%). 1H NMR (500 MHz, CDC1 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(lH)-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 ^χ 40.0 mL), and the resulting organic layers were combined and dried over MgS0 ₄ and concentrated in vacuo to afford the title compound.

4-Ethoxy-3-iodo-2-methyl-1.7-napthyridrne compound was synthesised using, 3-Iodo-2-methyl-napthyrid-4(lH)-one (720 mg, 2.5 mmol) following general procedure C. To give the title compound as brown gum (244 mg, 0.8 mmol, 33%). 1H NMR (500 MHz, CDC1 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 x 20 mL). The organic phases were combined and washed with water (3 x 20 mL) and then dried with brine (1 x 10 mL) and MgSC>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-l,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 %). *H 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 A molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HC1 (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-l ,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 %). *H NMR (400 MHz, CDC1 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-methylnapth yridone (1 equiv.) in acetic acid (2 mL mmol ^"1 ) was added hydrogen bromide (>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-napth yrid-4(lH)-one

The title compound was synthesised from 4-Ethy l-3(4-(4- trifluoromethoxyphenoxy)phenyl)-2-methyl-l,7-napthyridone (31 mg, 0.07 mmol). To give the title compound as a colouress solid (13 mg, 0.03 mmol, 45%). 1H NMR (400 MHz, CDCI 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 C22H15F3N2O3 requires 413.1107).

a) 4-Hydroxybenzene boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ (aq), DMF 80 °C, b) 2,4,6 trichloropyridine, K ₂ C0 ₃ , DMF, 100 °C.

3-phenol-2-methyl-5.6.7.8-tetrahvdroquinolin-4(lH)-one

The title compound was synthesised from 4(lH)-3-iodo-2-methyl-5, 6,7,8- tetrahydroquinolin-4(lH)-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 x 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%). *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 (Ci ₆ Hi ₇ N0 ₂ requires 255.1259).

3-(4- (2.6-dichloropyridin-4-yl)oxy1phenyl}-2-methyl-5.6 .8-tetrahydro-lH-quinolin-4-one

3-phenol-2-methyl-5,6,7,8-tetrahydroquinolin-4(lH)-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 *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,

(C21H18CI2N2O2 requires 400.0745).

a) 2-Chlorpyridine-5-boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ (aq), DMF 80 °C, b) Phenol, K ₂ C0 ₃ , DMF, 100 °C. 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 x 20 mL). The organic phases were combined and washed with water (3 x 20 mL) and then dried with brine (1 x 10 mL) and MgS0 ₄ , before concentration in vacuo. The resulting residue was purified by column chromatography (PetEtOAc), to yield the title compound as a yellow platelets (330 mg, 1.09 mmol, 23%). HPLC; 2.17 mm (100% ref area); *H NMR (500 MHz, CDC1 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, Ci ₇ Hi ₉ ClN ₂ 0 requires 303.1259). 4-Ethoxy-3-(6-(4-trifluoromethoxyphenoxy)pyrdin-3-yl) -2-methyl-5.6.7.8- tetrahy droquinoline

tetrahy droquinoline (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 x 20 mL). The organic phases were combined and washed with water (3 x 20 mL) and then dried with brine (1 x 10 mL) and MgS0 ₄ , before concentration in vacuo. The resulting residue was purified by reverse phase column chromatography (H ₂ 0 : acetonitrile), to yield the title compound as a yellow oil (75 mg, 0.17 mmol, 20 %). *H NMR (400 MHz, CDC1 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, C24H23F3N2O3 requires 445.1739).

3-(6-(4-Trifluoromethoxyphenoxy)pyrdin-3-yl) -2-methyl-5.6.7.8-tetrahvdroquinolin-(4)-one

The title compound was synthesised from 4-ethoxy-3-(6-(4- trifluoromethoxyphenoxy)pyrdin-3-yl)-2-methyl-5,6,7,8-tetrah ydroquinoline (70 mg, 0.15 mmol) according to general procedure J. The title compound was isolated as colourless solid (13 mg, 0.03 mmol, 20%). *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, C22H19F3N2O3 requires 417.1421).

a) i) Ethanol, ii) Dowtherm A, 250 °C, b) Pt0 ₂ , H ₂ , AcOH, c) NIS, Acetonitrile, 80 °C, d) Etl, K ₂ C0 ₃ D F, 80 °C, e) 4- Hydroxyp enyl boronic acid, Pd(PPH ₃ ) ₄ , Na ₂ C0 ₃ , DMF, 80 °C, f) Phenyl boronic acid, Cu(OAc) ₂ , Pyridine, TEA, DCM, g) HBr (40% aq), Acetic acid, 120 °C, h) i) MeOH, ii) DiBAI.

General method B

The 4-hydroxylquinolone (1 equiv.) was dissolved in acetic acid (10.0 niL) 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(lH)-one

The title compound was synthesised following general procedure B from 2-

(methoxycarboxylate)quinolin-4(lH)-one ( 500 mg, 2.5 mmol). The title compound was isolated as colourless solid (470 mg, 2.4 mmol, %). ^J H NMR (500 MHz, CDC1 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 _n H ₁₃ N03 requires 208.0974).

1.5 General method C

The tetrahydroquinolin-4(lH)-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(lH)-one The title compound was synthesised following general procedure C from 2- (methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(lH)-one (450 mg, 2.20 mmol). The title compound was isolated as colourless solid (612 mg, 1.8 mmol, 84 %). 1H 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 _n Hi ₂ IN0 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 ^χ 40.0 mL), and the resulting organic layers were combined and dried over MgS0 ₄ and concentrated in vacuo to afford the title compound. 4-Ethoxy-3-iodo-2-(methoxycarboxylate)-5.6.7.8-tetrahydroqui noline

The title compound was synthesised following general procedure D from 3- iodo-2-(methoxycarboxylate)-5,6,7,8-tetrahydro quinolin-4(lH)-one (500 mg, 1.5 mmol). The title compound was isolated as colourless cyrstals (450 mg, 1.25 mmol, 83 %). *H NMR (300 MHz, CDC1 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, Ci ₃ Hi ₆ IN0 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 x 20 mL). The organic phases were combined and washed with water (3 x 20 mL) and then dried with brine (1 x 10 mL) and MgS0 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 %). *H NMR (500 MHz, CDCl;,) 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 N0 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 A molecular sieves. The reaction mixture was stirred over 16 hours at room temperature. The reaction mixture was quenched with HC1 (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-(methox ycarboxylate)-5.6.7.8- tetrahy droquinoline

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 %). 1H NMR (500 MHz, CDC1 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)-hydroxyquinolone (1 equiv.) in acetic acid (2 mL mmol ^"1 ) was added hydrogen bromide (>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-tetrahvdroquinolin-4(lH)- one The title compound was synthesised following general procedure G from 4-ethoxy-3(4-(4-trifluoromethoxyphenoxy)phenyl)-2-(methoxyca rboxylate)-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 %). 1H 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, C23H18F3NO5 requires 446.1210).

3(4-(4-Trifluoromethoxyphenoxy)phenyl)-2-(methylhydroxy)- 5.6.7.8-tetrahydroquinolin- 4(lH)-one

tetrahydroquinolin-4(lH)-one (80 mg, 0.17 mmol) was dissolved in methanol (5 mL) with the addition of HCl (1 mL, cone.) heated to 80 °C for 24 hours. The reaction mixture was diluted with water (10 mL) and the organics extracted with EtOAc (3 x 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 %). ^J H 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, C23H20F3NO4 requires 432.1423).

1.2-dimethyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5. 6.7.8-tetrahvdroquinolin-4-one 2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-5,6,7,8- tetrahydroquinolin-4(lH)-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%). *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).

a) Urea, NaO e, Ethanol, 80 °C, b) 4-phenoxyphenyl boronic acid, CuOAc ₂ , Pyridine, triethylamine, Ethanol 1,2,3,4,5, 6,7, 8-Octahydroqwnazoline-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 x 10 mL) to afford the title compound as a white solid. (526 mg 3.17mmol, 53 %). ^! 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 HioN ₂ 02 requires 167.0815).

3-(4-Phenonxyphenyl)-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 %). *![ 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 ₂ oHi ₈ N ₂ 0 ₃ requires 335.1390).

a) Cu(OAc) ₂ , Pyridine, TEA, DCM,b)i) Ethylacetoacetate, PdOAc ₂ , JohnPhos, K ₃ P0 ₄ , Tol, 90 °C, b) ii) pyrazole/triazole, AcOH, 120 °C

General Procedure B

Toluene (2.00 mL) was added to a flask flushed with nitrogen and charged with l-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 0 (2.00 ml) caused precipitation of a white solid. Precipitate was filtered and washed with H ₂ 0 (2 x 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)pyrazo lo[1.5-alpyrimidin-7(4H)- one.

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, C2iHi ₆ F ₃ N ₃ 0 ₃ requires 416.1217).

5-methyl-2-(methylthio)-6-(4-(4-(trifluoromethoxy)phenoxy )phenyl)-[L2,41triazolo [1.5- alpyrimidin-7(4H)-one

was synthesised from 3-amino-5-methio- l,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, C20H15F3N4O3S requires 449.0893).

5-methyl-7-oxo-6-(4-(4-(trifluoromethoxy)phenoxy)phenyl)- 4.7-dihvdropyrazolo[1.5- alpyrimidine-3-carbonitrile.

was synthesised from 3-amino-4-carbonitrile- l,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%); 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 Hi ₃ F ₃ N ₄ 0 ₃ requires 427.1012). 5-methyl-2-phenyl-6-i4-(4-itrifluoromethoxy)phenoxy)phenyl)p yrazolo[1.5-alpyrimidin-

7(4H)-one.

title compound was synthesised from 3-amino-4-carbonitrile- l,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 %) . ¾ NMR (500 MHz, DMSO) δ 12.47 (s, 1H, NH), 8.01 (d, J = 6.8 Hz, 2H, H-2* & 6*), 7.53 - 7.40 (m, 5H, H-3*, 4*, 5*,2' & 6' ), 7.38 (d, J = 8.7 Hz, 2H, H-2" & 6"), 7.20 (d, J = 9.1 Hz, 2H, H-3' & 5'), 7.11 (d, J = 8.7 Hz, 2H, H-3 ^: ' & 5"), 6.62 (s, 1H, H-3), 2.22 (s, 3H, Me); M/Z (ESI+); 478.1378 (Found MH+, C26HI 8F3N3O3 requires 478.1373).

In Vitro Challenge Assay for Toxoplasma Tachyzoites

Protocol adapted from Fomovska, et. al. (Fomovska A, Huang Q, El Bissati K, Mui

EJ, Witola WH, 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 RD, Mui E, Dubey JP, Ferreira LR, Hickman MR, 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 (lx, [+] glutamine, [+] 25 mM HEPES, [+] Phenol red, 10% FBS [gibco, Denmark]) was removed from each well and replaced with IMDM-C(lx, [+] 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 Jan [cited 2015 Jul 8];47(1):309— 16.). Various concentrations of the compounds were made using IMDM-C, and 20 μΐ 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 (lx, [+] 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 3x104 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.

Biological Activity Studies

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 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.

(uM)

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

JAG01 D6, C235, W2, C2B 0.71 0.94 1.35 0.99

JAG015 D6, C235, W2, C2B >20 N/A >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 >20 N/A

JAG039 D6, C235, W2, C2B 9.595 0.9532 >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

JAG015 D6, C235, W2, C2B >20 N/A >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 >20 N/A >20 N/A

JAG039 D6, C235, W2, C2B >20 N/A >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 >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 (Figure 19 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'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 Al: Wildtype mice on a C57B16/J background, mice in which the Apolipoprotein Al gene was knocked out (Apo Al -/-) 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. "Protwith high score" has 3,359 proteins identified by more than 1 peptide and with ProteinProphet probability > 0.8 (= FDR <1%). Among these 3,3359 proteins with high confidence, 10 proteins up >2-fold in either of the 3 infected cells vs. controls, while 28 proteins down >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 (Figure 19a). 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 (Fig.19 b-d). PGLYRP2 (N-acetylmuramoyl-L-alanine amidase) and Apolipoprotein Bl were depressed. miR-17-92, which T. gondii RH strain markedly increases in HFF cultures, also was increased in sera of the ill children, as was miR-124 (Figure 19b,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 ApoAl 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 alternatiely spliced genes and immunofluresce were also perfomed. 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 Ι,ΙΙ,ΙΙΙ 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 Figure 19 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-Al 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's disease, Huntingtons disease, and Parkinson's disease by encysted EGS, and for example pathway s of response to oxidative stress, regulation of apotosis, and alternativ e 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.

ApoAl may also be a useful treatment.