Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

Abstract

Histone deacetylases (HDACs) play an essential role in the transcriptional regulation of cells through the deacetylation of nuclear histone and non-histone proteins and are promising therapeutic targets for the treatment of various diseases. Here, the synthesis of new compounds in which a hydroxamic acid residue is attached to differently substituted pyrimidine rings via a methylene group bridge of varying length as potential HDAC inhibitors is described. The target compounds were obtained by alkylation of 2-(alkylthio)pyrimidin-4(3H)-ones with ethyl 2-bromoethanoate, ethyl 4-bromobutanoate, or methyl 6-bromohexanoate followed by aminolysis of the obtained esters with hydroxylamine. Oxidation of the 2-methylthio group to the methylsulfonyl group and following treatment with amines resulted in the formation of the corresponding 2-amino-substituted derivatives, the ester group of which reacted with hydroxylamine to give the corresponding hydroxamic acids. The synthesized hydroxamic acids were tested as inhibitors of the HDAC4 and HDAC8 isoforms. Among the synthesized pyrimidine-based hydroxamic acids N-hydroxy-6-[6-methyl-2-(methylthio)-5-propylpyrimidin-4-yloxy]hexanamide was found to be the most potent inhibitor of both the HDAC4 and HDAC8 isoforms, with an IC₅₀ of 16.6 µM and 1.2 µM, respectively.

Keywords: HDAC inhibitors; alkylation; aminolysis; hydroxamic acid; pyrimidine.

Figure 1

FDA-approved HDAC inhibitors with a hydroxamic acid moiety.

Scheme 1

Synthesis of compounds 3–18. Reagents and conditions: (a) ethyl 2-bromoethanoate, TBAB, TEA, 50–60 °C, 0.5 h; (b) oxone, DMF, 40 °C, 0.5 h; (c) corresponding amine, DMSO, 50–70 °C, 0.5 h; (d) H₂O, DMSO, 100 °C, 0.5 h; (e) H₂O, reflux, 1 h; (f) aqueous NaOH, dioxane, rt, 12 h, then, conc. HCl to pH 2; (g) NH₂OH^.HCl, KOH, H₂O (H₂O/MeOH for 7), 0–5 °C, 1–4 h (rt, 96 h for 7), then, conc. HCl to pH 5–6.

Scheme 2

Synthesis of compounds 20–31. Reagents and conditions: (a) ethyl 2-bromoethanoate (for 22) (or ethyl 4-bromobutanoate (for 20, 23), or methyl 6-bromohexanoate (for 21, 24)), TBAB, TEA, 50–60 °C, 0.5–4 h; (b) NH₂OH^.HCl, KOH, MeOH, 0–5 °C, 1 h, then ester 20–24, 0–5 °C,1 h, then conc. HCl to pH 5–6.

Figure 2

The conformational and tautomeric forms of hydroxamic acids according to [36].

Figure 3

Fragment of the ¹H NMR spectrum in DMSO-d₆ of compound 12.