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

Abstract

The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities (K a or K d) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.

Frameworks for targeting RNA with small molecules

“…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 ).…”

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

“…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.…”

RNA sequence and ligand binding alter conformational profile of SARS-CoV-2 stem loop II motif

“…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 .…”

“…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.…”