Synthesis and Application of KγT Peptide Nucleic Acids.

Displaying ligands in a succinct and predictable manner is essential for elucidating multivalent molecular-level binding events. Organizing ligands with high precision and accuracy provides a distinct advantage over other ligand-display systems, such as polymers, because the number and position of the ligand(s) can be accurately and fully characterized. Here we describe the synthesis of peptide nucleic acids (PNAs), which are oligonucleotide mimics with a pseudopeptide backbone that can hybridize to oligonucleotides through Watson-Crick base pair to form highly predictable and organized scaffold for organizing a ligand.

PNA-Based Multivalent Scaffolds Activate the Dopamine D2 Receptor.

Peptide nucleic acid scaffolds represent a promising tool to interrogate the multivalent effects of ligand binding to a membrane receptor. Dopamine D2 receptors (D2R) are a class of G-protein coupled receptors (GPCRs), and the formation of higher-ordered structures of these receptors has been associated with the progression of several neurological diseases. In this Letter, we describe the synthesis of a library of ligand-modified PNAs bearing a known D2R agonist, (±)-PPHT.

Programmable nanoscaffolds that control ligand display to a G-protein-coupled receptor in membranes to allow dissection of multivalent effects.

A programmable ligand display system can be used to dissect the multivalent effects of ligand binding to a membrane receptor. An antagonist of the A2A adenosine receptor, a G-protein-coupled receptor that is a drug target for neurodegenerative conditions, was displayed in 35 different multivalent configurations, and binding to A2A was determined. A theoretical model based on statistical mechanics was developed to interpret the binding data, suggesting the importance of receptor dimers.

Direct observation of aminoglycoside-RNA binding by localized surface plasmon resonance spectroscopy.

RNA is involved in fundamental biological functions when bacterial pathogens replicate. Identifying and studying small molecules that can interact with bacterial RNA and interrupt cellular activities is a promising path for drug design. Aminoglycoside (AMG) antibiotics, prominent natural products that recognize RNA specifically, exert their biological functions by binding to prokaryotic ribosomal RNA and interfering with protein translation, ultimately resulting in bacterial cell death.

Cooperative, heparan sulfate-dependent cellular uptake of dimeric guanidinoglycosides.

Oligoarginine and guanidinium-rich molecular transporters have been shown to facilitate the intracellular delivery of a diverse range of biologically relevant cargos. Several such transporters have been suggested to interact with cell-surface heparan sulfate proteoglycans as part of their cell-entry pathway. Unlike for other guanidinium-rich transporters, the cellular uptake of guanidinoglycosides at nanomolar concentrations is exclusively heparan sulfate dependent.

Antibiotic selectivity for prokaryotic vs. eukaryotic decoding sites.

A FRET assembly reports antibiotic affinities to two different RNA targets. A binder was labeled with a fluorophore that acts both as an acceptor for the emissive nucleoside on the bacterial A-site and a donor fluorophore for the terminally-labeled human A-site. Unlabeled drugs were used to dissociate the labeled antibiotic.

FRET enabled real time detection of RNA-small molecule binding.

A robust analysis and discovery platform for antibiotics targeting the bacterial rRNA A-site has been developed by incorporating a new emissive U surrogate into the RNA and labeling the aminoglycosides with an appropriate fluorescence acceptor. Specifically, a 5-methoxyquinazoline-2,4(1H,3H)-dione-based emissive uracil analogue was identified to be an ideal donor for 7-diethylaminocoumarin-3-carboxylic acid. This donor/acceptor pair displays a critical Forster radius (R(0)) of 27 A, a value suitable for an A-site-aminoglycoside assembly.

Antibacterial activity of (-)-deoxypseudophrynaminol versus its racemate and derivatives.

(-)-Deoxypseudophrynaminol 1 possesses 43-fold greater antibacterial potency than the racemate toward Staphylococcus aureus, indicating that the (-)-enantiomer is the biologically active isomer in this assay. Comparison of the percent growth inhibition by derivatives of 1 indicates that prenylation of N8 and replacement of N1-methyl by methyl carbamate are detrimental to antibacterial potency. (-)-1 is a promising lead structure for the development of the novel hexahydropyrrolo[2,3-b]indole class of antibacterial agents.