RNA aptamers as pathway-specific MAP kinase inhibitors

Background: In eukaryotic cells, many intracellular signaling pathways have closely related mitogen activated protein kinase (MAPK) paralogs as centra l components. Although MAPKs are therefore obvious targets to control the c ellular responses resulting from the activation of these signaling pathways , the development of inhibitors which target specific cell signaling pathwa ys involving MAPKs has proven difficult. Results: We used an RNA combinatorial approach to isolate RNAs that inhibit the in vitro phosphorylation activity of extracellular regulated kinase 2 (ERK2). These inhibitors block phosphorylation by ERK1 and ERK2, but do not inhibit Jun N-terminal kinase or p38 MAPKs. Kinetic analysis indicates the se inhibitors function at high picomolar concentrations through the steric exclusion of substrate and ATP binding. In one case, we identified a compac t RNA structural domain responsible for inhibition. Conclusions: RNA reagents can selectively recognize and inhibit MAPKs invol ved in a single signal transduction pathway. The methodology described here is readily generalizable, and can be used to develop inhibitors of MAPKs i nvolved in other signal transduction pathways. Such reagents may be valuabl e tools to analyze and distinguish homologous effectors which regulate dist inct signaling responses.