Probing the Chemical Space for Non-Promiscuous Nucleic Acid Binders
Creators: name: Sandoval, Jorge
Publisher: name: My University
Year: 2023
Subjects: subject: Nucleic-acid targeted probes
subject: Probing chemical repertoire for inhibition of Dicer Mediated Maturation of pre-miRNA
subject: Identification of structural elements that may drive preferential towards the major groove
subject: Natural Product, surfactins, Identified via HTS technique, cat-ELCCA, binds to pre-miRNA
subject: Crystal Violet derivatives require different structural elements to drive either major or minor groove binding
subject: Biological Chemistry
subject: Chemistry
subject: Science

description: Our understanding of DNA, RNA &amp; RNA motifs has catapulted in the last few decades, and as we have begun to better understand their role in disease, we’ve seen an influx of therapeutic tools &amp; technologies that are actively changing how we understand these molecules and how our overall knowledge translates into novel tools or therapeutic strategies. To further our knowledge of nucleic acid biology, novel probes were developed for reassessing the targetability of select nucleic acid motifs. In particular, the two nucleic-acid-based target sites studied were: the major groove pockets of select DNA sequences and a select library of pre-miRNAs. Corrupted DNA sequences or dysregulation of DNA transcription has been implicated in almost every disease, despite being highly conserved and regulated. DNA’s localization in the nucleus makes it incredibly difficult to make DNA-targeted probes &amp; therapeutics. The biological events at the major groove of DNA are of particular interest because several regulatory proteins and transcription factors associate at specific major groove unit sequences. Through the rational design of 2nd generation probes, we were able to derivatize our crystal violet library and confirm a previous observation that an alkene or alkyne linker is necessary for major groove binding. Alkyl &amp; aliphatic linkers were found to be strongly associated in the minor groove, and thereby also observing that not all crystal violet analogs discriminately associate with the major groove. The molecules described do not show significant levels of sequence selectivity, however, a mild affinity for tighter major groove sequences from bulky trimeric analogs might reveal a structural basis for achieving some level of shape recognition and subsequently, sequence selectivity. MicroRNAs (miRNAs) are a conserved, non-coding class of RNAs that regulate more than 60% of protein expression via RNA Induced Silencing Complex (RISC). Dysregulation of miRNA expression has been linked to diabetes, obesity, cancer, cardiovascular, neurodegenerative, and other diseases. These correlations have made probing miRNAs an attractive target for therapeutic innovation. However, the development pre-miRNA specific probes have remained poorly explored largely due to their inherent challenges as targetable substrates. By employing a novel screening technique, catalytic-enzyme linked click chemistry assay (cat-ELCCA), and an activity-guided fractionation strategy, we were able to isolate and identify a series of surfactin-based analogs, the hermicidins, and their novel ability to bind premiR21 and inhibit Dicer mediated maturation. These probes may prove to be useful tools in studying the processes regulating pre-miRNA biogenesis. There are currently FDA-approved, surfactin-based drugs on the market, therefore, these findings may provide the basis for a novel therapeutic strategy by modulating dicer-mediated pre-miRNA maturation. Furthermore, our efforts in the total synthesis of similar surfactin-based probes were successful, providing preliminary insight into structural features necessary for their inhibitory activity. Furthermore, novel molecules capable of inhibiting or modulating Dicer activity are briefly described and could serve useful in the study of Dicer-specific studies. Altogether, these preliminary findings provide some key insight into structural elements necessary for major groove binding &amp; identify a class of macrocycles capable of interfering with dicer-mediated maturation. Ideally, the results from this work can be further explored to further our understanding of how nucleic acids interact with their surroundings and elucidate the mechanisms by which nucleic acids can be exploited for therapeutic purposes.