Selective Small Molecule Recognition of RNA Base Pairs

Many types of RNAs exist in the human transcriptome, yet only the bacterial ribosome has been exploited as a small molecule drug target. Aside from rRNA, other cellular RNAs such as noncoding RNAs have primarily secondary structure and limited tertiary structure. Within these secondary structures of noncanonically paired and unpaired regions, more than 50% are base paired, with most efforts to target these structures focused on looped regions. A void exists in the availability of small molecules capable of targeting RNA base pairs. Using chemoinformatics, an RNA-focused library enriched for nitrogen-containing heterocycles was developed and tested for binding RNA base pairs, leading to the identification of six selective and previously unknown binders. While all binders were derivatives of benzimidazoles, those with expanded aromatic polycycles bound selectively to AU pairs, while those with flexible urea side chains bound selectively to GC pairs. Two of the three selective GC pair binders can distinguish between two different orientations, 5′GG/3′CC and 5′GC/3′CG pairs. Furthermore, all six molecules showed >50-fold selectivity for RNA over DNA. These studies provide foundational knowledge to better exploit RNA as targets for small molecule chemical probes or lead therapeutics by using modules that target RNA base pairs

Superfluorescent Squaraine With Efficient Two-Photon Absorption And High Photostability

The synthesis, linear photophysical, two-photon absorption (2PA), femtosecond transient absorption, and superfluorescence properties of a new symmetrical squaraine derivative (1) are reported. Steady-state linear spectral and photochemical properties, fluorescence lifetimes, and excitation anisotropy of 1 were investigated in various organic solvents. High fluorescence quantum yields (≈0.7) and very high photostability (photodecomposition quantum yields ≈10-6-10-8) were observed. An open-aperture Z-scan method was used to obtain 2PA spectra of 1 over a broad spectral range (maximum 2PA cross section ≈1000 GM). Excited-state absorption (ESA) and gain was observed by femtosecond transient absorption spectroscopy, in which both reached a maximum at approximately 500 fs. Squaraine 1 exhibits efficient superfluorescence. The quantum chemical study of 1 revealed the simulated vibronic nature of the 1PA and 2PA spectra were in good agreement with experimental data; this may provide the ability to predict potential advanced photonic materials. Super fluoro to the rescue! Large two-photon absorption (2PA), femtosecond transient absorption kinetics, and efficient superfluorescence properties of a new symmetrical squaraine derivative (1) are reported along with extremely high photochemical stability. The density functional theory (DFT)-based quantum chemical study of 1 reveals the vibronic nature of the 2PA spectra in the main linear absorption band that is in good agreement with experimental data. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif–small molecule interactions identified via selection. Named High Throughput Structure–Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif–small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule–RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs