Toward conditional control of Smac mimetic activity by RNA-templated reduction of azidopeptides on PNA or 2'-OMe-RNA

Towards a templated reaction that translates RNA in cells into a proaptotic peptide-PNA conjugate

Nucleic acid-templated chemistry opens the intriguing prospect of triggering the synthesis of drugs only in diseased cells. Herein, we explore the feasibility of using RNA-templated chemical reactions for the activation of a known Smac peptidomimetic compound (SMC), which has proapoptotic activity. Two peptide nucleic acid (PNA) conjugates were used to enable conditional activation of a masked SMC by reduction of an azide either by Staudinger reduction or catalytic photoreduction using a ruthenium complex. The latter provided ~135 nM SMC-PNA on as little as 10 nM (0.01 eq.) template. For the evaluation of the templated azido-SMC reduction system in cellulo, a stable HEK 293 cell line was generated, which overexpressed a truncated, non-functional form of the XIAP mRNA target. We furthermore describe the development of electroporation protocols that enable a robust delivery of PNA conjugates into HEK 293 cells. The action of the reactive PNA conjugates was evaluated by viability and flow cytometric apoptosis assays. In addition, electroporated probes were re-isolated and analyzed by ultra-high performance liquid chromatography (UPLC). Unfortunately, the ruthenium-PNA conjugate proved phototoxic, and treatment of cells with PNA-linked reducing agent and the azido-masked SMC conjugate did not result in a greater viability loss than treatment with scrambled sequence controls. Intracellular product formation was not detectable. A control experiment in total cellular RNA isolate indicated that the templated reaction can in principle proceed in a complex system. The results of this first-of-its-kind study reveal the numerous hurdles that must be overcome if RNA molecules are to trigger the synthesis of pro-apoptotic drugs inside cells.

DNA-Templated Reactions with High Catalytic Efficiency Achieved by a Loss-of-Affinity Principle

Nucleic-acid-templated chemical reactions are currently explored for applications in DNA-encoded drug discovery, nucleic acid diagnostics, and theranostics. Of particular interest are reactions enabling the template to gain catalytic activity, so that enzymatic amplification of low copy targets would no longer be necessary. Herein, we introduce a new reaction design relying on the template-controlled cleavage of PNA-spermine conjugates. With turnover frequencies in the range of 3-10 min^-1 and a k_cat/K_M = 1.3 × 10⁶ M^-1 s^-1, the loss of affinity upon reaction provides a catalytic efficiency equal to most enzymatic conversions and superior to nucleic-acid-templated reactions reported to date.