Synthesis and in Vitro Evaluation of Biotinylated RG108:  A High Affinity Compound for Studying Binding Interactions with Human DNA Methyltransferases

• Published in: Bioconjugate chemistry 2006-03, Vol.17 (2), p.261-266
• Main Authors: Schirrmacher, Esther, Beck, Carmen, Brueckner, Bodo, Schmitges, Frank, Siedlecki, Pawel, Bartenstein, Peter, Lyko, Frank, Schirrmacher, Ralf
• Format: Article
• Language: English
• Subjects: Biochemistry; Biotin - chemistry; Biotin - metabolism; Cell-Free System; Deoxyribonucleic acid; DNA; DNA Modification Methylases - antagonists & inhibitors; DNA Modification Methylases - metabolism; Enzymes; Human body; Humans; Indoles - chemistry; Indoles - metabolism; Medical research; Molecular Structure; Nuclear Magnetic Resonance, Biomolecular; Phthalimides; Prescription drugs; Propionates - chemistry; Propionates - metabolism; Protein Binding; Proteins; Tryptophan - analogs & derivatives
• ISSN: 1043-1802; 1520-4812
• DOI: 10.1021/bc050300b

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.