Trisubstituted Pyrimidines as Efficacious and Fast-Acting Antimalarials

Abstract

In this paper we describe the optimization of a phenotypic hit against Plasmodium falciparum, based on a trisubstituted pyrimidine scaffold. This led to compounds with good pharmacokinetics and oral activity in a P. berghei mouse model of malaria. The most promising compound (13) showed a reduction in parasitemia of 96% when dosed at 30 mg/kg orally once a day for 4 days in the P. berghei mouse model of malaria. It also demonstrated a rapid rate of clearance of the erythrocytic stage of P. falciparum in the SCID mouse model with an ED90 of 11.7 mg/kg when dosed orally. Unfortunately, the compound is a potent inhibitor of cytochrome P450 enzymes, probably due to a 4-pyridyl substituent. Nevertheless, this is a lead molecule with a potentially useful antimalarial profile, which could either be further optimized or be used for target hunting.

Figure 1

Published analogue compound 2, codes TCMDC-125419 (GSK) and GNF-Pf-1034/GNF-Pf-1447 (Novartis).

Figure 2

(a) In vivo efficacy data for compound 13 in P. falciparum infected SCID mice. (b) Levels of compound 13 in blood of the mice of the efficacy experiment during 23 h after the first oral dose. The symbols represent the same individuals depicted in plot a. (c) In vitro PRR data for compound 13 when parasites were treated at 10 × EC₅₀. Comparator data for other standard drugs are included for reference (data previously reported). Compound 13 showed a similar rate of kill to pyrimethamine. (d) Comparison of morphology of parasitized human RBC in vehicle and compound 13 treated mice. Erythrocytes with only remnants of parasites showing nuclear condensation were seen following 2-day treatment with compound 13. Compound dosed as the fumarate salt.

Scheme 1

(i) Dimethyl malonate (DMM), NaOMe, MeOH, reflux, 3 days, 55%; or DMM, NaOMe, N-methylpyrrolidinone, microwave, 1 h, 150 °C, 70%; (ii) POCl₃, 90°C, 58%; (iii) amine, DIPEA, THF, rt ; (iv) boronic ester/acid, K₃PO₄, Pd(PPh₃)₄, DMF/water, microwave, 120 °C, 20 min.

Scheme 2

(i) Amine, Et₃N, ethanol, −5 °C, 4 h; (ii) boronic acid/ester, 2 M aq Na₂CO₃, Pd(PPh₃)₄, 1,4-dioxane/water, microwave at 120 °C, 20 min; (iii) amine, Et₃N, acetonitrile, 40–70°C; (iv) 3-pyridyl boronic acid, K₃PO₄, Pd(PPh₃)₄,DMF/water 3/1, microwave at 120 °C, 20 min.

Scheme 3

(i) Amine, Et₃N, ethanol, rt, 16 h, 56%; (ii) 3-pyridylboronic acid, K₃PO₄, Pd(PPh₃)₄, 1,4-dioxane/water 3/1, microwave at 130 °C, 20 min, 96%; (iii) boronic acid, thiophene-2-carbonyloxycopper, Pd(PPh₃)₄, 1,4-dioxane or THF, microwave at 130 °C, 1 h or 85 °C, 18 h.

Scheme 4

(i) CH₂I₂, t-BuONO, acetonitrile, 80 °C, 3 h 30 min, 64%; (ii) amine, Et₃N, ethanol, 0 °C, 3 h; (iii) acetylene, CuI, Et₃N, Pd(PPh₃)₂Cl₂, acetonitrile, rt, 18 h; (iv) amine, DIPEA, NMP, microwave at 200 °C, 15 min; (v) boronic acid/ester, 2 M aq Na₂CO₃, Pd(PPh₃)₂Cl₂, DME, microwave at 200 °C, 20 min; (vi) 3-pyridylboronic acid, K₃PO₄, Pd(PPh₃)₄, DMF, microwave at 120 °C, 20 min.