Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non-aminoglycoside Ligand for the Bacterial A-site RNA

Classical thiazole orange and its regioisomer as fluorogenic probes for nucleolar RNA imaging in living cells

In contrast to well-established DNA-selective dyes for live cell imaging, RNA-selective dyes have been less developed owing to the challenges of making small molecules have RNA selectivity over DNA. Two kinds of dyes are now commercially available for nucleolar RNA imaging in cells, but these two dyes do not apply to living cells and have limited use in fixed and permeabilized cells. Herein, we report on thiazole orange (TO), a well-known nucleic acid stain, as a promising fluorogenic dye for nucleolar RNA imaging in living cells. TO shows clear response selectivity for RNA over DNA with a significant light-up property upon binding to RNA (λ_em = 532 nm, I/I₀ = 580-fold, and Φ_bound/Φ_free = 380) and is even applicable to wash-free imaging of living cells. More interestingly, 2TO, a regioisomer of TO in which the benzothiazole unit is connected to position 2 in the quinoline ring, performs much better (λ_em = 532 nm, I/I₀ = 430-fold, Φ_bound/Φ_free = 1200), having superior selectivity for RNA in both solution and living cells. The comparison with TO derivatives carrying different substituents at N1 of the quinoline ring reveals that the slight change in the TO framework significantly affects RNA selectivity, photostability and membrane permeability.

Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule

We have developed a new class of triplex-forming peptide nucleic acid (PNA)-based fluorogenic probes for sensing of the panhandle structure of the influenza A virus (IAV) RNA promoter region. Here, a small molecule (DPQ) capable of selectively binding to the internal loop structure was conjugated with triplex-forming forced intercalation of the thiazole orange (tFIT) probe with natural PNA nucleobases. The resulting conjugate, tFIT-DPQ, showed a significant light-up response (83-fold) upon strong (K_d = 107 nM) and structure-selective binding to the IAV RNA promoter region under physiological conditions (pH 7.0, 100 mM NaCl). We demonstrated the conjugation of these two units through the suitable spacer was key to show useful binding and fluorogenic signaling functions. tFIT-DPQ facilitated the sensitive and selective detection of IAV RNA based on its binding to the promoter region. Furthermore, we found that tFIT-DPQ could work as a sensitive indicator for screening of test compounds targeting the IAV RNA promoter region in the fluorescence indicator displacement assay.

Naphthyridine Derivatives Induce Programmed Cell Death in Naegleria fowleri

Primary amoebic encephalitis (PAM) caused by the opportunistic pathogen Naegleria fowleri is characterized as a rapid and lethal infection of the brain which ends in the death of the patient in more than 90% of the reported cases. This amoeba thrives in warm water bodies and causes infection after individuals perform risky activities such as splashing or diving, mostly in non-treated water bodies such as lakes and ponds. Moreover, the infection progresses very fast and no fully effective molecules have currently been found to treat PAM. In this study, naphthyridines fused with chromenes or chromenones previously synthetized by the group were tested in vitro against the trophozoite stage of two strains of N. fowleri. In addition, the most active molecule was evaluated in order to check the induction of programmed cell death (PCD) in the treated amoebae. Compound 3 showed good anti-Naegleria activity (61.45 ± 5.27 and 76.61 ± 10.84 µM, respectively) against the two different strains (ATCC^® 30808 and ATCC^® 30215) and a good selectivity compared to the cytotoxicity values (>300 µM). In addition, it was able to induce PCD, causing DNA condensation, damage at the cellular membrane, reduction in mitochondrial membrane potential and ATP levels, and ROS generation. Hence, naphthyridines fused with chromenes or chromenones could be potential therapeutic agents against PAM in the near future.

New Approaches in Sensing and Targeting Bacterial rRNA A-site

New chemical agents that could combat increasing antibiotic resistance are urgently needed. In this mini-review, an old but highly relevant RNA sequence which is crucial for the continuation of bacterial life-cycle is covered. Some of the most significant advances of the last decade in sensing and targeting the bacterial rRNA A-site: a well-validated binding site of proverbially known aminoglycoside antibiotics are described. Some of the major advances in direct sensing of the bacterial decoding side (A-site) are described and also new fluorescent molecules that are capable of detecting lead compounds through high-throughput assays by displacement of fluorescent probe molecules are highlighted. Lastly, some of the recently discovered non-aminoglycoside small molecule binders of bacterial rRNA A-site as a new class of molecules that could provide future scaffolds and molecules for developing new antibacterial agents have been discussed.

Fused chromeno and quinolino[1,8]naphthyridines: Synthesis and biological evaluation as topoisomerase I inhibitors and antiproliferative agents

The synthesis of 1,8-naphthyridine derivatives fused with other heterocycles, such as chromenes and quinolines, as well as their behaviour as topoisomerase I inhibitors is studied. The preparation is carried out through a direct and simple process as an intramolecular [4 + 2] cycloaddition reaction between functionalized aldimines, obtained by the condensation of 2-aminopyridine and unsaturated aldehydes, and olefins. In particular, while no clear inhibitory activity is observed for chromeno[4,3-b][1,8]naphthyridine fused heterocycles, a very different result is observed for quinolino[4,3-b][1,8]naphthyridine derivatives. Experimental assays indicated that quinolino[4,3-b][1,8]naphthyridines inhibited the topoisomerase I enzymatic reaction behaving like a poison, as occurs with the natural TopI inhibitor, camptothecin. Furthermore, the cytotoxic effect on cell lines derived from human lung adenocarcinoma (A549), human ovarian carcinoma (SKOV3), and on non-cancerous lung fibroblasts cell line (MRC5) was also screened.

Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding

The bacterial A-site RNA is one of the key targets towards the development of new antibacterials including new treatment options for tuberculosis. Using DAPI as a prototype, we have explored the potential of bisamidines as a potential chemical motif for bacterial A-site recognition. We have demonstrated that the binding of DAPI shows a concentration-dependent thermal stabilization of the bacterial A-site RNA (ΔT_m = 9.9 °C). The binding, however, does not show pH-dependent changes upon lowering of pH. Both UV-vis and CD experiments show that the DAPI binding involves base stacking with the RNA bases in a manner that is analogous to intercalation. Scatchard analysis of the UV-vis titration data revealed a micromolar affinity of the DAPI to the bacterial rRNA A-Site (K_a = 1.14 × 10⁶ M^-1) which was corroborated by the FID-based relative binding affinity comparison with aminoglycosides. The molecular docking studies showed binding poses consistent with polar and stacking interactions with the RNA. These studies highlight the role of amidines in bacterial A-site recognition and the need for the development of their structural analogs towards the making of aminoglycoside mimics.

Small molecule-PNA oligomer conjugates for rRNA A-site at neutral pH for FID assays

A triplex-forming PNA oligomer conjugated with a naphthyridine derivative (ATMND-C₂-NH₂) showed high selectivity and strong binding for the bacterial rRNA A-site at pH 7.0 (K_d = 190 ± 72 nM), which was accompanied by fluorogenic signaling that allowed the potential use of this conjugate probe in fluorescent indicator displacement assays.

Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA

Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.

Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA

We report that TO-PRO-3 functions as a deep-red fluorescent indicator for the internal loop structure of the bacterial (Escherichia coli) A-site, which enables the assessment of A-site binding capability of various test compounds including blue and even-green-emitting compounds.