Synthesis and evaluation of non-peptidic cysteine protease inhibitors of P. falciparum derived from etacrynic acid.

A series of etacrynic acid derivatives was synthesized and screened for their in vitro activity against Plasmodium falciparum, as well as their activity against recombinantly expressed falcipain-2 and -3. The two most active compounds of the series displayed IC(50) values of 9.0 and 18.8 microM against Plasmodia.

Introduction

Malaria is still a major cause of global human morbidity and mortality, with Plasmodium falciparum being the deadliest among the four Plasmodium species that infect humans. Annually 350–500 million clinical malaria episodes occur, causing more than 1 million deaths each year [1]. The increasing spread of P. falciparum due to inadequate vector control, increasing drug resistance, and the lack of effective vaccine strengthens the need for the development of novel drugs for the treatment of malaria [2, 3]. New therapeutic strategies are therefore urgently needed. Cysteine proteases of P. falciparum represent attractive antiplasmodial drug targets due to their essential functions for the parasite erythrocytic cycle [4, 5, 6]. Among them are falcipain-2 and falcipain-3, which are located in the acidic food vacuole of the parasite, play a pivotal role in hemoglobin hydrolysis, and may also participate in erythrocyte rupture [5, 7]. Disruption of the hemoglobin degradation pathway is lethal for the parasite. Development of compounds targeting falcipain-2 and falcipain-3 is therefore currently a focus of research. A recent study has further shown that individual cysteine protease inhibitors significantly reduce microgametogenesis in P. falciparum, pointing to a potential role of these inhibitors for transmission blocking strategies [8]. So far several peptidic and peptidomimetic as well as non-peptidic cysteine protease inhibitors have been synthesized and tested against malaria parasites [9,10,11,12]. In the present work a set of non-peptidic cysteine protease inhibitors derived from the loop diuretic etacrynic acid as a lead compound were evaluated for their potency to inhibit recombinantly expressed falcipain-2 and falcipain-3 [13,14,15]. Furthermore, activities against chloroquine-sensitive P. falciparum strain 3D7 and the chloroquine-resistant strain W2 were investigated. Several of these compounds have initially been tested against papain, the prototype cysteine protease of the CAC1 family, and against the SARS coronavirus main protease Mpro, as described elsewhere [16, 17].

Results and Discussion

In these previous studies compounds possessing an activated double bond revealed covalent, but reversible binding to the cysteine residue of the respective protease. In addition to the structural modifications implemented in previous work [16, 17], namely within the compounds 1, 2, 8-21, we now included fluoro-substituted compounds 3-7, several analogues without an activated double bond 25-32, as well as derivatives with polar side chains 22-23, and finally, a biotin-labeled inhibitor 24. In summary, the structure of etacrynic acid was modified as follows (Scheme 1): A: substitution pattern of the aromatic ring, B: esters and amides, C: ortho-position of the double bond containing side chain (cpd. 2), D: removal of the double bond.

Scheme 1

Sites of modification of the etacrynic acid lead.

A: substitution pattern of the aromatic ring; B: esters, amides, acids; C: ortho-position; D: removal of the double bond.

The inhibitors were synthesized according to previously described pathways [16,17] which are summarized in Scheme 2. Halogen substituted anisoles were subjected to Friedel-Crafts acylation yielding the corresponding phenolic ketones. Further alkylation of the phenolic hydroxyl functions yielded amides 28, 30 – 32, and esters 1, 9 and 29. Introduction of the double bond was performed either by Mannich reaction with TMDM (➔ 3, 6, 7) or by aldol condensation with formaldehyde (➔ 4, 8). The latter yielded the free acids 4 and 8 due to concurrent hydrolysis of the ester function. The free acids were coupled to various amides to give the amides 5, 10 – 24. Amides 26 and 27 without activated double bond were also synthesized by standard amide coupling methods.

Scheme 2

Synthetic pathways to the etacrynic acid derivatives. HOSuc, N-hydroxysuccinimide; DCC, dicyclohexylcarbodiimide, TMDM, N,N,N’,N’ tetramethyldiaminomethane; EEDQ, ethyl 1,2-dihydro-2-ethoxyquinoline-1-carboxylate.

Recombinant falcipain-2 and falcipain-3 were produced as previously described [14, 18]. Inhibitory activities against recombinant falcipain-2 and falcipain-3 were evaluated in fluorometric microplate assays using the substrates Cbz-Phe-Arg-AMC and Cbz-Leu-Arg-AMC (AMC, 7-amino-4-methyl-coumarin) [19]. The cysteine protease inhibitor E-64 was used as a positive control [20]. The solvent DMSO was used as negative control. Compounds 1-6, 8-11 and 13-28 were tested in vitro against the CQ-sensitive 3D7 P. falciparum strain or the CQ-resistant W2 P. falciparum strain. The corresponding IC50 values are shown in Table 1. The in vitro data for the etacrynic acid derivatives are compared to those of the well known drug chloroquine and to E-64. In addition, the cytotoxicity of the inhibitor 23 was studied on human kidney epithelium cell-line 293T, as described previously [21, 22], resulting in an IC50 value of >160 mM.

Table 1

Inhibition of falcipain-2 / -3 (FP-2 / -3) as well as antiplasmodial activity of non-peptidic Michael-acceptors derived from etacrynic acid.

Cpd.	R1	X	Y	R2	FP-2 IC50, (mM)	FP-3 IC50, (mM)	P. f. 3D7/W2, IC50 (µM)
1	H5C2	H	Cl	O-CH2-CO2Et	498±8	346±14	nic
2	H5C2	O-CH2-CO2Et	H	Cl	110±5	381±21	nic
3	H5C2	H	F		ni	nd	142±5b
4	H5C2	H	F	O-CH2CO2H	nd	nd	79.8±6b
5	H5C2	H	F		80±5	nd	205±9b
6	H5C2	H	F		ni	nd	141±4b
7	H5C2	H	F		ni	nd	nd
8	H5C2	Cl	Cl	O-CH2-CO2H	443±17	ni	nic
9	H5C2	Cl	Cl	O-CH2-CO2Et	60.6±4.2	163±5.6	nic
10	H5C2	Cl	Cl		178±14	56.7±5.7	nic
11	H5C2	Cl	Cl		333±5	158±11	nic
12	H5C2	Cl	Cl		165±12	nd	nd
13	H5C2	Cl	Cl		269±21	87.2±6	nic
14	H5C2	Cl	Cl		318±14	ni	29.3±3.4c
15	H5C2	Cl	Cl		212±17	ni	nic
16	H5C2	Cl	Cl		242±19	ni	nic
17	H5C2	Cl	Cl		305±30	479±23	nic
18	H5C2	Cl	Cl		255±4	153±16	nic
19	H5C2	Cl	Cl		144±11	557±23	27.4±4.1c
20	H5C2	Cl	Cl		184±17	158±17	nic
21	H5C2	Cl	Cl		182±9	123±8	nic
22	H5C2	Cl	Cl		ni	ni	nic
23	H5C2	Cl	Cl		57.1±13	96.5±0.6	18.8±0.9c
24	H5C2	Cl	Cl		3.0±1.1	11.9±1.1	9.0±0.4c
25					531a	ni	nic
26					484a	ni	nic
27					713a	ni	nic
28					80±6	nd	66.4±2.2c
29					80±6	nd	nd
30					ni	nd	nd
31					ni	nd	nd
32					ni	nd	nd
E-64					0.015±0.008	0.075±0.02	5.3±1.05c
CQ (W2)					nd	nd	0.24[19]
CQ (3D7)					nd	nd	0.01±0.0048

a Only one experiment; ni, no inhibition; nd, not determined; CQ, chloroquine; b 3D7 strain;

c W2 strain.

Inspection of the data in Table 1 allows the following conclusions to be drawn: in general, the etacrynic acid derivatives are weak or moderate inhibitors of falcipains and P. falciparum. Nevertheless, some structure-activity relationship can be found:

The ethyl ester derivative (9) is more potent than the etacrynic acid (8), both against falcipain-2 and -3. This is in accordance with the results for papain and the SARS-CoV Mpro. The dichloro-substituted compounds (e.g. 9, 20) are better inhibitors than the mono-chloro- (e.g. 1) or fluoro-substituted (6) compounds, with one exception, namely inhibitor 5 (compared to 18). The α,ß-unsaturated system appears to be favourable for activity against falcipains when comparing the analogous dichloro-compounds 20 and 27 or compounds 18 and 26. Short voluminous moieties such as the tertbutyl moiety of compounds 5, 28, 29, seem to be advantageous if combined with the fluoro-substituted aromate. In these cases, the activated double bond is apparently not essential for inhibition.

Nearly all etacrynic acid amides show better inhibition properties than the free acid (8). A longer acidic side-chain significantly enhances the activity (23, compared to 20, 21), making 23 the most active inhibitor of falcipains and P. falciparum within the series. However, insertion of an additional acidic group (e.g. 22) diminishes the inhibiting activity. The cytotoxicity/antiplasmodial ratio for the most active compound 23 is >8.5, indicating selectivity against the parasite. As the data against the target enzymes and the parasites do not correlate in all cases (e.g. 14), the question arises whether there are additional or other targets. In order to allow further affinity binding studies the biotinylated dichloro-substituted etacrynic acid amide 24 was included and synthesized according to the methods recently described [17,23] (Scheme 2). Notably, this compound emerged as the most potent inhibitor of falcipains and P. falciparum within the series.

Conclusions

In summary, this paper describes a comprehensive screening of non-peptidic Michael acceptors using etacrynic acid as lead structure. The best inhibition against recombinantly synthesized falcipain-2 and falcipain-3 revealed the compound 24. Moreover, this etacrynic acid amide as well as compound 23 displayed modest antiplasmodial activity in vitro with IC50 values of 9 and 18.8 µM, respectively, which are in the range of the standard cysteine protease inhibitor E-64. In addition, the high IC50 value of >160 µM for compound 23 obtained from cytotoxicity assays using the human kidney epithelium cell-line 293T indicates selectivity against the parasite. These results provide basic information for the development of further non-peptidic irreversible cysteine protease inhibitors with etacrynic acid amides as lead compounds. In addition, the good inhibitory properties of 24 allow further affinity binding studies.

Experimental

General

Melting points were determined in open capillary on a melting point apparatus, model 530, from Büchi, Switzerland. NMR spectra were recorded on an AVANCE 400 MHz spectrometer from Bruker Biospin GmbH, Germany [solvent CDCl3 (unless otherwise noted); 1H-NMR, 400.13 MHz; 13C-NMR, 100.61 MHz]. The optical rotation values were determined on a Perkin-Elmer 241 polarimeter. ESI mass spectra were recorded on an Agilent 1100 ion trap equipped with an Agilent HPLC system. Hydrostatic column chromatography was performed with silica gel 60 (0.063-0.2 mm). All solvents were purified and dried prior to use according to standard literature procedures. Chloroquine, E64 and DMSO (dimethyl sulfoxide) were obtained from Sigma-Aldrich, Deisenhofen, Germany. Alamar Blue® was purchased from Trinova Biochem, Giessen, Germany. DMEM (Dulbecco’s Modified Eagle’s Medium) high glucose was delivered from Gibco/Sigma-Aldrich, Deisenhofen, Germany. Hygromycin was obtained from Merck, Darmstadt, Germany.

Syntheses of inhibitors

The syntheses of compounds 1, 2, 8-21, and 25 are described in [17].

Method A: Introduction of the double bond. To substances 29, 30 or 32 (1 equiv.) and TMDM (N,N,N’,N’-tetramethyldiaminomethane, 20 equiv.), acetic anhydride (20 equiv.) was added slowly. The mixture was heated under reflux at 85 °C. The reaction is followed by 1H-NMR spectroscopy. After completion of the reaction the mixture was cooled to room temperature and saturated K2CO3 solution was added until gas evolution stopped. The product was extracted with Et2O, washed with water and brine and dried with Na2SO4. The solvent was removed in vacuo and the product purified by column chromatography.

Method B: Syntheses of bromoacetamides. Bromoacetyl bromide (1 equiv.) in absolute CH2Cl2 was cooled to -30 °C. Amine (1 equiv.) and triethylamine (1 equiv.) in absolute CH2Cl2 were added dropwise. After the addition, the reaction mixture was warmed up to room temperature and stirred for 1-2 h further. The solvent was removed in vacuo, the product was dissolved in acetone and filtered off. The bromoacetamides were used directly without further purification.

Method C: Coupling of the bromoacetamide or bromoacetic acid ester with 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one. 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (1 equiv.), K2CO3 (1.5 equiv.) and KI (0.1 equiv.) were refluxed in dry acetone for 1 h. Bromoacetamide (method B) or bromoacetic acid ester (2 equiv.) were added and the mixture heated to reflux for a further 4 h. The mixture was cooled to room temperature, filtered and the solvent was removed in vacuo. The product was dissolved in Et2O, washed with brine, KOH solution (5%) and water, and dried with Na2SO4. The solvent was removed in vacuo and the product was purified by column chromatography.

Tert-butyl 2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetate (3). Method A: Tert-butyl-2-(4-butyryl-2-fluorophenoxy)acetate (29, 558 mg, 1.89 mmol), TMDM (5.14 mL, 37.7 mmol), acetic anhydride (3.56 mL, 37.7 mmol). Rf: 0.73 (cyclohexane/ethyl acetate: 1/1); yield 180 mg (0.58 mmol, 31 %); yellow oil; LOOP-ESI-MS: calcd. for C16H21FO4 308.35, found [M+H]+ 309.2; LC-MS: Rt = 38.2 min, purity 100 %; 1H-NMR: δ 1.09 (t, 3H, 3J = 7.5 Hz, CH2CH2CH), 1.47 (s, 9H, Cq(CH)3), 2.45 (q, 2H, 3J = 7.4 Hz, CH2CHCH3), 4.64 (s, 2H, OCHC=O), 5.50 (s, 1H, Cq=CH), 5.74 (s, 1H, Cq=CH), 6.88 (dd, 1H, J = 8.4 Hz, CH), 7.54–7.59 (m, 2H, CH); 13C-NMR: δ 12.30 (CqCH2CH3), 25.51 (CqCH2CH3), 28.01 (Cq(CH3)3), 66.48 (OCH2C=O), 82.95 (C(CH3)3), 114.09 (CHarom.), 117.98 (CHarom.), 122.82 (Cq=CH2), 126.52 (CHarom.), 131.64 (CC=O), 149.39 (C=CH2), 150.58 (CF or COCH2C=O), 153.06 (CF or COCH2C=O), 166.96 (OCH2C=O), 196.12 (CqC=O).

2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetic acid (4): 1-(3-fluoro-4-hydroxyphenyl)butan-1-one. 2-Fluoroanisole (4.00 g, 31.7 mmol) and butyric acid chloride (5.07 g, 47.6 mmol) were dissolved under a N2 atmosphere in absolute CH2Cl2 (50 mL) and the mixture was cooled to 0-10 °C. AlCl3 (6.35 g, 47.6 mmol) was added within 30 minutes, and the mixture was stirred for 2-3 h. An additional amount of AlCl3 (6.35 g, 47.6 mmol) was added, and the mixture was heated under reflux for 2 h. The mixture was poured on ice and acidified with concentrated HCl to pH 1. Tartaric acid was added for complexation of aluminum until the solution was clear. The solution was extracted with Et2O and the organic layer was washed with KOH solution (10%) and brine. The organic layer was dried with Na2SO4 and solvent was removed in vacuo. Yield 4.97 g (27.3 mmol, 86 %); white solid; mp. 91 °C (water); 1H-NMR: δ 0.98 (t, 3H, 3J = 7.3 Hz, CH2CH2CH), 1.74 (sext, 2H, 3J = 7.3 Hz, CH2CHCH3), 2.87 (t, 2H, 3J = 7.3 Hz, CHCH2CH3), 6.04 (bs, 1H, OH), 7.04 (dd, 1H, J = 8.5 Hz, CH), 7.67–7.73 (m, 2H, CH).

Ethyl-2-(4-butyryl-2-fluorophenoxy)acetate. 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (2.00 g, 11.0 mmol), bromoacetic acid ethyl ester (3.67 g, 22.0 mmol), K2CO3 (2.28 g, 16.5 mmol) and KI (183 mg, 1.10 mmol) were refluxed in dry acetone for 5-6 h. The reaction mixture was cooled to room temperature and filtered off. The solvent was removed in vacuo and the product was extracted with Et2O, washed with NaOH solution (10%), water and brine, dried with Na2SO4, and the solvent was removed in vacuo. Yield 2.30 g (8.60 mmol, 78%); white solid; mp. 79-80 °C (Et2O). 1H-NMR (DMSO-d6): δ 0.90 (t, 3H, 3J = 7.5 Hz, CH2CH2CH), 1.20 (t, 3H, 3J = 7.2 Hz, OCH2CH), 1.60 (sext, 2H, 3J = 7.3 Hz, CH2CHCH3), 2.93 (t, 2H, 3J = 7.1 Hz, CHCH2CH3), 4.17 (q, 2H, 3J = 7.1 Hz, OCHCH3), 4.99 (s, 2H, OCHC=O), 7.20 (dd, 1H, J = 8.5, CH), 7.74–7.78 (m, 2H, CH).

2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetic acid (4). Ethyl-2-(4-butyryl-2-fluorophenoxy)-acetate (2.11 g, 7.87 mmol), formaldehyde solution (40%, 1.08 mL, 15.7 mmol) and K2CO3 (2.17 g, 15.7 mmol, dissolved in water) were refluxed in ethanol for 24 h. The reaction mixture was cooled to room temperature, acidified with concentrated HCl to pH 1 and the product was extracted with Et2O. The solvent was removed in vacuo. Yield 556 mg (2.20 mmol, 28%); white solid; mp 99-101 °C (Et2O); LOOP-ESI-MS: calcd. for C13H13FO4 252.24, found [M+H]+ 253.1; LC-MS: Rt = 23.8 min, purity 100 %; 1H-NMR: δ 1.10 (t, 3H, 3J = 7.5 Hz, CqCH2CH). 2.46 (q, 2H, 3J = 7.4 Hz, CqCHCH3), 4.81 (s, 2H, OCHC=O), 5.52 (s, 1H, Cq=CH), 5.78 (s, 1H, Cq=CH), 6.95 (dd, 1H, J = 8.4 Hz, CH), 7.56–7.60 (m, 2H, CH); 13C-NMR: δ 12.30 (CqCH2CH3), 25.44 (CqCH2CH3), 65.65 (OCH2C=O), 114.50 (CHarom), 118.19 (CHarom), 123.35 (Cq=CH2), 126.59 (CHarom), 132.35 (CC=O), 148.87 (C=CH2), 149.33 (CF or COCH2C=O), 153.11 (CF or COCH2C=O), 172.29 (OCH2C=O), 196.16 (CqC=O).

N-tert-butyl-2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetamide (5). 2-(2-Fluoro-4-(2-methylene-butanoyl)phenoxy)acetic acid (4, 767 mg, 3.00 mmol) and N-hydroxysuccinimide (336 mg, 3.00 mmol) were dissolved under a N2 atmosphere in absolute CH2Cl2 (10 mL). Dicyclohexylcarbodiimide (DCC) (619 mg, 3.00 mmol) was added in small portions and the mixture was stirred overnight. The mixture was filtered into a flask with tert-butylamine (219 mg, 3.00 mmol) in CH2Cl2 (10 mL), stirred for 3 h at room temperature and filtered. The reaction mixture was washed with brine and KOH solution (5%), dried with Na2SO4 and the solvent was removed in vacuo. The product was purified by column chromatography. Rf: 0.43 (cyclohexane/ethyl acetate: 2/1); yield 314 mg (1.02 mmol, 34 %); white solid; mp 85 °C (cyclohexane/ethyl acetate); LOOP-ESI-MS: calcd. for C17H22FNO3 307.37, found [M+H]+ 308.4; LC-MS: Rt = 18.0 min, purity 100 %; 1H-NMR: δ 1.10 (t, 3H, 3J = 7.5 Hz, CqCH2CH), 1.40 (s, 9H, Cq(CH)3), 2.46 (q, 2H, 3J = 7.4 Hz, CqCHCH3), 4.46 (s, 2H, OCHC=O), 5.51 (s, 1H, Cq=CH), 5.78 (s, 1H, Cq=CH), 6.43 (bs, 1H, NH), 6.96 (dd, 1H, J = 8.2 Hz, CH), 7.56–7.62 (m, 2H, CH); 13C-NMR: δ 12.30 (CqCH2CH3), 25.45 (CqCH2CH3), 28.71 (Cq(CH3)3), 51.46 (C(CH3)3), 68.50 (OCH2C=O), 114.05 (CHarom), 117.73 (CHarom), 123.23 (Cq=CH2), 126.92 (CHarom), 132.23 (CC=O), 146.73 C=CH2), 148.87 (CF or COCH2C=O), 149.35 (CF or COCH2C=O), 165.95 (OCH2C=O), 196.01 (CqC=O).

N-butyl-2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetamide (6). Method A: N-butyl-2-(4-butyryl-2-fluorophenoxy)acetamide (30) (105 mg, 0.36 mmol), TMDM (0.97 mL, 7.11 mmol), acetic anhydride (0.67 mL, 7.11 mmol). Rf: 0.59 (cyclohexane/ethyl acetate: 1/2); yield 55.5 mg (0.18 mmol, 51 %); white solid; mp 73 °C (cyclohexane/ethyl acetate); LOOP-ESI-MS: calcd. for C17H22FNO3 307.37; found [M+H]+ 308.4; LC-MS: Rt = 15.8 min, purity 100 %; 1H-NMR: δ 0.93 (t, 3H, 3J = 7.4 Hz, NHCH2CH2CH2CH3), 1.11 (t, 3H, 3J = 7.4 Hz, CqCH2CH3), 1.36 (sext, 2H, 3J = 7.4 Hz, NHCH2CH2CH2CH3), 1.53 (sext, 3J = 7.3 Hz, NHCH2CH2CH2CH3), 2.46 (q, 2H, 3J = 7.5 Hz, CqCH2CH3), 3.37 (q, 2H, 3J = 6.7 Hz, NHCH2CH2CH2CH3), 4.57 (s, 2H, OCH2C=O), 5.51 (s, Cq=CH2), 5.78 (s, Cq=CH2), 6.60 (s, 1H, NH), 6.96 (dd, 1H, J = 8.1 Hz, CHarom.), 7.57–7.62 (m, 2H, CHarom.); 13C-NMR: δ 12.31 (CqCH2CH3), 13.69 (NHCH2CH2CH2CH3), 20.00 (NHCH2CH2CH2CH3), 25.45 (CqCH2CH3), 31.53 (NHCH2CH2CH2CH3), 38.90 (NHCH2CH2CH2CH3), 68.21 (OCH2C=O), 113.90 (CHarom.), 117.77 (CHarom.), 123.22 (Cq=CH2), 126.92 (CHarom.), 149 (CqF or CqOCH2C=O), 166.77 (OCH2C=O).

Methyl-2-(2-(2-fluoro-4-(2-methylenebutanoyl)phenoxy)acetamido)-3-methylpentanoate (7). Method A: Methyl-2-(2-(4-butyryl-2-fluorophenoxy)acetamido)-3-methylpentanoate (32, 58.0 mg, 0.16 mmol), TMDM (0.43 mL, 3.16 mmol), acetic anhydride (0.30 mL, 3.16 mmol). Rf: 0.75 (cyclohexane/ethyl acetate: 1/1); yield 41.5 mg (0.11 mmol, 68 %); colorless oil; LOOP-ESI-MS: calcd. for C20H26FNO5 379.43; found [M+H]+ 380.4; LC-MS: Rt = 18.9 min, purity 100 %; [α]: 61.1 (CHCl3, c = 0.1). 1H-NMR: δ 0.90–0.94 (m, 6H, Ile-CH2CH and Ile-CHCH), 1.11 (t, 3H, 3J = 7.5 Hz, CqCH2CH), 1.14–1.22 (m, 2H, Ile-CHCH3), 1.40–1.48 (m, 1H, Ile-C=O), 1.93–1.99 (m, 1H, Ile-CHCH3), 2.47 (t, 2H, 3J = 7.3 Hz, CqCHCH3), 3.74 (s, 3H, OCH), 4.62 (s, 2H, OCHC=O), 5.51 (s, Cq=CH), 5.78 (s, Cq=CH), 6.98 (dd, 1H, 3J = 8.2 Hz, CH), 7.08 (d, 1H, J = 8.5 Hz, NH), 7.57–7.63 (m, 2H, CH); 13C-NMR: δ 11.51 (Ile-CH2CH3 or Ile-CHCH3), 12.31 (CqCH2CH3), 15.50 (Ile-CH2CH3 or Ile-CHCH3), 25.08 (CqCH2CH3 or Ile-CHC=O), 25.43 (CqCH2CH3 or Ile-NCHC=O), 37.79 (Ile-CHCH3), 52.23 (OCH3), 68.32 (OCH2C=O), 114.25 (CHarom.), 117.86 (CHarom.), 123.26 (Cq=CH2), 126.81 (CHarom.), 132.46 (CC=O), 149.37 (COCH2C=O), 150.66 (C=CH2), 153.14 (CF), 166.83 (OCH2C=O), 171.68 (COCH3), 195.98 (CqC=O).

2-{2-[2,3-Dichloro-4-(2-methylene-butyryl)-phenoxy]acetylamino}pentanedioic acid (22). Compound 22 was synthesized according to [17] starting from etacrynic acid (240 mg, 0.79 mmol), N-hydroxy-succinimide (91 mg, 0.79 mmol), DCC (163 mg, 0.79 mmol) in THF. The solvent was removed and a solution of glutamic acid (116 mg, 0.79 mmol) and KOH (133 mg, 2.37 mmol) in water was added. After stirring 7 days at room temperature the mixture was acidified with conc. HCl and extracted with dichloro­methane. The crude product, which still contained etacrynic acid, was suspended in hot benzene and filtered. The solid residue yielded the pure amide as a white powder. Yield: 55 mg (0.127 mmol, 16 %). 1H-NMR (d-MeOH): δ = 1.14 (t, 3H, = 8.0 Hz, CH2CH), 2.05 (m, 1H), 2.27 (m, 1H), 2.38 – 2.47 (m, 4H, 2 CH2), 4.57 (m, 1H, NHCH), 4.75 (s, 2H, OCH2CO), 5.60 (s, 1H, C=CH), 6.02 (s, 1H, C=CH), 7.10 (d, 1H, = 8.0 Hz, Ar-H), 7.24 (d, 1H, = 8.0 Hz, Ar-H); LC-MS (negative mode): m/z: 431.2 (100) [M-H]-, Rt = 2.3 min.

6-{2-[2,3-Dichloro-4-(2-methylene-butyryl)-phenoxy]acetylamino}-hexanoic acid (23). Compound 23 was synthesized according to [17] starting from etacrynic acid (201 mg, 0.66 mmol), N-hydroxy-succinimide (76 mg, 0.66 mmol), DCC (137 mg, 0.66 mmol) in dichloromethane (20 mL). The solvent was removed and the residue taken up in THF. This solution was added to a solution of 6-amino-hexanoic acid (130 mg, 0.99 mmol) and KOH (111 mg, 1.98 mmol) in water (10 mL). After 3 days stirring at room temperature the mixture was acidified with conc. HCl and extracted with dichloro­methane. After removal of the organic solvent the crude product yielded a yellow oil which was purified by column chromatography (MeOH/CHCl3 10:2). Product: colourless oil, which solidified to a white solid. Yield: 93 mg (0.22 mmol, 34 %); 1H-NMR (d-MeOH): δ = 1.14 (t, 3H, = 8.0 Hz, CH2CH), 1.33 – 1.40 (m, 2H, CH2), 1.53 – 1.66 (m, 4H, 2 CH2), 2.28 (t, 2H, = 8.0 Hz, CH2), 2.44 (q, 2H, = 8.0 Hz, CHCH3), 3.30 (m, 2H, NHCH), 4.68 (s, 2H, OCH2CO), 5.59 (s, 1H, C=CH), 6.03 (s, 1H, C=CH), 7.07 (d, 1H, = 8.0 Hz, Ar-H), 7.24 (d, 1H, = 8.0 Hz, Ar-H); 13C-NMR (d-MeOH): δ = 13.0 (CH3), 24.5 (CH2), 25.7 (CH2), 27.4 (CH2), 30.1 (CH2), 34.9 (CH2), 40.0 (CH2), 69.5 (OCH2CO), 112.9 (Ar-CH), 124.0 (Ar-qC), 128.5 (Ar-CH), 129.9 (C=CH2), 131.8 (Ar-qC), 135.0 (Ar-qC), 151.7 (qC, C=CH2), 156.9 (Ar-qC), 169.7 (qC, NHCONH), 177.6 (qC, COOH), 197.3 (qC, C=O); LC-MS: m/z: 418.0 (15), Rt = 0.5 min.

5-(2-Oxo-hexahydro-thieno[3,4-d]imidazol-4-yl)pentanoic acid (6-{2-[2,3-dichloro-4-(2-methylene-butyryl)-phenoxy]acetylamino}-hexyl)-amide (24)

(A) Coupling of Boc-diaminohexane and D-biotin: Boc-diaminohexane (443 mg, 2.05 mmol) and D-biotin (500 mg, 2.05 mmol) were suspended in absolute DMF (45 mL) and cooled to 0 °C. DPPA (620 mg, 2.25 mmol) and triethylamine (229 mg, 2.25 mmol) were added and the mixture was stirred at 4 °C for 8 days. Dichloromethane (25 mL) was added and the organic phase was washed twice with citric acid (10%). Upon addition of water to the organic phase the amide precipitated as a white solid which was filtered off.

(B) Removal of the Boc-protecting group: The solid obtained in step (A) was suspended in dichloromethane (9 mL) and treated with TFA (3 mL) at 0 °C. Excess TFA was repeatedly removed in vacuo. For better evaporation dichloromethane was added to the residue. Quantitative removal of the protecting group was verified by 1H-NMR.

(C) Amide coupling to etacrynic acid: Biotin-(6-amino)-hexylamide (TFA-salt) (175 mg, 0.383 mmol), triethylamine (39 mg, 0.383 mmol) and etacrynic acid (232 mg, 0.767 mmol) were dissolved in DMF (2 mL). EEDQ (190 mg, 0.767 mmol) was added and the mixture was stirred at room temperature for 14 days. Ethyl acetate (50 mL) was added. Treatment of the organic phase with Na2CO3-solution (2%, 25 mL) yielded the desired product as a white precipitate which was filtered off. Overall yield: 62 mg (0.0988 mmol) as a white solid; 1H-NMR (DMSO-d): δ = 1.07 (t, 3H, = 7.4 Hz, CH2CH), 1.23 – 1.57 (m, 14H, CH2), 2.03 (t, 2H, = 7.2 Hz, CH2), 2.36 (q, 2H, = 7.4 Hz, CHCH3), 2.56 (d, 1H, = 12.3 Hz, SCH), 2.80 (dd, 1H, = 12.4 Hz, = 4.8 Hz, SCH), 2.97 – 3.12 (m, 5H, 2 NHCH2, SCH), 4.11 (m, 1H, NHCH), 4.29 (m, 1H, NHCH), 4.70 (s, 2H, OCH2CO), 5.55 (s, 1H, C=CH), 6.06 (s, 1H, C=CH), 6.33 (s, 1H, biotin-NH), 6.39 (s, 1H, biotin-NH), 7.07 (d, 1H, = 8.6 Hz, Ar-H), 7.32 (d, 1H, = 8.6 Hz, Ar-H), 7.70 (br s, 1H, CONH), 8.01 (br s, 1H, CONH); 13C-NMR (DMSO-d): δ = 12.3 (CH3), 22.9 (CH2CH3), 25.3 (CH2), 26.0 (CH2), 26.0 (CH2), 28.0 (CH2), 28.2 (CH2), 28.9 (CH2), 29.1 (CH2), 35.2 (CH2), 38.2 (CH2), 38.3 (CH2), 39.8 (SCH2), 55.4 (SCH), 59.2 (NHCH), 61.0 (NHCH), 67.9 (OCH2CO), 111.9 (Ar-CH), 121.2 (Ar-qC), 127.4 (Ar-CH), 129.3 (C=CH2), 129.9 (Ar-qC), 132.4 (Ar-qC), 149.3 (qC, C=CH2), 155.5 (Ar-qC), 162.6 (qC, NHCONH), 166.3 (qC, CONH), 171.7 (qC, CONH), 195.1 (qC, C=O); LC-MS: m/z 628.0 (100) [M+H]+, Rt = 16.3 min.

N-tert-butyl-2-(4-butyryl-2,3-dichloro-phenoxy)-acetamide (26). Compound 26 was synthesized according to [17] starting from 2,3-dichloro-4-butyrylphenoxyacetic acid (500 mg, 1.72 mmol), N-hydroxysuccinimide (198 mg, 1.72 mmol), DCC (354 mg, 1.72 mmol) and t-butylamine (251 mg, 3.43 mmol) in dichloromethane (15 mL). Reaction time: 21 d stirring at room temperature. The crude product was purified by column chromatography (SiO2, Cy/EtOAc 1:1). Yield: 374 mg (1.08 mmol, 63 %) as white solid; 1H-NMR: δ = 0.97 (t, 3H, = 7.4 Hz, CH2CH), 1.41 (s, 9H, (CH3)3), 1.72 (sext, 2H, = 7.3 Hz, CHCH3), 2.88 (t, 2H, = 7.2 Hz, COCHCH2CH3), 4.44 (s, 2H, OCH2), 6.62 (br s, 1H, NH), 6.84 (d, 1H, = 8.6 Hz, Ar-H), 7.38 (d, 1H, = 8.6 Hz, Ar-H). 13C-NMR: δ = 13.7 (CH2CH3), 17.8 (CH2CH3), 28.7 (C(CH3)3), 44.7 (COCH2), 51.5 (C(CH3)3), 68.4 (OCH2), 111.1 (Ar-CH), 123.2 (Ar-qC), 127.6 (Ar-CH), 131.4 (Ar-qC), 134.9 (Ar-qC), 155.2 (Ar-qC), 165.5 (qC, CONH), 201.8 (C=O).

N-butyl-2-(4-butyryl-2,3-dichloro-phenoxy)-acetamide (27). Compound 27 was synthesized according to [17] starting from 2,3-dichloro-4-butyrylphenoxyacetic acid (500 mg, 1.72 mmol), N-hydroxy-succinimide (198 mg, 1.72 mmol), DCC (354 mg, 1.72 mmol) and n-butylamine (251 mg, 3.43 mmol) in dichloromethane (15 mL). Reaction time: 21 d stirring at room temperature. The crude product was purified by column chromatography (SiO2, Cy/EtOAc 1:1). Yield: 270 mg (0.880 mmol, 45 %) as a white solid; 1H-NMR: δ = 0.92 – 0.98 (m, 6H, NH(CH2)3CH, COCH2CH2CH), 1.38 (sext, 2H, = 7.4 Hz, NHCH2CH2CHCH3), 1.55 (quint, 2H, = 7.3 Hz, NHCH2CHCH2CH3), 1.72 (sextett, 2H, = 7.3 Hz, COCH2CHCH3), 2.88 (t, 2H, = 7.3 Hz, COCHCH2CH3), 3.37 (q, 2H, = 6.7 Hz, NHCH), 4.55 (s, 2H, OCH2), 6.72 (br s, 1H, NH), 6.85 (d, 1H, = 8.8 Hz, Ar-H), 7.38 (d, 1H, = 8.6 Hz, Ar-H); 13C-NMR: δ = 13.7 (n-butyl-CH3, CH2CH3), 17.8 (CH2CH3), 20.0 (NHCH2CH2CH2CH3), 31.5 (NHCH2CH2CH2CH3), 38.9 (NHCH2), 44.8 (COCH2CH2CH3), 68.2 (OCH2), 111.0 (Ar-CH), 123.3 (Ar-qC), 127.6 (Ar-CH), 131.4 (Ar-qC), 135.0 (Ar-qC), 155.1 (Ar-qC), 166.4 (qC, CONH), 201.8 (C=O).

N-tert-butyl-2-(4-butyryl-2-fluorophenoxy)acetamide (28). Method B: Bromoacetyl bromide (2.94 g, 14.6 mmol), tert-butylamine (1.07 mg, 14.6 mmol), triethylamine (2.05 mL, 14.6 mmol); Method C: 1-(3-fluoro-4-hydroxyphenyl)butan-1-one (856 mg, 4.70 mmol), K2CO3 (974 mg, 7.05 mmol), KI (78.0 mg, 0.47 mmol), 2-bromo-N-tert-butylacetamide (see method B). Rf: 0.31 (cyclohexane/ethyl acetate: 2/1); yield 1.00 g (3.38 mmol, 72%); white solid; mp 80 °C (cyclohexane/ethyl acetate). 1H-NMR: δ 0.99 (t, 3H, 3J = 7.5 Hz, CH2CH2CH), 1.37 (s, 9H, Cq(CH)3), 1.75 (sext, 2H, 3J = 7.3 Hz, CH2CHCH3), 2.88 (t, 2H, 3J = 7.2 Hz, CHCH2CH3), 4.46 (s, 2H, OCHC=O), 6.41 (bs, 1H, NH), 6.97 (dd, 1H, J = 8.4 Hz, CH), 7.72–7.76 (m, 2H, CH).

Tert-butyl-2-(4-butyryl-2-fluorophenoxy)acetate (29). Method C: 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (1.00 g, 5.49 mmol), K2CO3 (1.19 g, 8.64 mmol), KI (91.0 mg, 0.55 mmol), bromoacetic acid tert-butylester (1.50 mL, 10.2 mmol); Rf: 0.69 (cyclohexane/ethyl acetate: 1/1); yield 1.46 g (4.93 mmol, 90 %); white solid; mp 62 °C (cyclohexane/ethyl acetate); 1H-NMR: δ 0.98 (t, 3H, 3J = 7.3 Hz, CH2CH2CH), 1.47 (s, 9H, Cq(CH)3), 1.74 (sext, 2H, 3J = 7.3 Hz, CH2CHCH3), 2.86 (t, 2H, 3J = 7.2 Hz, CHCH2CH3), 4.64 (s, 2H, OCHC=O), 6.89 (dd, 1H, J = 8.5 Hz, CH), 7.68–7.72 (m, 2H, CH).

N-butyl-2-(4-butyryl-2-fluorophenoxy)acetamide (30). Method B: Bromoacetyl bromide (2.08 g, 10.3 mmol), n-butylamine (753 mg, 10.3 mmol), triethylamine (1.45 mL, 10.3 mmol). Method C: 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (750 mg, 4.12 mmol), K2CO3 (853 mg, 6.17 mmol), KI (68.4 mg, 0.41 mmol), 2-bromo-N-n-butylacetamide (see method B). Rf: 0.32 (cyclohexane/ethyl acetate: 1/2); yield 1.00 g (3.39 mmol, 82 %); white solid; mp 75 °C (cyclohexane/ethyl acetate); 1H-NMR: δ 0.93 (m, 3H, NHCH2CH2CH2CH), 0.99 (t, 3H, 3J = 7.4 Hz, CH2CH2CH), 1.36 (sext, 2H, 3J = 7.3 Hz, NHCH2CH2CHCH3), 1.53 (sext, 3J = 7.3 Hz, NHCH2CHCH2CH3), 1.75 (sext, 2H, 3J = 7.3 Hz, CH2CHCH3), 2.88 (t, 2H, 3J = 7.3 Hz, CHCH2CH3), 3.36 (q, 2H, 3J = 6.8 Hz, NHCHCH2CH2CH3), 4.57 (s, 2H, OCHC=O), 6.59 (s, 1H, NH), 6.97 (dd, 1H, J = 8.3 Hz, CH), 7.72–7.76 (m, 2H, CH); 13C-NMR: δ 13.68 und 13.82 (CH2CH2CH und NHCH2CH2CH2CH), 17.76 (CH2CHCH3), 19.98 (NHCH2CH2CHCH3), 31.52 (NHCH2CHCH2CH3), 38.89 (NHCHCH2CH2CH3), 40.24 (CHCH2CH3), 68.15 (OCHC=O), 114.04 (CHarom.), 116.03 (CHarom.), 125.31 (CHarom.), 131.22 (CC=O), 149.12 (CF or COCH2C=O), 153.30 (CF or COCH2C=O), 166.69 (OCH2C=O), 197.84 (CqC=O).

2-(4-Butyryl-2-fluorophenoxy)-N-(1-hydroxy-2-methylpropan-2-yl)acetamide (31). Method B: Bromoacetyl bromide (0.76 mL, 8.75 mmol), 2-amino-2-methyl-1-propanol (780 mg, 8.75 mmol), triethylamine (1.23 mL, 8.75 mmol). Method C: 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (495 mg, 2.72 mmol), K2CO3 (563 mg, 4.08 mmol), KI (45.2 mg, 0.27 mmol), 2-bromo-N-(1-hydroxy-2-methylpropan-2-yl)acetamide (see method B). Rf: 0.28 (cyclohexane/ethyl acetate: 1/2); yield 455 mg (1.46 mmol, 54 %); white solid; mp 84 °C (cyclohexane/ethyl acetate); 1H-NMR: δ 0.99 (t, 3H, 3J = 7.5 Hz, CH2CH2CH), 1.35 (s, 6H, Cq(CH)2), 1.75 (sext, 2H, 3J = 7.4 Hz, CH2CHCH3), 2.88 (t, 2H, 3J = 7.3 Hz, CHCH2CH3), 3.65 (s, 2H, CqCHOH), 4.52 (s, 2H, OCHC=O), 6.66 (s, 1H, NH), 6.98 (dd, 1H, J = 8.1 Hz, CH), 7.73–7.76 (m, 2H, CH); 13C-NMR: δ 13.83 (CH2CH2CH3), 17.74 (CH2CH2CH3), 24.66 (Cq(CH3)2), 40.26 (CH2CH2CH3), 56.50 (C(CH3)2), 68.24 (OCH2C=O), 70.17 (CqCH2OH), 114.38 (CHarom.), 116.30 (CHarom.), 125.28 (CHarom.), 132.21 (CC=O), 148.87 (CF or COCH2C=O), 153.34 (CF or COCH2C=O), 167.42 (OCH2C=O), 197.85 (CqC=O).

Methyl 2-(2-(4-butyryl-2-fluorophenoxy)acetamido)-3-methylpentanoate (32). Method B: Bromoacetyl bromide (2.00 g, 9.92 mmol), isoleucine methylester HCl (1.80 mg, 9.92 mmol), triethylamine (2.79 mL, 19.8 mmol). Method C: 1-(3-Fluoro-4-hydroxyphenyl)butan-1-one (600 mg, 3.29 mmol), K2CO3 (683 mg, 4.94 mmol) KI (54.6 mg, 0.33 mmol), methyl-2-(2-bromoacetamido)-3-methyl-pentanoate (see method B)). Rf: 0.65 (cyclohexane/ethyl acetate: 1/1); yield 616 mg (1.68 mmol, 51 %); white solid; mp 74 °C (cyclohexane/ethyl acetate); [α] = 61.1 (CHCl3, c = 0.1); 1H-NMR: δ 0.90–0.94 (m, 6H, Ile-CH2CH and Ile-CHCH), 0.99 (t, 3H, 3J = 7.5 Hz, CH2CH2CH), 1.12–1.23 (m, 2H, Ile-CHCH3), 1.40–1.49 (m, 1H, Ile-CHC=O), 1.75 (sext, 3J = 7.3 Hz, CH2CHCH3), 1.92–1.99 (m, 1H, Ile-CHCH3), 2.88 (t, 2H, 3J = 7.3 Hz, CHCH2CH3), 3.74 (s, 3H, OCH), 4.62 (s, 2H, OCHC=O), 6.99 (dd, 1H, 3J = 8.5 Hz, CH), 7.08 (d, 1H, J = 8.5 Hz, NH), 7.72–7.77 (m, 2H, CH).

Protein expression and purification

Falcipain-2 and falcipain-3 were recombinantly expressed in E. coli and refolded to active enzyme as previously described [13,24].

Enzyme assays, in-vitro assays

IC50 values for inhibition of falcipain-2 and falcipain-3 were determined as described previously using the fluorogenic substrates Cbz-Phe-Arg-AMC and Cbz-Leu-Arg-AMC, respectively (AMC, 7-amino-4 methylcoumarin) [7, 13, 14]. As a positive control the well-known cysteine protease inhibitor E-64 [7, 25, 26] and as a negative control the solvent (DMSO) was used. Dose-dependent effects of compounds on parasite development (P. falciparum strain W2) were quantified by flow cytometry according to a previously published method [27]. First, a screening with inhibitor concentrations of 100, 10 and 1 mM was performed and the percentage activity of infected red blood cells (RBCs) relative to the negative control was determined. Compounds showing concentration dependent inhibition in these assays were selected for determination of IC50 values (Table 1). Chloroquine [20] and E-64 were used as positive controls, and the solvent DMSO was used as a negative control. For selected compounds assays with the P. falciparum strain 3D7 were performed using a fluorometric assay with Hoechst-33258 [28], or the microculture tetrazolium test measuring parasite lactate dehydrogenase activity [12, 29]. The parasites were cultivated in vitro as described previously [30]. Compounds were screened at concentrations between 1 nM and 100 μM. Synchronized ring stages were plated in 96-well plates at a parasitemia of 1%, in the presence of the compounds (dissolved in DMSO). Incubation of parasites with DMSO alone at a concentration of 0.5% v/v was used as a negative control. IC50 values were calculated by non-linear regression analyses using the programs GaphPad® Prism 4 and GraFit® [31, 32].

In vitro cytotoxicity assay

The human kidney epithelium-cell line 293T was cultured in DMEM medium supplemented with 20% fetal bovine serum and 1% l-glutamine (200 mM) at 37 °C in a humidified atmosphere containing 5% CO2. For the experimental procedures, cells were detached from the flasks with a rubber policeman, washed twice with PBS (phosphate-buffer saline) containing 1 mL trypsin-EDTA (1 x), and suspended at 2 x 106 cells mL-1 in complete medium. Inhibitor assays were carried out as described elsewhere except that the cell concentration used in this study was 2 x 104 mL-1 well-1 [33].