Selection, design, and characterization of a new potentially therapeutic ribozyme

Abstract

An in vitro selection was designed to identify RNA-cleaving ribozymes predisposed for function as a drug. The selection scheme required the catalyst to be trans-acting with phosphodiesterase activity targeting a fragment of the Kras mRNA under simulated physiological conditions. To increase stabilization against nucleases and to offer the potential for improved functionality, modified sequence space was sampled by transcribing with the following NTPs: 2′-F-ATP, 2′-F-UTP, or 2′-F-5-[(N-imidazole-4-acetyl) propylamine]-UTP, 2′-NH₂-CTP, and GTP. Active motifs were identified and assessed for their modified NMP and divalent metal dependence. The minimization of the ribozyme's size and the ability to substitute 2′-OMe for 2′-F and 2′-NH₂ moieties yielded the motif from these selections most suited for both nuclease stability and therapeutic development. This motif requires only two 2′-NH₂-Cs and functions as a 36-mer. Its substrate sequence requirements were determined to be 5′–Y-G-H–3′. Its half-life in human serum is >100 h. In physiologically relevant magnesium concentrations [∼1 mM] its k_cat = 0.07 min⁻¹, K_m = 70 nM. This report presents a novel nuclease stable ribozyme, designated Zinzyme^TM, possessing optimal activity in simulated physiological conditions and ready for testing in a therapeutic setting.