Study and Development of new RNA-targeted probes

Targeting non-coding RNAs with small molecules is a promising frontier in addressing unmet medical needs, especially the microRNAs, which have been recognized as established biological targets playing fundamental roles in cellular processes. This research focused on developing inhibitors targeting processing of pre-miR-21 by Dicer, to rebalance cellular regulatory networks and mitigate the oncogenic impacts associated with mature miR-21 overexpression. In our project, a medium-throughput screening was carried out against the precursor of miR-21 (pre-miR-21) and two other RNA strands (A-site and TAR). Approximately 4,000 compounds underwent testing, identifying hits 1 and 2, featuring a morpholinone- and cyclopentene-based scaffold, respectively. The synthetic design of these hits led to the development of two synthetic pathways, enabling the preparation of a diverse array of different functionalized analogs for both series. While the synthesis of hit 1 employed an enantiospecific approach using commercial enantiopure starting materials, the synthetic design for hit 2 required a novel organic methodology to address the proper trans stereochemistry of the substituents in the main scaffold. Subsequent Structure-Activity Relationship (SAR) investigations revealed that the chemical class of hit 1 showed limited activity, triggering its abandonment in favor of the more promising hit 2. SAR studies on hit 2 and analogs demonstrated that enhancements in affinity to pre-miR-21 could be achieved, culminating in the identification of promising compounds 36, 39, 52 and 65. During a research period at Prof. F. L. Gervasio’s lab (University of Genève), computational studies on pre-miR-21's active/inactive conformations were conducted. These efforts resulted in developing a robust model for describing and predicting compound interactions with pre-miRNA-21 and, possibly, inhibiting the processing of premiR-21 by Dicer.