Elise Prost

Investigation of RNA–Ligand Interactions by 19F NMR Spectroscopy Using Fluorinated Probes†

Ribonucleic acid (RNA) is now recognized as playing a key role in many biological functions, and is emerging as an important new drug target. However, its therapeutic potential is still underexploited. Indeed, the limited understanding of the interactions between small molecules and RNA still hampers rational drug development of RNA-targeting molecules. Among the different methods available to investigate binding between small molecules and RNA, NMR spectroscopy is particularly attractive as it can deliver information on molecular interactions at the atomic level, including conformational rearrangements that can occur before or upon binding. The dynamic nature of this interaction is particularly important in RNA-regulated pathways. Many NMR spectroscopy techniques have been developed to visualize dynamic RNA–ligand interactions, most of them based on the observation of either the target or ligand H nuclei. However, some difficulties can occur when studying larger strands of RNA, as the number of detectable signals will increase. Introducing a specific label is one way to overcome this problem. An elegant method based on F NMR spectroscopy was proposed some years ago by Micura and co-workers. Introduction of a fluorine atom at a specific position of RNA allows local monitoring of binding events at this site. One technical difficulty with this approach is the need to chemically modify the RNA, which can be difficult for large RNAs or for RNAs with modified nucleotides. Furthermore, this modification can affect RNA– ligand interactions. We have recently shown that F NMR spectroscopy can be used to monitor the binding of racemic fluorinated molecules to various RNAs and that chiral recognition can be used to monitor the local conformation of the binding site. The use of ligand-based binding-competition NMR screening using fluorinated ligands has been described by Dalvit for the investigation of protein–ligand interactions (FAXS technique), but has not been applied to the study small molecules interacting with RNA. We report herein that competitive binding of fluorinated probes can be used to detect and quantify the interaction between unlabeled RNA and non-fluorinated ligands and to monitor dynamic RNA folding events (Figure 1).

Fluorinated Diaminocyclopentanes as Chiral Sensitive NMR Probes of RNA Structure

The supramolecular chiral recognition between rac-2a and several structured RNA leads to a distinct (19)F NMR signal splitting. The (19)F NMR analysis of the diastereomeric pairs formed upon binding of this racemic probe delivers a topological footprint of the RNA. This phenomenon can be exploited to investigate dynamic events involving structural equilibria, as demonstrated in a melting experiment. This work provides a proof of concept that small fluorinated moderate binders can act as external probes of RNA structures.

Chemical compounds from Eperua falcata and Eperua grandiflora heartwood and their biological activities against wood destroying fungus (Coriolus versicolor)

AbstractThe chemical analysis of the compounds present in dichloromethane and ethanolic fractions as well as bioassays enable to understand the differences in the durability of Eperua falcata and Eperua grandiflora. The main distinction between these two species is the acidic subfraction of diterpenoid extract, which is antifungal in Eperua falcata when tested under in-vitro conditions. This study also shows that ethanolic fraction plays an important role in the mechanism of natural durability. Furthermore, it reports the first isolation of cativic acid in Eperua falcata wood. ZusammenfassungAnhand chemischer Analyse der in Dichlormethan- und Ethanolfraktionen vorhandenen Verbindungen sowie biologischer Prüfungen können die Unterschiede in der Dauerhaftigkeit von Eperua falcata und Eperua grandiflora aufgezeigt werden. Der Hauptunterschied zwischen den beiden Arten besteht in der sauren Fraktion des Diterpenoid-Extraktstoffes, der sich bei Prüfungen unter in-vitro Bedingungen bei Eperua falcata als pilzwidrig erwies. Anhand dieser Arbeit konnte auch gezeigt werden, dass die Ethanolfraktion eine wichtige Rolle bezüglich der natürlichen Dauerhaftigkeit spielt. Darüber hinaus wird über die erstmalige Isolierung von Cativinsäure aus Eperua falcata Holz berichtet.

Synthesis of Substituted 1,2,3,4-Tetrahydro-1-thiacarbazole and Spiro[pyrrolidinone-3,3′-indolinones] through a Common Intermediate Obtained by Condensation of Indolin-2-one, (Aryl)aldehydes, and Meldrum's Acid

Trimolecular adducts resulting from condensation between indolin-2-one (or indoline-2-thione), (aryl)aldehydes, and Meldrum’s acid are useful intermediates for the synthesis of either 1,2,3,4-tetrahydro-1-thiacarbazoles or spiro[pyrrolidino-3,3′-oxindoles] related to the natural product horsfiline. These latter compounds were obtained in a three-step procedure characterized by acyl azide formation, Curtius rearrangement, and subsequent thermal spiro cyclization. The relative stereochemistry of the spiro derivatives was determined by comparison of NOESY data and calculated conformational analyses. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

Solvent/Base Effects in the Selective Domino Synthesis of Phenanthridinones That Involves High‐Valent Palladium Species: Experimental and Theoretical Studies

The domino reaction of o-bromobenzamides 1a-m in the presence of K(2)CO(3) and the [PdCl(2)(PPh(3))(2)] catalyst granted a selective access to phenanthridinones 2 or to the new 1-carboxamide phenanthridinones 3 depending on the solvent, DMF or 1,4-dioxane, respectively. Investigations of the reaction parameters provided the first example of a direct correlation between the base dissociation and the solvent polarity on the selectivity observed. Moreover, mechanistic studies (NMR spectroscopy and ESI-MS monitoring) allowed us to characterize Pd(II) palladacycle 4 and biaryl species as common intermediates for these two domino processes. On that basis, C(sp(2))-C(sp(2)) bond formation is envisaged by generation of a Pd(IV) complex after oxidative addition of 1 into Pd(II) palladacycle 4, a rationale that is supported by DFT calculations. A general catalytic cycle is proposed to account for these observations.

Strychnohexamine from Strychnos icaja, a naturally occurring trimeric indolomonoterpenic alkaloid

Abstract A reinvestigation of Strychnos icaja roots has resulted in the isolation, from the EtOAC extract, of one tertiary trisindole alkaloid, named strychnohexamine. Its structure has been investigated by means of spectroscopic data interpretation (UV, IR, HRESIMS, 1D and 2D NMR). This is the first time that a natural trimeric indolomonoterpenic alkaloid has been isolated directly from a plant species. This compound is one of the largest alkaloids ever discovered.

Relative Stereochemical Determination and Synthesis of the C17–C25 δ-Lactone Fragment of Hemicalide

Hemicalide is a novel marine metabolite polyketide distinguished by a unique mechanism of action. Because of insufficient quantities of purified material, this natural product has evaded complete stereochemical assignments. Recently, we have determined the relative stereochemistry of the C8-C13 hexad by synthesizing the C1-C13 fragment. Presently, we report the assignment of the C17-C25 δ-lactone fragment. NMR analysis of authentic hemicalide along with a computational conformation study allowed us to reduce the number of putative relative isomers from 16 to 4. Concise syntheses of the four candidate diastereomers were achieved using a common strategy based on a Dias aldehyde allylation reaction, an intramolecular Horner-Wadsworth-Emmons olefination, and a dihydroxylation reaction. Finally, thorough NMR comparisons enabled us to deduce the relative stereochemistry of the C1-C17 fragment with high certainty.

Carbene‐Mediated Functionalization of the Anomeric CH Bond of Carbohydrates: Scope and Limitations

Herein we investigate the scope and limitations of a new synthetic approach towards α- and β-ketopyranosides relying on the functionalization of the anomeric C-H bond of carbohydrates by insertion of a metal carbene. A key bromoacetate grafted at the 2-position is the cornerstone of a stereoselective glycosylation/diazotransfer/quaternarization sequence that makes possible the construction of a quaternary center with complete control of the stereochemistry. This sequence shows a good tolerance toward protecting groups commonly used in carbohydrate chemistry and gives rise to quaternary disaccharides with good efficiency. In the case of a disaccharide with a more restricted conformation, this functionalization process can be hampered by the steric demand next to the targeted anomeric position. In addition, the formation of transient orthoesters during the glycosylation step may also reduce the overall efficiency of the synthetic sequence.

Synthetic Studies on Hemicalide: Development of a Convergent Approach toward the C1–C25 Fragment

Synthetic studies on hemicalide, a recently isolated marine natural product displaying highly potent antiproliferative activity and a unique mode of action, have highlighted a reliable Horner-Wadsworth-Emmons olefination to create the C6-C7 alkene and a remarkable efficient Suzuki-Miyaura coupling to form the C15-C16 bond, resulting in the development of a convergent approach toward the C1-C25 fragment.