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ACS Medicinal Chemistry Letters
ACS Med Chem Lett. Oct 14, 2010; 1(7): 331–335.
Published online Jul 7, 2010. doi:  10.1021/ml100096t
PMCID: PMC2992447
NIHMSID: NIHMS220292

Discovery of Potent and Selective Inhibitors of CDPK1 from C. parvum and T. gondii

Abstract

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The protozoans Cryptosporidium parvum and Toxoplasma gondii are parasites of major health concern to humans. Both parasites contain a group of calcium-dependent protein kinases (CDPKs) which are found in plants and ciliates but not in humans or fungi. Here, we describe a series of potent inhibitors that target CDPK1 in C. parvum (CpCDPK1) and T. gondii (TgCDPK1). These inhibitors are highly selective for CpCDPK1 and TgCDPK1 over the mammalian kinases SRC and ABL. Furthermore, they are able to block an early stage of C. parvum invasion of HCT-8 host cells, which is similar to their effects on T. gondii invasion of human fibroblasts.

Keywords: Phosphorylation, protozoans, calcium-dependent protein kinases, Cryptosporidium parvum, Toxoplasma gondii, apicomplexan

The apicomplexan protozoans Cryptosporidium parvum and Toxoplasma gondii are ubiquitous parasites that infect humans and domesticated animals. C. parvum is a parasite of major health concern in humans as it is a common cause of illness transmitted by water.1C. parvum infection results in debilitating diarrhea that can be life-threatening in immunocompromised patients. Recent studies have implicated C. parvum in around 15−20% of childhood diarrheal disease in the developing world.2,3 Currently, nitazoxanide is the only approved therapy for cryptosporidiosis, but it is expensive and has not been shown to be effective in treating immunocompromised hosts. T. gondii may be the most common infectious eukaryotic parasite in humans, based on serosurveys.4 Transmitted primarily through undercooked meat or accidental ingestion of cat feces, T. gondii infection presents major health concerns in immunocompromised hosts, where it causes toxoplasmic encephalitis, and in pregnancy, where it can result in severe birth defects or miscarriage. Sulfadiazine and pyrimethamine are the current therapies for toxoplasmosis, but they can cause nephrotoxicity, rash, and additional complications in pregnancy. Thus, new therapies for treating infections caused by both parasites are greatly needed.

In T. gondii, calcium-regulated signaling is associated with a number of cellular functions such as secretion, gliding motility, and host cell invasion.5,6 The proper control of intracellular calcium levels is important for host cell invasion, and T. gondii uses several mechanisms for the uptake and release of calcium. Furthermore, this organism contains specialized calcium-regulated signaling enzymes, including a unique family of calcium-dependent protein kinases (CDPKs), which are present in plants, ciliates, and green algae but not in animals.7 These kinases are believed to be mediators of secretion, invasion, and gliding motility.5,6,8T. gondii and C. parvum are highly related obligate intracellular parasites. While much less is known about the role of calcium signaling in C. parvum, it appears that many calcium-regulated signaling processes are conserved between T. gondii to C. parvum.9C. parvum also possesses CDPKs that are believed to play important roles in calcium-regulated processes. The roles that CDPKs play in calcium signaling in T. gondii and C. parvum make this family of kinases intriguing targets for the development of antiparasitic agents. Previous studies have demonstrated that TgCDPK1 plays an important role in T. gondii invasion of mammalian cells.8 Pharmacological agents that selectively inhibit the catalytic activity of TgCDPK1 block parasitic invasion of human fibroblast cells.10,11 Furthermore, we have demonstrated that a unique sequence and structural variation in the ATP-binding cleft of TgCDPK1 provides an opportunity to develop highly selective inhibitors of this kinase.10 Specifically, TgCDPK1 contains a glycine residue at the “gatekeeper” position, which allows inhibitors to access a large hydrophobic pocket that is adjacent to the site of ATP binding (hydrophobic pocket II).12 As all known human kinases possess larger residues (threonine, valine, or a larger amino acid) at the gatekeeper position, it is possible to gain selectivity by developing inhibitors that optimize interactions with the enlarged ATP-binding pocket of TgCDPK1.13,14 Indeed, Shokat and co-workers have shown that mutant mammalian kinases that contain an alanine or glycine residue at the gatekeeper position are uniquely sensitive to pyrazolopyrimidine inhibitors that contain bulky substituents at the 3-position (compounds 13, Figure Figure11).1517

Figure 1
(a) TgCDPK1 and CpCDPK1 inhibitors 13. IC50 values shown are the average of three assays ± SEM. (b) C. parvum parasite numbers (Y-axis) present after a 24 h infection of human intestinal cells (HCT-8) with C. parvum sporozoites (1:1 ratio ...

Compounds 2 and 3 potently inhibit the catalytic activity of TgCDPK1 and block T. gondii invasion of human fibroblasts (Figure (Figure11a).10 A homologue of TgCDPK1 is also found in C. parvum (CpCDPK1), but its role in parasitic invasion has yet to be elucidated. CpCDPK1 and TgCDPK1 share 70% sequence identity in the kinase catalytic domain, and both enzymes have a glycine residue at the gatekeeper position. Because pyrazolopyrimidines that contain bulky substituents at the 3-position are potent inhibitors of TgCDPK1, we wished to determine if this class of compounds can serve as dual inhibitors of TgCDPK1 and CpCDPK1. First, the sensitivity of CpCDPK1 to compounds 13 was determined with an in vitro activity assay (Figure (Figure1a).1a). Both TgCDPK1 and CpCDPK1 show similar levels of inhibition by these compounds, with analogue 2 as the most potent inhibitor. Next, the phenotypic response of C. parvum cells to 13 was tested by measuring the number of parasites present after 24 h of infection of human intestinal cells (HCT-8) with C. parvum sporozoites in the presence of these inhibitors. These assays were performed under two different sets of conditions: one in which the sporozoites were exposed to each inhibitor at the time of infection (Figure (Figure1b,1b, left graph) and a second assay in which the sporozoites were exposed to each inhibitor 1 h after infection (Figure (Figure1b,1b, right graph). Importantly, reduced levels of C. parvum sporozoites are observed with increasing concentrations of 13 under both sets of conditions, with analogue 2 demonstrating the most potent effect on parasite proliferation. The potencies of the pyrazolopyrimidine inhibitors were dramatically increased when they were added at the time of sporozoite infection rather than 1 h after C. parvum had been incubated with HCT-8 host cells. This suggests that these inhibitors affect an early stage of C. parvum host cell invasion, which is similar to their effects on T. gondii invasion. In all cases, the relative ability of each inhibitor to block C. parvum proliferation correlates with its in vitro activity against CpCDPK1.

On the basis of the promising ability of pyrazolopyrimidine inhibitors to block T. gondii and C. parvum host cell invasion, we decided to further optimize compounds based on this scaffold as potent and selective dual inhibitors of TgCDPK1 and CpCDPK1. Inhibition of TgCDPK1 and CpCDPK1 was determined using a luminescent kinase assay (KinaseGlo).10 Notably, both kinases were tested at the same ATP concentration, which allows direct comparison of inhibitor potencies due to these enzymes possessing similar Km values for this cofactor.21 To profile the sensitivity of CDPK1 to ATP-competitive kinase inhibitors, we tested the ability of a diverse panel of previously described kinase inhibitors to inhibit TgCDPK1 (Supporting Information, Figure S1). While several compounds were weak inhibitors of TgCDPK1, none were as potent as compounds 2 and 3.

Encouraged by the similar potency of inhibitor 3 against TgCDPK1 (IC50 = 150 ± 20 nM) and CpCDPK1 (IC50 = 130 ± 40 nM), pyrazolopyrimidine analogues that contain a naphthylmethylene group at the 3-position and various alkyl substituents at the 1-position were tested for their ability to inhibit both kinases (Table 1). Derivatives containing smaller alkyl groups (5ac) were found to have reduced potencies for both enzymes relative to 3. Furthermore, a significant increase in potency was not observed for inhibitors that contain bulkier substituents at the 1-position (5df). However, the reduced potencies of compounds with larger substituents are not due to a size restriction in the ATP-binding pocket because derivatives that contain a basic piperidine group (derivatives 5gi) were found to be significantly more potent inhibitors of TgCDPK1 and CpCDPK1. Notably, compound 5h, which contains a methylene linkage between the pyrazolopyrimidine core and the piperidine ring, has an 8- and 16-fold lower IC50 for CpCDPK1 and TgCDPK1 than parent compound 3, respectively. Derivatization of 5gi with an acetyl (5jl), ethyl (5mo), or sulfonylmethyl (5pr) group reduces the enhanced potency that the piperidine substituent confers, with only modified versions of piperidine 5g showing similar inhibition as the parent compound. Notably, most compounds from this series are near equipotent inhibitors of both TgCDPK1 and CpCDPK1, demonstrating the overall similarity in this region of the ATP-binding pockets of both kinases.

Table 1
In Vitro Activities of 3 and 5ar against TgCDPK1 and CpCDPK1a

To further probe the hydrophobic pocket adjacent to the gatekeeper residue (hydrophobic pocket II), a series of analogues that contain an isopropyl group at the 1-position and various aryl substituents at the 3-position were tested for their ability to inhibit both kinases (Table 2, compounds 7aab). We felt that this series of compounds would provide insight into which substituents can be accommodated in this region. As shown in Table 2, a large number of aryl substituents are accommodated by both kinases. Almost all of the compounds from this series have an IC50 less than 1 μM, with several inhibitors demonstrating very high potency against both enzymes. Inhibitors that contain aryl rings that are monosubstituted with smaller substituents at the meta (7b, 7e, 7g, and 7ab) or para positions (7a, 7d, 7f, and 7j) are accommodated in the ATP-binding sites of both kinases but are more potent against TgCDPK1 than CpCDPK1. Analogues that contain meta- and para-substituted aryl rings (7c, 7i, 7k, and 7m) are potent against both enzymes and show reduced selectivity for TgCDPK1. Consistent with this observation, pyrazolopyrimidine derivatives that contain a 2-naphthyl (7p-7r) or quinoline group (7t) are potent inhibitors of both enzymes. However, bicyclic substituents that are not planar show reduced potency (7uw). In general, most inhibitors from this series are 2−12-fold selective for TgCDPK1 over CpCDPK1. However, several compounds (for example, compounds 7l, 7q, and 7t) are equipotent or slightly selective for CpCDPK1. This fact demonstrates that while the ATP-binding pockets of both kinases are very similar, they are not identical.

Table 2
In Vitro Activities of 7aab against TgCDPK1 and CpCDPK1a

Key to the use of pyrazolopyrimidine-based kinase inhibitors as antiparasitic agents is the potential to selectively inhibit TgCDPK1 and CpCDPK1 over mammalian kinases. To determine the potency of these compounds against mammalian kinases, a subset of inhibitors were tested against the tyrosine kinases SRC and ABL. We felt that these two kinases would be a suitable counterscreen because they both contain the most permissive gatekeeper residue found in mammalian kinases (threonine) and the pyrazolopyrimidine core was originally developed as a kinase inhibitor scaffold against SRC family kinases.22 Most of the pyrazolopyrimidines tested have limited activity against SRC and ABL (Supporting Information, Table S1). Consistent with earlier studies, previously characterized “bumped” inhibitors 1 and 3 do not potently inhibit SRC or ABL kinase. Despite the increased activity of analogue 2 against TgCDPK1 and CpCDPK1, this compound only weakly inhibits SRC and ABL (IC50 > 1 μM). As expected, pyrazolopyrimidine inhibitors that contain smaller aryl groups at the 3-position (7c and 7e) are less selective for both parasite kinases due to their increased potency against SRC and ABL. However, analogues that contain a substituted naphthyl (7q and 7r) or quinoline (7t) substituent at the 3-position are much more selective due the increased size of these functional groups. Presumably, the larger threonine gatekeeper residues of SRC and ABL restrict access of these inhibitors to hydrophobic pocket II. While the substituent at the 3-position is the major contributor to inhibitor selectivity, substitution at the 1-position affects the potency of these compounds against TgCDPK1 and CpCDPK1 relative to SRC and ABL. For example, piperidine-containing analogues 5m and 5p are less selective for TgCDPK1 and CpCDPK1 than parent compound 1. However, several analogues restore the high selectivity of this class of compounds, with secondary piperidine 5h demonstrating over 1000-fold selectivity for the CDPKs. To test the overall toxicity of our pyrazolopyrimidines inhibitors, they were assayed for their ability to inhibit the growth of four human cell lines (Table S1): glioma derived (SF539), human lymphocyte (CRL8155), human promyelocytic leukemia (HL-60), and colorectal carcinoma (HC 2998). For all four cell lines tested, the inhibitors showed little or no growth inhibition at the highest concentration tested (10 μM).

We have previously reported crystal structures of inhibitors 2 and 3 bound to TgCDPK1.10 Similar to the structures of other pyrazolopyrimidines bound to tyrosine kinases, these inhibitors occupy the ATP-binding cleft of TgCDPK1. The pyrazolopyrimidine scaffold superimposes with the purine ring of ATP, with the exocyclic amine and nitrogen at the 5-position forming hydrogen-bonding interactions with the hinge region. In addition, the glycine gatekeeper residue of TgCDPK1 allows bulky substituents at the 3-position unobstructed access to hydrophobic pocket II. Replacing glycine with a larger amino acid at this position clearly creates a steric clash with the 2-naphthyl and 1-naphthylmethylene groups of inhibitors 2 and 3, respectively.10 On the basis of the similar sensitivities of TgCDPK1 and CpCDPK1 to pyrazolopyrimidines, we predicted that inhibitors of this class would bind in a similar orientation in both enzymes. The structure of compound 3 bound to CpCDPK1 shows that this is indeed the case (Figure (Figure2,2, top panel). Superposition of the active sites of TgCDPK1 and CpCDPK1 bound to 3 shows that the inhibitor has an identical mode of binding in both kinases. Furthermore, all of the residues surrounding the inhibitor are nearly superimposable, which is remarkable because TgCDPK1 is in the calcium-free inactive conformation, while CpCDPK1 is in the calcium-bound active conformation (Supporting Information, Figure S2). It is therefore clear that the inhibitors are able to bind the ATP-binding site of CDPK1 whether it is active or not. While structures of both enzymes bound to 2 and 3 provided direct insight into how large substituents can be accommodated at the 3-position, we were interested in further exploring how substitution at the 1-position affects the potencies of these inhibitors. Structures of inhibitor 5h bound to TgCDPK1 and CpCDPK1 show how increased potency can be obtained (Figure (Figure2,2, bottom panel). While the pyrazolopyrimidine cores and 3-position substituents of inhibitors 3 and 5h make identical contacts with both enzymes, the piperidine ring of 5h forms a salt bridge with a glutamate residue that lines the ATP-binding cleft. Importantly, this interaction is present in the structures of 5h bound to both TgCDPK1 and CpCDPK1. Alkylation, acetylation, or sulfonylation of the piperidine ring disrupts this interaction and accounts for the lower potency of compounds 5jr. Furthermore, the reduced potency of 5h against SRC and ABL demonstrates that these kinases cannot form a similar interaction.

Figure 2
Superposition of the active sites of TgCDPK1·3 (green sticks and light green ball and sticks) and CpCDPK1·3 (orange sticks and light orange ball and sticks) complexes (PDB entries 3I7B(10) and 3NCG, respectively) (top). Overlay of the ...

In conclusion, we have demonstrated that selective pyrazolopyrimidine kinase inhibitors are indeed potent inhibitors of CpCDPK1 and that they are able to inhibit an early stage of C. parvum cell invasion. This class of compounds has similar effects on the ability of T. gondii to invade human fibroblast cells.10,11 On the basis of these promising results, a diverse panel of pyrazolopyrimidine analogues was generated, and their activities against CpCDPK1 and TgCDPK1 were determined. By exploiting a unique sequence and structural variation in the ATP-binding clefts of TgCDPK1 and TgCDPK1, potent dual inhibitors of these enzymes were obtained. Importantly, many of these inhibitors show minimal inhibition of the tyrosine kinases SRC and ABL and are not toxic to human cell lines. Future efforts will focus on increasing the potency and selectivity of these compounds and on optimizing their PK/ADME/Tox properties. Furthermore, optimized inhibitors will be used to investigate the role of CpCDPK1 in C. parvum host cell invasion.

Acknowledgments

Dr. Raymond Hui (Structural Genomics Consortium, University of Toronto) kindly provided an expression construct for C. parvum CpCDPK1. Portions of this research were carried out at the Stanford Synchrotron Radiation Light Source, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences.

Funding Statement

National Institutes of Health, United States

Notes

These authors contributed equally to the manuscript.

Notes

This work was funded by National Institute of Allergy and Infectious Diseases Grants R01AI080625 (W.C.V.V.) and R01AI067921 (C.L.M.J.V., E.A.M., and W.C.V.V.), National Institute of General Medical Sciences Grant R01GM086858 (D.J.M.), and financial support from G. and K. Pigotti.

Supporting Information Available

Supporting Information Available

Three figures, two tables and details for synthetic procedures, analytical data, biological assays, and structural studies. This material is available free of charge via the Internet at http://pubs.acs.org.

Supplementary Material

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