Features of Modularly Assembled Compounds That Impart Bioactivity Against an RNA Target

Abstract

Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the non-coding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)exp. Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). Based on activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely PTAs, are optimal. Notably, we determined that r(CUG)exp is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived and faster on rates than the protein that binds r(CUG)exp, the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs

“…(67, 68) Indeed, the affinity and selectivity of a multivalent compound that targets RNA is controlled by the nature of the scaffold that displays the RNA-binding modules, valency, and the distance between RNA-binding modules. (36, 47, 69)…”

Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells

“…Total RNA was then incubated with the beads, and RNAs that bound the small molecule were identified by qRT-PCR. Indeed, this approach was used to confirm that small molecules can be designed to bind a desired target (18, 79). In one study, we showed that a small molecule designed to bind the r(CGG) repeat that causes FXTAS pulls down more of the desired target than an oligonucleotide complementary to the repeat (18).…”

“…If RNAs cause disease by sequestering protein, as in the case of DM1, then the small molecule could displace RNA-bound protein in cellulo or in vivo and improve cellular defects caused by sequestration. Indeed, monomeric and multivalent compounds have been developed against the RNAs that cause DM1, DM2, c9ALS/FTD, and fragile X-associated tremor ataxia syndrome (FXTAS) (18, 78, 79). In general, bioactive compounds improve disease-associated defects in cellulo in the low- to mid-micromolar range (18, 78, 79).…”

Esperdimina como agente inhibidor de la proteína de la distrofia muscular miotónica tipo 1 (MBNL‐1) empleando química computacional

“…3 [26] se realizó una minimización de energías para la estructura MBNL-1, usando el método de "steepest descent", seguidamente se tomó la estructura minimizada de la MBNL-1 y se procedió a realizar la Dinámica Molecular, agregándole condiciones periódicas de contorno (PBC) [27] usando la funcional CAMB3LYP [28], la cuál es una funcional híbrida de intercambio correlación que combina las cualidades híbridas del B3LYP y una corrección de largo alcance. Además de la funcional CAMB3LYP, se utilizó el set de base TZVP para obtener una convergencia más rápida y mejor de las energías y geometrías a nivel de DFT (Density Theory Function) [29] y así evitar las frecuencias negativas al momento de la optimización.…”

“…5. Dichos aminoácidos logran interaccionar con los nitrógenos presentes en la espermidina logrando obtener sitios favorables de interacción con la estructura del fosfodiéster cargada negativamente en el ligando [28]. Revista TECNIA Vol.27 N°1 Enero-Junio Tabla 1.…”