Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA–Small Molecule Interactions

Juru, Aline Umuhire; Hargrove, Amanda E.

doi:10.1021/acschembio.8b00945

Cited by 34 publications

(16 citation statements)

References 139 publications

(364 reference statements)

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“…For each framework, we will first discuss how it is generally conceived and implemented and then we will provide a critical evaluation in relation to other frameworks. Having focused our analysis mainly on major themes, we will not discuss important work that may not fit into the three main frameworks such as modulation of the RNA conformational landscape, which we discussed in a previous review article ( 43 ), or the use of small molecules to induce degradation of pathogenic RNAs ( 44 ).…”

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confidence: 99%

Frameworks for targeting RNA with small molecules

Juru

Hargrove

2021

Journal of Biological Chemistry

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Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including proteins, DNA, other RNAs, and metabolites. Through these interactions, RNAs mediate cellular processes such as the regulation of gene transcription and the enhancement or inhibition of protein activity. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, and RNA molecules have been increasingly recognized as potential targets for drug development efforts, which in the past had focused primarily on proteins. Although both small molecule–based and oligonucleotide-based therapies have been pursued in efforts to target RNA, small-molecule modalities are often favored owing to several advantages including greater oral bioavailability. In this review, we discuss three general frameworks (sets of premises and hypotheses) that, in our view, have so far dominated the discovery of small-molecule ligands for RNA. We highlight the unique merits of each framework as well as the pitfalls associated with exclusive focus of ligand discovery efforts within only one framework. Finally, we propose that RNA ligand discovery can benefit from using progress made within these three frameworks to move toward a paradigm that formulates RNA-targeting questions at the level of RNA structural subclasses.

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confidence: 99%

Frameworks for targeting RNA with small molecules

Juru

Hargrove

2021

Journal of Biological Chemistry

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“…The distribution of defined structures can be greatly altered by interactions with substrate molecules or ions. There may even be novel structures that would not be stable without those interactions ( 25 ). Cations, especially divalent Mg 2+ ions, are essential in stabilizing tertiary RNA structures and are thus required for most aptamers to fold into their native and binding-competent state.…”

Section: Resultsmentioning

confidence: 99%

What defines a synthetic riboswitch? – Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials

Kaiser

Schneider

Groher

et al. 2021

Nucleic Acids Research

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Among the many in vitro-selected aptamers derived from SELEX protocols, only a small fraction has the potential to be applied for synthetic riboswitch engineering. Here, we present a comparative study of the binding properties of three different aptamers that bind to ciprofloxacin with similar KD values, yet only two of them can be applied as riboswitches. We used the inherent ligand fluorescence that is quenched upon binding as the reporter signal in fluorescence titration and in time-resolved stopped-flow experiments. Thus, we were able to demonstrate differences in the binding kinetics of regulating and non-regulating aptamers. All aptamers studied underwent a two-step binding mechanism that suggests an initial association step followed by a reorganization of the aptamer to accommodate the ligand. We show that increasing regulatory potential is correlated with a decreasing back-reaction rate of the second binding step, thus resulting in a virtually irreversible last binding step of regulating aptamers. We suggest that a highly favoured structural adaption of the RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch. In addition, our results provide an explanation for the fact that so few aptamers with regulating capacity have been found to date. Based on our data, we propose an adjustment of the selection protocol for efficient riboswitch detection.

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“…Small molecules binding to noncoding RNA elements can directly block the binding of endogenous factors and also can alter the conformational profile of the RNA, thus disrupting the RNA element's cellular function [ 13 ]. The enzymatic probing changes we observed in the presence of polymyxin B and colistin are consistent with a ligand-induced change in the conformational profile of S2M G35U .…”

Section: Discussionmentioning

confidence: 99%

“…Together, the data indicate that the stem-loop II motif in SARS-CoV-2 has a different conformational profile compared to that of SARS-CoV due to a G to U base transversion and that this conformational profile is altered upon ligand binding. Consequently, since the conformation of noncoding RNA elements often determines their function [ 13 ], we suggest that the coronavirus stem-loop II motif may be a druggable target.…”

Section: Introductionmentioning

confidence: 99%