Unveiling the druggable RNA targets and small molecule therapeutics

The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.     

Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles

SARS-CoV is a newly identified coronavirus that causes severe acute respiratory syndrome (SARS). Currently, there is no effective method available for prophylaxis and treatment of SARS-CoV infections. In the present study, the influence of small interfering RNA (siRNA) on SARS-CoV nucleocapsid (N) protein expression was detected in cultured cells and mouse muscles. Four siRNA expression cassettes driven by mouse U6 promoter targeting SARS-CoV N gene were prepared, and their inhibitory effects on expression of N and enhanced green fluorescence protein (EGFP) fusion protein were observed. A candidate siRNA was proved to down-regulate N and EGFP expression actively in a sequence-specific manner. The expression vector of this siRNA was constructed and confirmed to reduce N and EGFP expression efficiently in both cultured cells and adult mouse muscles. Our findings suggest that the siRNA should provide the basis for prophylaxis and therapy of SARS-CoV infection in human.     

非编码小RNA的多样性

RNA是一类广泛存在的极其重要的生物大分子,它不仅种类繁多,而且不同种类的RNA在结构方面有着显著的差异。RNA种类和结构的多样性决定了RNA具有很多重要的生物学功能。随着对非编码RNA(non-coding RNA,ncRNA)研究的不断深入,ncRNAs同样呈现出前所未有的复杂性和多样性。主要介绍了tRNA、snRNA、scRNA、rRNA、siRNA、miRNA、pi RNA和nat-si RNA等两大类持家ncRNA和调控ncRNA的结构和功能,为便于了解生物体内小的非编码RNA的多样性,进一步挖掘和利用ncRNAs提供一定的参考,促使人们对RNA的认识和地位作出新的思考。     

Recent progress in human telomere RNA structure and function

Human telomeric DNA is transcribed into telomeric RNA in cells. Telomeric RNA performs the fundamental biological functions such as regulation and protection of chromosome ends. This digest highlights the human telomere RNA G-quadruplex structures, telomere RNA functions, G-quadruplex-binding small molecules, and future prospects.     

Small molecule SUMOylation activators are novel neuroprotective agents

Neuronal loss characterizes many of the most intractable nervous system diseases that deprive our ageing population of their quality of life. Neuroprotective pharmacological modalities are urgently needed to address this burgeoning population. Small ubiquitin-like modifier (SUMO) conjugation has been established as an endogenous neuroprotective response, and we have discovered several classes of small molecules that enhance SUMO conjugation. Herein we describe the hit to lead campaign that enabled the discovery of 3 diverse classes of drug-like SUMOylation activators. Optimized compounds were ultimately validated in cell-based models of neuronal loss and provide a foundation for establishing systemically active SUMO activators to treat degenerative diseases such as Parkinson’s disease, Alzheimer’s disease, and stroke.     

Endogenous Small RNA Clusters in Plants

In plants, small RNAs（sRNAs） usually refer to non-coding RNAs（ncRNAs） with lengths of 20–24 nucleotides. sRNAs are involved in the regulation of many essential processes related to plant development and environmental responses. sRNAs in plants are mainly grouped into microRNAs（miRNAs） and small interfering RNAs（siRNAs）, and the latter can be further classified into trans-acting siRNAs（ta-siRNAs）, repeat-associated siRNAs（ra-siRNAs）, natural anti-sense siRNAs（nat-siRNAs）, etc. Many sRNAs exhibit a clustered distribution pattern in the genome. Here, we summarize the features and functions of cluster-distributed sRNAs, aimed to not only provide a thorough picture of sRNA clusters（SRCs） in plants, but also shed light on the identification of new classes of functional sRNAs.     

Small RNA species in maize tissue

The low molecular weight RNA components of maize have been analyzed after labeling callus and leaf tissue with [³H]uridine in vitro. Electrophoresis of the isolated RNA on acrylamide slab gels reveals, apart from 5S and transfer RNA, three major and about five minor RNA species with chain lengths between 140 and 280 nucleotides. These RNA molecules are labeled as rapidly as 5S, transfer RNA, and do not represent degradation products of large ribosomal RNA molecules. Furthermore, like 5S and transfer RNA, these small RNA species are stable and show no detectable turnover within forty-eight hours. Fractionation of the tissue into crude subcellular fractions indicates a preferential association of some of the small stable RNA species with the nucleus, while others appear to be located in the cytoplasm. The low molecular weight RNA spectrum from the leaf is similar to that observed in callus, with the major small RNA species equally present in both tissues.Abbreviations tRNA transfer RNA - hnRNA heterogenous nuclear RNA - mRNA messenger RNA - scRNA small cytoplasmic RNA - snRNA small nuclear RNA     

Ligand-inducible formation of RNA pseudoknot

Here, we demonstrate that a series of naphthyridine derivatives, naphthyridine carbamate tetramer (NCTn), can bind to the RNA CGG/CGG triad comprised of two single-stranded regions of a hairpin loop and a tail. Complete suppression of the binding by a single mutation indicated simultaneous binding of NCTn between hairpin loop and single stranded tail, leading to the formation of NCTn-induced pseudoknot.     

RNA as a small molecule druggable target

Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents.     

piRNA：一类新的非编码小RNA

piRNA（Piwi-interacting RNA）是从哺乳动物生殖细胞中分离得到的一类长度约为30nt的小RNA,并且这种小RNA与PIWI蛋白家族成员相结合才能发挥它的调控作用。目前,越来越多的文献表明piRNA在生殖细胞的生长发育中的调控是由于Piwi-piRNA复合物引起的基因沉默导致的,但由于对piRNA的研究尚处于初级阶段,它的一些具体的功能和生源论尚在研究当中。本文主要综述了piRNA的最新研究进展。     

植物核仁小分子RNA及其研究进展

自从６０年代末Ｗｅｉｎｂｅｒｇ等在哺乳动物中发现了第一个核仁小分子ＲＮＡ（ｓｍａｌｎｕｃｌｅｏｌａｒＲＮＡ,ｓｎｏＲＮＡ）Ｕ３以来,这一领域的研究特别是９０年代以来的进展引起了人们的广泛关注。这些富集于核仁区的代谢稳定的ｓｎｏＲＮＡ暗示了它们在核糖体...     

RNA interference and its application in bone-related diseases

RNA interference (RNAi) is the most exciting insight in biology in past decades, which provided new perspectives into the genome-wide surveys of gene function by targeted degradation of mRNA with the introduction of small interfering RNAs (siRNAs) or small hairpin RNAs (shRNAs) in a large variety of organisms, and turned out to be a more efficient and convenient method compared with the traditional knockout pathway. What's more, as the enhancement of its stability and improvement of its delivery vehicles, RNAi is bound to be a practical tool in determine gene function first in vitro and then in vivo. In this paper, we will focus on the recent achievements of RNAi and also depict the development of RNAi as a potentially powerful tool in studying bone-related diseases.     

Case studies in rare disease small molecule discovery and development

This review covers case studies in rare disease small molecule drug discovery with an emphasis on the use of new technologies and innovative target approaches. Case studies include examples of covalent modification, inducement of alternative splicing, stop codon readthrough, allosteric activation, and a repurposing example. The review highlights effective use of rare disease animal models, inducible pluripotent stem cells, and biomarkers.     

New approaches to target RNA binding proteins

RNA binding proteins (RBPs) are a large and diverse class of proteins that regulate all aspects of RNA biology. As RBP dysregulation has been implicated in a number of human disorders, including cancers and neurodegenerative disease, small molecule chemical probes that target individual RBPs represent useful tools for deciphering RBP function and guiding the production of new therapeutics. While RBPs are often thought of as tough-to-drug, the discovery of a number of small molecules that target RBPs has spurred considerable recent interest in new strategies for RBP chemical probe discovery. Here we review current and emerging technologies for high throughput RBP-small molecule screening that we expect will help unlock the full therapeutic potential of this exciting protein class.