Combinatorial synthesis of cholesterol ester transfer protein-mRNA ligandsand screening by nondenaturating gel-electrophoresis

RNA, as one of the biomolecules with the most structural and functional div ersity, is an attractive therapeutic target.(1) Employing combinatorial che mistry methods, small peptide ligands were found, which bind to a short RNA with important biological functions. A 23-nt RNA oligonucleotide from the cholesterol ester transfer protein mRNA was chosen as a molecular target.(2 ) A 27-nt RNA oligonucleotide from the human immunodeficiency virus type-1 (HN-1) TAR RNA was used to control the binding specificity.(3) Tetrapeptide libraries, composed of the amino acids Lys, Tyr, Leu, lie, and Arg, with a nd without C- and N-terminal lysines, were synthesized by a combination of combinatorial and divergent solid-phase synthesis. Gel-shift affinity scree ning was used to extract the peptides with the best RNA binding properties. The peptide Lys-Tyr-Lys-Leu-Tyr-Lys-Cys-NH2 (1) showing micromolar affinit y to its RNA target was characterized with circular dichroism (CD), ultra v iolet (UV) measurement, and H-1 NMR spectroscopy.