Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA

Zhang, Peiyuan; Park, Hye-Jin; Zhang, Jie; Junn, Eunsung; Andrews, Ryan J.; Velagapudi, Sai Pradeep; Abegg, Daniel; Vishnu, Kamalakannan; Costales, Matthew G.; Childs‐Disney, Jessica L.; Adibekian, Alexander; Moss, William C.; Mouradian, M. Maral; Disney, Matthew D.

doi:10.1073/pnas.1905057117

Cited by 77 publications

(96 citation statements)

References 81 publications

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“…Particular focus is on the development of novel therapeutic agents to target and inhibit processes critical to SARS-CoV-2 infection and replication. To help address this important need, we have analyzed the SARS-CoV-2 genome using an RNA structural analysis and motif discovery pipeline, ScanFold, which has been previously applied to two other RNA viruses: Zika and HIV-1 4 ; as well as human mRNAs for MYC 5 and α-synuclein 6 . A significant innovation of ScanFold is that unique consensus secondary structural motifs are generated from bases pairs with the strongest evidence of being functional, while not necessarily focusing on evolutionary conservation (as in a recent analysis of SARS-CoV-2 7 ).…”

Section: Introductionmentioning

confidence: 99%

Anin silicomap of the SARS-CoV-2 RNA Structurome

Andrews

Haniff

et al. 2020

Preprint

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SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis. Δ G° z-score region is the 3′UTR, which was found to yield mostly positive z-scores; despite a higher than average GC content for this region (0.45 on average; Table S1), MFE values here were less stable than expected, averaging Δ G° z-scores of +0.98 (or roughly one standard deviation less stable than random). Scans were also performed in the negative sense of the genome, revealing slightly less propensity for structure. The MFE values ranged from -42.9 to -6.0 and averaged -23.25 kcal/mol; z-scores in the negative sense had a similar range of Δ G° z-scores as the positive sense (-5.76 to 2.66) but averaged lower at -1.12 (Table S1). Interestingly, Δ G° z-scores for the 3′ UTR in negative sense were more skewed to the negative (finding minimums as low as -2.32) resulting in an average z-score of 0.16 for the region.

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Section: Introductionmentioning

confidence: 99%

Anin silicomap of the SARS-CoV-2 RNA Structurome

Andrews

Haniff

et al. 2020

Preprint

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“…Experiments that assess off-target interactions and RNA selectivity are clearly important when it comes to testing novel RNA-binders in vitro and in vivo (Naro et al 2018;Zhang et al 2020;Costales et al 2017;Abulwerdi et al 2019;Donlic et al 2018). However, our survey of the HIV-1 TAR literature ( Supplementary Table S2) revealed that these controls are not always performed (Gelus et al 1999;He et al 2005;Hwang et al 2003).…”

Section: Rnasmentioning

confidence: 99%

“…Such compounds with demonstrated cellular activity have been enumerated in the R-BIND database (Morgan et al 2019). Some of these compounds have been shown to bind specific RNAs and inhibit their cellular activities with well-validated selectivity (Costales et al 2017(Costales et al , 2019Zhang et al 2020;Shi et al 2019;Haga et al 2015;Naro et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…When performed, drug-like RNA-targeted small molecules are often found to have broad, promiscuous activity (Schmidt 2014;Murchie et al 2004;Mischiati et al 2001;Nahar et al 2014) and/or to interact with assay reporter proteins (Thorne et al 2010). Because few studies comprehensively report on the selectivity of these drug-like molecules at both the in vitro and cellular level (Zhang et al 2020;Mischiati et al 2001;Richter et al 2004), it is unclear what capacity this new class of RNA-targeted compounds has to bind RNAs non-specifically and what structural features define this behavior.…”

Section: Introductionmentioning

confidence: 99%

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Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

Kelly

Chu²,

Shi

et al. 2020

Preprint

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Identifying small molecules that selectively bind a single RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to non-specific binding of aminoglycosides and intercalators to a variety of RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities, however the ability of such compounds to discriminate against RNA stem-loops commonly found in the transcriptome has not been thoroughly assessed in all cases. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activity of three distinct RNAs, to non-specifically bind two HIV-1 stem-loop RNAs: the transactivation response element (TAR) and stem IIB in the rev response element (RREIIB). All three compounds bound to TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting substantial off-target interactions consistent with non-specific cellular activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, much like aminoglycosides, and in contrast to ligands that specifically bind riboswitches. Our results support extending the group of non-selective RNA-binders beyond aminoglycosides and intercalators to encompass drug-like compounds with capacity for non-specific hydrogen-bonding and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.

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“…Further, multiple occurrences of bulged nucleotides and internal loops within a helix can establish a structural and dynamics pattern unique to the RNA molecule containing those features. Although non-canonical elements within regular helices offer clear opportunities for targeting specific ncRNAs, progress towards the identification of small molecules that selectively bind such nonstandard features has only recently begun to gain momentum [6][7][8][9][10] .…”

Section: Introductionmentioning

confidence: 99%

2-amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)

Nikonowicz

Zhang

Chang

et al. 2020

Preprint

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RNA helices are often punctuated with non-Watson-Crick features that can be the target of chemical compounds, but progress towards identifying small molecules specific for non-canonical elements has been slow. We have used a tandem UU:GA mismatch motif (5'-UG-3':5'-AU-3') embedded within the helix of an RNA hairpin as a model to identify compounds that bind the motif specifically. The three-dimensional structure of the RNA hairpin and its interaction with a small molecule compound identified through a virtual screen are presented. The G-A of the mismatch forms a sheared pair upon which the U-U base pair stacks. The hydrogen bond configuration of the U-U pair involves the O2 of the U adjacent to the G and the O4 of the U adjacent to the A. The G-A and U-U pairs are flanked by A-U and G-C base pairs, respectively, and the mismatch exhibits greater stability than when the motif is within the context of other flanking base pairs or when the 5'-3' orientation of the G-A and U-U is swapped.Residual dipolar coupling constants were used to generate an ensemble of structures against which a virtual screen of 64,480 small molecules was performed to identify candidate compounds that the motif specifically binds. The tandem mismatch was found to be specific for one compound, 2-amino-1,3-benzothiazole-6-carboxamide, which binds with moderate affinity but extends the motif to include the flanking A-U and G-C base pairs. The finding that affinity for the UU:GA mismatch is flanking sequence dependent emphasizes the importance of motif context and potentially increases the number of small non-canonical features within RNA that can be specifically targeted by small molecules.

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Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA

Cited by 77 publications

References 81 publications

Anin silicomap of the SARS-CoV-2 RNA Structurome

Anin silicomap of the SARS-CoV-2 RNA Structurome

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

2-amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)

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