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Small-molecule inhibitors of DNA methyltransferases such as RG108 represent promising candidates for cancer drug development. We report the synthesis and in vitro analysis of a biotinylated RG108 conjugate, 2-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-3-(5-{3-[5-(2-oxo-hexahydro-thieno[3,4-d]imidazol-4-yl)pentanoylamino]propoxy}-1H-indol-3-yl)propionic acid (bio-RG108), for the evaluation of interactions with DNA methyltransferase enzymes. The structural design of the chemically modified inhibitor was aided by molecular modeling, which suggested the possibility for extensive chemical modifications at the 5-position of the tryptophan moiety in RG108. The inhibitory activity of the corresponding derivative was confirmed in a cell-free biochemical assay, where bio-RG108 showed an undiminished inhibition of DNA methyltransferase activity (IC50 = 40 nM). Bio-RG108 therefore represents a suitable bioconjugate for the elucidation of inhibitory mechanisms and for the affinity purification of RG108-associated proteins.

DNA methyltransferases are promising targets for cancer therapy. In many cancer cells promoters of tumor suppressor genes are hypermethylated, which results in gene inactivation. It has been shown that DNA methyltransferase inhibitors can suppress tumor growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. To discover novel compounds for the inhibition of human DNA methyltransferases, we have screened a set of small molecules available from the NCI database. Using a 3-dimensional model of the human DNA methyltransferase 1 and a modified docking and scoring procedure, we have identified a small list of molecules with high affinities for the active site of the enzyme. The two highest scoring structures were found to inhibit DNA methyltransferase activity in vitro and in vivo. The newly discovered inhibitors validate our screening procedure and also provide a useful basis for further rational drug development.