Structure-Guided Identification of DNMT3B Inhibitors

Abstract

Methyltransferase 3 beta (DNMT3B) inhibitors that interfere with cancer growth are emerging possibilities for treatment of melanoma. Herein we identify small molecule inhibitors of DNMT3B starting from a homology model based on a DNMT3A crystal structure. Virtual screening by docking led to purchase of 15 compounds, among which 5 were found to inhibit the activity of DNMT3B with IC₅₀ values of 13-72 μM in a fluorogenic assay. Eight analogues of 7, 10, and 12 were purchased to provide 2 more active compounds. Compound 11 is particularly notable as it shows good selectivity with no inhibition of DNMT1 and 22 μM potency toward DNMT3B. Following additional de novo design, exploratory synthesis of 17 analogues of 11 delivered 5 additional inhibitors of DNMT3B with the most potent being 33h with an IC₅₀ of 8.0 μM. This result was well confirmed in an ultrahigh-performance liquid chromatography (UHPLC)-based analytical assay, which yielded an IC₅₀ of 4.8 μM. Structure-activity data are rationalized based on computed structures for DNMT3B complexes.

Figure 1

DNMT1/DNA complex crystal structure from the Protein Data Bank (PDBID: 3PTA). The partially buried SAM methyl donor is shown in blue.

Figure 2

DNA methyltransferase inhibitors.

Figure 3

Schematic of the computational methodology used here.

Figure 4

Structures of the purchased (1–15) obtained from the virtual screening. Compounds 16, 17–22, and 23, analogues of 7, 10, and 12, respectively, were also purchased and tested.

Figure 5

(A) Docking pose from Glide XP for 11 obtained from the virtual screening for DNMT3B. (B) Substituents R and R′ of 11.

Scheme 1. Indole Core Series

Reagents and conditions: (a) CH₃NH₂, NaBH₄, CH₃OH, 23 °C, 94–99%; (b) H₂SO₄ (aq), NaNO₂ (aq), KI, H₂O, 23 °C, 92%; (c) Indole, Pd(OAc)₂, dppm, KOAc, H₂O, 110 °C, 50%; (d) 25, HATU, DIPEA, DMF, 23 °C, 52–77%.

Scheme 2. Benzimidazole and Adenine Core Series

Reagents and conditions: (a) 25a–25j, PyBOP, DMF, 23 °C, 70–87%; (b) 34 or 35, Pd₂(dba)₃, P(Cy)₃, K₃PO₄ (aq), dioxane, 100 °C, 17%–40%.

Figure 6

(A) Inhibition of methyltransferase activity by the addition of DNMT3B inhibitor 33h. (B) Docking pose from Glide XP for 33h.