Identification and development of a series of disubstituted piperazines for the treatment of Chagas disease

Abstract

Approximately 6-7 million people around the world are estimated to be infected with Trypanosoma cruzi, the causative agent of Chagas disease. The current treatments are inadequate and therefore new medical interventions are urgently needed. In this paper we describe the identification of a series of disubstituted piperazines which shows good potency against the target parasite but is hampered by poor metabolic stability. We outline the strategies used to mitigate this issue such as lowering logD, bioisosteric replacements of the metabolically labile piperazine ring and use of plate-based arrays for quick diversity scoping. We discuss the success of these strategies within the context of this series and highlight the challenges faced in phenotypic programs when attempting to improve the pharmacokinetic profile of compounds whilst maintaining potency against the desired target.

Graphical abstract

Fig. 1

The structure of initial hit compound TCMDC-143497 and compound 1 with key profiling data.

Fig. 2

Results of acute T. cruzi infection efficacy study. Treatments: vehicle b.i.d. 10 mL/kg for 5 days, benznidazole 50 mg/kg b.i.d. for 5 days and 1-ABT (1-aminobenzotriazole) b.i.d. 50 mg/kg as a pre-treatment 30 min prior to each dose of compound 1 b.i.d. 50 mg/kg for 5 days (a) Study outline. Blue arrows indicate imaging days, red arrows indicate immunosuppression days. 5 day dosing begins on day 14 (b) Quantification (Total Flux [p/s]) of combined ventral and dorsal bioluminescence for the mice shown in (c). Black line and grey line represent limit of detection of the imaging system and are the mean and mean + 2 SDs, respectively, for infected untreated control mice. Vehicle (purple), benznidazole (red), 1-ABT + compound 1 (green). Blue box indicates dosing period, red box indicates immunosuppression period (c) Whole body imaging – dorsal and ventral. Heat-maps are on log₁₀ scales and indicate intensity of bioluminescence from low (blue) to high (red), minimum and maximum radiance values as indicated. The mice were immunosuppressed on days 28, 32 and 36 post-infection using cyclophosphamide (200 mg/kg i.p.). Study shows reduction in parasite burden when dosing compound 1 compared to vehicle but relapse is observed post immunosuppression (d) Exposure data (n = 3) for compound 1 from efficacy study showing sustained whole blood levels over EC₉₉ for the duration of the study on day 1 and day 5. Free blood levels are over or around EC₅₀ on day 1 but drop below EC₅₀ after 5 h on day 5. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Comparison of T. cruzi pEC₅₀ of purified and non-purified material for test set.

Fig. 4

Plot showing number of compounds in each clogD bracket included in the plate-based array.

Fig. 5

(a) the loss of parent and appearance of metabolites when compound 1 was incubated with mouse liver microsomes; (b) the proposed structures of the metabolites.

Fig. 6

Plot of potency vs microsomal clearance. Green lines show desired property cut offs of pEC₅₀ > 6 and clearance <5 mL/min/g. Desired property space is coloured in green. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Scheme 1

Synthesis of varied sulphonamide compounds 1-9^{a a}Reagents and conditions: (a) NaBH(OAc)₃, anh. MgSO₄, DCM, rt, 5 h (b) 4 M HCl in dioxane, DCM, rt, 16 h (c) triethylamine, DCM, 0°C-rt, 16 h or pyridine, 0°C-rt, 16 h ¹Nitrogen linked directly to aromatic ring of core structure.

Scheme 2

Synthesis of varied amide compounds 10–22^{a a}Reagents and conditions: (a) DCM, rt, 16 h (b) TFA, DCM, rt, 20 h (c) T3P, triethylamine, DCM, rt, 5 h.

Scheme 3

Synthesis of piperazine replacement compound 37^{a a}Reagents and conditions: (a) NaBH(OAc)₃, DCM, 0°C-rt, 22 h (b) Zn, NH₄Cl, THF:water, 0°C-rt, 16 h (c) triethylamine, DCM, 0°C-rt, 5 h (d) TFA, DCM, 0°C-rt, 4 h (e) HATU, DIPEA, DCM, 0°C-rt, 16 h.

Scheme 4

Synthesis of piperazine replacement compound 39^{a a}Reagents and conditions: (a) Pd₂(dba)₃, XPhos, K₃PO₄, 1,4-dioxane, 100 °C, 16 h (b) NaBH(OAc)₃, THF, rt, 3 h (c) 4 M HCl dioxane, MeOH, rt, 16 h (d) HOBt, EDC.HCl, triethylamine, DCM, rt, 18 h.

Scheme 5

Synthesis of piperazine replacement compound 40^{a a}Reagents and conditions: (a) K₂CO₃, MeCN, rt 16 h (b) 4 M HCl in dioxane, MeOH, rt, 24 h (c) HOBt, EDC.HCl, DIPEA, DCM, rt, 72 h (d) Zn, AcOH, DCM, rt, 2.5 h (e) DIPEA, DCM, 0°C-rt, 16 h.

Scheme 6

Synthesis of phenyl replacement compound 41^{a a}Reagents and conditions: (a) NaH, DMF, 0°C-rt, 2 h (b) LiAlH₄, THF, −78 °C, 1 h (c) NaBH(OAc)₃, anh. MgSO₄, DCM, 0°C-rt, 12 h.

Scheme 7

Synthesis of phenyl replacement compound 44^{a a}Reagents and conditions: (a) NaBH(OAc)₃, DCM, rt, 16 h (b) Zn, NH₄Cl, THF:H20, rt, 24 h (c) pyridine, 0°C-rt, 1 h (d) TFA, DCM, 0°C-rt, 5 h (e) T3P, DIPEA, DCM, rt, 16 h.

Scheme 8

Synthesis of phenyl replacement compounds 43 and 45^{a a}Reagents and conditions: (a) Pyridine, 60 °C, 16 h (b) LiBH₄, EtOH:Et₂O:THF, 0°C-rt, 20 h (c) PBr₃, DCM, 0°C-rt, 1 h (d) K₂CO₃, DMF, rt, 16 h (e) [Pd(OAc)₂]₃, BINAP, Cs₂CO₃, toluene, 100 °C, 5 h (f) HCl, MeOH, rt, 16 h.