Resveratrol-salicylate derivatives as selective DNMT3 inhibitors and anticancer agents

Figures & data

Figure 1. Chemical structures of resveratrol, NSC 14778 and aspirin. The hybrid resveratrol-salicylate derivatives possess the combined chemical features of these three different types of agents; the methylene bridge in NCS 14778 is replaced by an ethylene linkage between a phenol on one side, and the salicylate on the other.

Figure 2. Chemical structures of representative examples of nucleoside and non-nucleoside DNMT inhibitors.

Table 1. Concentration (µM) of test compounds required to inhibit by 50% the enzymatic activity of DNMT1, DNMT3A, and DNMT3B.

	IC50 (µM)
Compounds	DNMT3A/3L	DNMT3B/3L	DNMT1
3	282	>300	NI^a
4	>300	>300	NI^a
5	>300	>300	NI^a
6	>300	>300	NI^a
7	>300	>300	NI^a
8	281	156	NI^a
9	40	52	NI^a
10	25	62	NI^a
11	186.6	190	NI^a
12	100	215	NI^a
TMS	>300	>300	NI^a
Resveratrol	105	65	>300
SAH	ND^b	0.25^c	2

Results are expressed as IC₅₀ values using a cell-free biochemical assay. To generate the enzyme inhibition curves, duplicate reactions were performed for each concentration; IC₅₀ values were calculated using the GraphPad Prism v6 software.

^aNI, no inhibition at the maximum test compound concentration (300 µM).

^bND, not determined.

^cTaken from Ref.37.

Figure 3. Comparison of the binding modes calculated for compounds 9 (blue), 10 (purple), and resveratrol (orange) as predicted by AutoDock 4.2, in the presence and in the absence of the co-factor SAH (yellow) in the active site of DNMT1, DNMT3A and DNMT3B enzymes.

Figure 4. Comparison of the binding modes of compounds 3 (magenta), 4 (yellow), 5 (pink), 6 (gray), 7 (violet), 8 (green), 9 (blue), 10 (purple), 11 (pink), 12 (cyan), TMS (brown) and resveratrol (orange) predicted by AutoDock 4.2 in the presence and absence of co-factor SAH of DNMT1, DNMT3A and DNMT3B.

Table 2. Calculated binding free energies of resveratrol-salicylate analogs in human DNMTs.

	DNMT1		DNMT3A		DNMT3B
Compound	Without cofactor	With cofactor	Without cofactor	With cofactor	Without cofactor	With cofactor
3	−7.52	−6.58	−8.11	−7.08	−7.32	−7.16
4	−8.47	−5.83	−8.99	−5.84	−8.02	−6.78
5	−8.26	−6.26	−8.52	−6.27	−8.76	−6.17
6	−7.05	−6.39	−5.06	−6.29	−8.28	−7.02
7	−7.44	−6.14	−8.40	−5.76	−7.82	−7.85
8	−8.37	−6.91	−9.41	−7.84	−9.05	−8.54
9	−8.13	−7.67	−9.66	−8.17	−8.85	−7.54
10	−7.43	−6.42	−9.27	−7.01	−8.99	−8.82
11	−−8.94	−7.21	−7.65	−7.72	−9.33	−8.23
12	−7.95	−8.96	−8.42	−7.50	−7.88	−8.44
TMS	−7.36	−6.02	−7.95	−5.67	−8.23	−7.53
Resveratrol	−7.74	−5.83	−9.03	−6.57	−7.95	−6.22

Table 3. Concentration (µM) of the test compounds required to inhibit cell proliferation by 50 % (IC₅₀) using the MTT assay.

	IC50 (µM)
Compounds	HT-29	HepG2	SK-BR-3
10	44.3	18.9	11.3
Resveratrol	130.0	54.9	110.3
TMS	14.0	>100	111.8

Each IC₅₀ value represents the mean of three different experiments in triplicate. To generate the cell proliferation inhibition curves, six concentrations (in the 0.03–125 µM range) were used for each compound. IC₅₀ values were generated using the GraphPad v6 Prism software.

Kuck D, Singh N, Lyko F, Medina-Franco JL. Novel and selective DNA methyltransferase inhibitors: docking-based virtual screening and experimental evaluation. Bioorg Med Chem 2010;18:822–9

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