Small molecule based therapeutics development via targeting (CAG)n repeats RNA that causes Huntington's disease (HD) and spinocerebellar ataxia (SCAs)

Abstract

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological processes. Previously, RNA was solely considered as a protein-coding messenger. However, in the last two decades, extensive research on RNA has recognized its varied activities including catalytic and regulatory functions. The recognition of the ability of RNA to self-replicate has opened a whole new RNA world for researchers. RNA itself can exist in a complex form and involves in a multi-faceted role in cellular homeostasis rather than being a mere messenger of the information. It has different structural and functional forms that involve in diverse functions including RNA processing (e.g., small nuclear RNAs [snoRNAs], transfer RNAs [tRNAs] and translation, e.g., ribosomal RNAs [rRNAs]. Some other less characterized RNAs like Piwi-interacting RNA [piRNAs], Y RNAs and vault RNAs also exist in nature. Long or short non-coding RNAs also share this class and regulate gene expression transcriptionally or post-transcriptionally. RNA has a propensity tofold into the 3D structure using partly the Watson-Crick pairing and partially the non-canonical hydrogen bonds formed by either Hoogsteen base pairing or ribose-phosphate backbone. One such structure formed in trinucleotide repeat sequences is one of the most common types of simple sequence repeats found in mRNAs of all eukaryotic genome. These mutation-prone sequences are a rich source of genetic variations and sometimes mutations like slipped-strand mispairing during DNA replication leads to pathogenic expansion of trinucleotide repeats, causing several neurological disorders, commonly known as Trinucleotide Repeat (TNRs) Disorders. TNRs have a threshold limit for each repeat, and the increase in repeat length beyond the threshold limit causes the disease condition. There were six different types of TNRs, reported in literature so far, such as (CAG)n, (CUG)n, (CCG)n, (AAG)n, (CGG)n, (GCG)n and have been studied in translated or non-translated sequences of 17 genes showing their involvement in neurological disorders. The location of these repeats in genomes varies from 5′UTR like (CGG)n causing fragile X syndrome of FRAXA and FARXE, introns such as (AAG)n repeats implicated in Friedreich’s ataxia, ORFs like (CAG)n involving Huntington’s disease, Kennedy’s disease and several spinocerebellar ataxias (SCAs), 3′ UTR such as (CUG)n causing myotonic dystrophy type 1 (DM1) and (GCG)n repeats causes Oculopharyngeal Muscular Dystrophy (OPMD). The characteristic features of all these TNRs are that the early onset and the severity of the disease increase with the increase in the length of TNRs. However, why such repeats preferably expand more than the other triplet repeats is still not very well understood. For example, myotonic dystrophy type 1 (DM1) patient harbor 50-5000 repeats while HD patient has only 38-180 repeats in their pathogenic allele. The most suitable model of repeats expansion comprises the looped intermediates formation in DNA. Nevertheless, the intermediate loops of different TNRs have almost similar physical properties. For example, inspite of having very low energy difference (1-2 kcal/mol) between CAG and CTG repeats, these two sequence forms different length expansion as earlier involves in short expansion while later forms the longer expansion for the disease progression.