Vibrational circular dichroism of adenosine crystals.

Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals.

Novel analogues of a nonnucleoside SARS-CoV-2 RdRp inhibitor as potential antivirotics.

The RNA-dependent RNA polymerase (RdRp) represents a prominent target in the discovery and development of new antivirotics against RNA viruses, inhibiting the replication process. One of the most targeted RNA viruses of the last years is, without doubt, SARS-CoV-2, the cause of the recent COVID-19 pandemic. HeE1-2Tyr, a known inhibitor of flaviviral RdRp, has been discovered to also have antiviral potency against this coronavirus. In this study, we report three distinct modifications of HeE1-2Tyr: conversion of the core from a benzothiazole to a benzoxazole moiety and two different scaffold simplifications, respectively. We provide a novel synthetic approach and, in addition, evaluate the final molecules in an in vitro polymerase assay for biological activity.

Photocatalytic Generation of Trifluoromethyl Nitrene for Alkene Aziridination.

N-Trifluoromethylated organics may be applied in drug design, agrochemical synthesis, and materials science, among other areas. Yet, despite recent advances in the synthesis of aliphatic, cyclic and heterocyclic N-trifluoromethyl compounds, no strategy based on trifluoromethyl nitrene has hitherto been explored. Here we describe the formation of triplet trifluoromethyl nitrene from azidotrifluoromethane, a stable and safe-to-use precursor, by visible light photocatalysis. The addition of CF3 N to alkenes via biradical intermediates afforded previously unknown aziridines substituted with trifluoromethyl group on the nitrogen atom. The obtained aziridines were converted into either N-trifluoromethylimidazolines, via formal [3+2] cycloaddition with nitriles, mediated by a Lewis acid, or into N-trifluoromethylaldimines, via ring opening and aryl group migration mediated by a strong Brønsted acid. Our findings open new opportunities for the development of novel classes of N-CF3 compounds with possible applications in the life sciences.

Synthesis and Cycloaddition Reactions of 1-Azido-1,1,2,2-tetrafluoroethane.

A new fluorinated azidoethane─1-azido-1,1,2,2-tetrafluoroethane─was prepared in quantitative yield by the addition of an azide anion to tetrafluoroethylene in a protic medium. The title azide was shown to be thermally stable and insensitive to impact. Copper(I)-catalyzed [3 + 2] cycloaddition with alkynes afforded 4-substituted N-tetrafluoroethyl-1,2,3-triazoles which underwent rhodium(II)-catalyzed transannulation with nitriles to novel N-tetrafluoroethylimidazoles or the reaction with triflic acid to enamido triflates. [3 + 2] Cycloaddition of the title azide with primary amines afforded novel 5-difluoromethyl tetrazoles.

Correction: Rhodium(II)-catalyzed transannulation approach to N-fluoroalkylated indoles.

Correction for 'Rhodium(II)-catalyzed transannulation approach to N-fluoroalkylated indoles' by Olga Bakhanovich et al., Org. Biomol. Chem., 2023, https://doi.org/10.1039/d3ob01415k.

Rhodium(II)-catalyzed transannulation approach to N-fluoroalkylated indoles.

Copper(I)-catalyzed cycloaddition of substituted cyclohexenyl acetylenes with azido(per)fluoroalkanes afforded 4-cyclohexenyl-substituted N-(per)fluoroalkylated 1,2,3-triazoles. Their rhodium(II)-catalyzed transannulation led to fused N-(per)fluoroalkyl pyrroles and subsequent oxidation provided N-(per)fluoroalkyl indoles.

N-Acyl-1,2,3-triazoles - key intermediates in denitrogenative transformations.

Elusive N-acyl-1,2,3-triazoles formed by direct acylation of NH-1,2,3-triazoles were isolated and fully characterized, including X-ray crystallography. A preference for the formation of thermodynamic N2 isomers was established. Direct evidence of interconversion between N1- and N2-acyltriazoles confirmed their value in denitrogenative transformations. Efficient synthesis of enamido triflates from NH-triazoles via the intermediacy of N2-acyl-1,2,3-triazoles was developed.

Synthesis of Azidodifluoromethyl Phenyl Sulfone and Its Use as a Synthetic Equivalent of the Azidodifluoromethyl Anion.

Azidodifluoromethyl phenyl sulfone, a new stable fluorinated azide, was synthesized on a multi-gram scale from difluoromethyl phenyl sulfone. The synthetic utility of the title azide in the preparation of N-difluoro(phenylsulfonyl)methyl-1,2,3-triazoles was demonstrated on examples of azide-alkyne cycloaddition reactions. Subsequent reductive desulfonylation/silylation afforded N-difluoro(trimethylsilyl)methyl-1,2,3-triazoles, and rhodium(II)-catalyzed transannulation with nitriles provided N-difluoro(phenylsulfonyl)methyl-substituted imidazoles. The title azide thus represents a synthetic equivalent of the azidodifluoromethyl anion.

Lewis-Acid-Mediated Intramolecular Cyclization of 4-Aryl-5-allyl-1,2,3-triazoles to Substituted Cyclopentene Derivatives.

4-Aryl-5-allyl-N-fluoroalkyl-1,2,3-triazoles available by a three-component reaction of fluoroalkyl azides, copper acetylides, and allyl halides underwent aluminum halide-mediated transformation to N-(4-halo-2-aryl-cyclopentenyl) imidoyl halides by cyclization of vinyl cation intermediates, followed by halide capture. Utilization of the cyclic products was demonstrated by the synthesis of N-alkenyl amides, amidines, isoquinolines, and tetrazoles or by the subsequent modification of the cyclopentene ring.

Synthesis of Polycyclic Hetero-Fused 7-Deazapurine Heterocycles and Nucleosides through C-H Dibenzothiophenation and Negishi Coupling.

A new approach for synthesizing polycyclic heterofused 7-deazapurine heterocycles and the corresponding nucleosides was developed based on C-H functionalization of diverse (hetero)aromatics with dibenzothiophene-S-oxide followed by the Negishi cross-cooupling with bis(4,6-dichloropyrimidin-5-yl)zinc. This cross-coupling afforded a series of (het)aryl-pyrimidines that were converted to fused deazapurine heterocycles through azidation and thermal cyclization. The fused heterocycles were glycosylated to the corresponding 2'-deoxy- and ribonucleosides, and a series of derivatives were prepared by nucleophilic substitutions at position 4. Four series of new polycyclic thieno-fused 7-deazapurine nucleosides were synthesized using this strategy. Most of the deoxyribonucleosides showed good cytotoxic activity, especially for the CCRF-CEM cell line. Phenyl- and thienyl-substituted thieno-fused 7-deazapurine nucleosides were fluorescent, and the former one was converted to 2'-deoxyribonucleoside triphosphate for enzymatic synthesis of labeled oligonucleotides.

Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase.

Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2'-deoxyribonucleosides and their corresponding 5'-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1-hydroxypropyl)pyrimidine nucleosides were separated and their absolute configuration was determined by a combination of X-ray and NMR analysis. The modified dNXTPs were used as substrates for PCR synthesis of modified DNA templates used for the study of transcription with bacterial RNA polymerase. Fundamental differences in transcription efficiency were observed, depending on the various modifications. The most notable effects included pronounced stimulation of transcription from 5-ethyluracil-bearing templates (200% transcription yield compared to natural thymine) and an enhancing effect of 5-acetylcytosine versus inhibiting effect of 5-acetyluracil. In summary, these results reveal that RNA polymerase copes with dramatically altered DNA structure and suggest that these nucleobases could potentially play roles as artificial epigenetic DNA nucleobases.

(E)-7-Ethylidene-lithocholic Acid (7-ELCA) Is a Potent Dual Farnesoid X Receptor (FXR) Antagonist and GPBAR1 Agonist Inhibiting FXR-Induced Gene Expression in Hepatocytes and Stimulating Glucagon-like Peptide-1 Secretion From Enteroendocrine Cells.

Bile acids (BAs) are key signaling steroidal molecules that regulate glucose, lipid, and energy homeostasis via interactions with the farnesoid X receptor (FXR) and G-protein bile acid receptor 1 (GPBAR1). Extensive medicinal chemistry modifications of the BA scaffold led to the discovery of potent selective or dual FXR and GPBAR1 agonists. Herein, we discovered 7-ethylidene-lithocholic acid (7-ELCA) as a novel combined FXR antagonist/GPBAR1 agonist (IC50 = 15 µM/EC50 = 26 nM) with no off-target activation in a library of 7-alkyl substituted derivatives of BAs. 7-ELCA significantly suppressed the effect of the FXR agonist obeticholic acid in BSEP and SHP regulation in human hepatocytes. Importantly, 7-ELCA significantly stimulated the production of glucagon-like peptide-1 (GLP-1), an incretin with insulinotropic effect in postprandial glucose utilization, in intestinal enteroendocrine cells. We can suggest that 7-ELCA may be a prospective approach to the treatment of type II diabetes as the dual modulation of GPBAR1 and FXR has been supposed to be effective in the synergistic regulation of glucose homeostasis in the intestine.

Stereoselective Synthesis of (Z)-ß-Enamido Fluorides from N-Fluoroalkyl- and N-Sulfonyl-1,2,3-triazoles.

A reaction of N-sulfonyl-1,2,3-triazole with boron trifluoride etherate afforded a (Z)-ß-ensulfonylamido fluoride instead of the previously erroneously assigned E isomer. The correction of the stereochemistry was based on a ge-1D ROESY NMR experiment and X-ray crystal structure analyses. Application of the reaction to N-fluoroalkyl-1,2,3-triazoles afforded new (Z)-ß-enamido fluorides in a stereoselective manner. A mechanism involving coordination of BF3 with the triazole ring and vinyl diazonium and vinyl cation intermediates was proposed.

Di(benzothienyl)cyclobutenes: Toward Strained Photoswitchable Fluorophores.

Bis(benzothienyl)ethene sulfones are very interesting molecules for super-resolution microscopy due to their photoswitching properties. However, functionalization of the 'classical' bis(benzothienyl)ethene sulfones with a five-membered central ring leads to significant decrease of quantum yields of photoconversion of the fluorescent closed form of the dye to the non-fluorescent open form that limits their application in microscopy. Here, we designed and synthesized diarylethenes with a fluorinated four-membered central ring that adds extra strain to the closed form of the dye. The reaction mechanism of their formation was studied, and byproducts formed upon structural rearrangement of the benzothiophene fragment were characterized. The photochromic properties of the new molecules were investigated by NMR and absorption spectroscopy. Some of these compounds show enhanced tendency to ring opening and have quantum yields of the ring-opening reaction in the range of 0.2-0.5.

Binuclear Lanthanide(III) Complexes with Chiral Ligands: Dynamic Equilibria in Solution and Binding with Nucleotides Studied by Spectroscopic Methods.

Binuclear lanthanide complexes of Eu(III) and Sm(III) were obtained in the presence of chiral ligand 1,2-(R,R+S,S)-N,N'-bis(2-pyridylmethylene),2-diamine. An unusual structure of the Eu(III) compound with two lanthanide atoms connected through two chlorines was determined by X-ray crystallography. In solution, the dimer coexists with a monomeric complex, and the stability of the binuclear form depends on the solvent and concentration. The dimer-monomer equilibrium was monitored by circularly polarized luminescence (CPL) measured on a Raman optical activity (ROA) spectrometer, where both forms provided large CPL anisotropic ratios of up to 5.6×10-2 . Monomer formation was favored in water, whereas the dimer was stabilized in methanol. When mixed with adenosine phosphates, AMP gave much smaller CPL than ADP and ATP, indicating a high affinity of the Eu (III) complex for the phosphate group, which in connection with the ROA/CPL technique can be developed into a bioanalytical probe.

Synthesis and Cytotoxic and Antiviral Activity Profiling of All-Four Isomeric Series of Pyrido-Fused 7-Deazapurine Ribonucleosides.

All four isomeric series of novel 4-substituted pyrido-fused 7-deazapurine ribonucleosides possessing the pyridine nitrogen atom at different positions were designed and synthesized. The total synthesis of each isomeric fused heterocycle through multistep heterocyclization was followed by glycosylation and derivatization at position 4 by cross-coupling reactions or nucleophilic substitutions. All compounds were tested for cytostatic and antiviral activity. The most active were pyrido[4',3':4,5]pyrimidine nucleosides bearing MeO, NH2 , MeS, or CH3 groups at position 4, which showed submicromolar cytotoxic effects and good selectivity for cancer cells. The mechanism involved activation by phosphorylation and incorporation to DNA where the presence of the modified ribonucleosides causes double-strand breaks and apoptosis.

Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects.

Direct fluorination of ortho-, meta- and para-substituted aromatic thiols and disulfides using elemental fluorine afforded substituted (pentafluorosulfanyl)benzenes. This work thus represents the first study of the scope and limitation of direct fluorination for the synthesis of new SF5 -containing building blocks. Fluorinations in batch and flow modes were compared. A comprehensive computational study was carried out employing density functional and wave function methods to elucidate the reaction mechanism of the transformation of ArSF3 into ArSF5 . Eliminating various nonradical pathways, it has been shown that the reaction proceeds by a radical mechanism, initiated by the attack of the F. on the ArSF3 moiety, propagated via an almost barrierless F2 +ArSF4 . →ArSF5 +F. step and terminated by the ArSF4 . +F. →ArSF5 . Most of the calculated data are in very good agreement with experimental observations concerning the ortho-substituent effect on the reaction rates and yields.

Vicarious Nucleophilic Chloromethylation of Nitroaromatics.

Nitroaromatics substituted with electron-acceptor or electron-donor groups undergo vicarious nucleophilic substitution with the lithium salt of dichloromethane to provide chloromethyl-substituted nitroaromatics in good to high yields. The methodology represents a new strategy for the synthesis of benzyl chlorides.

Stereoselective Synthesis of (Z)-ß-Enamido Triflates and Fluorosulfonates from N-Fluoroalkylated Triazoles.

N-Fluoroalkylated 1,2,3-triazoles in the presence of triflic acid or fluorosulfonic acid underwent a cascade reaction consisting of triazole protonation, ring opening, nitrogen elimination, sulfonate addition, HF elimination, and hydrolysis to furnish novel trifluoromethanesulfonyloxy- or fluorosulfonyloxy-substituted enamides, respectively, in a highly stereoselective fashion. The vinyl triflates underwent cross-coupling reactions to a variety of substituted enamides and serve as sources of the aminovinyl cations. In reactions with triflic acid, electron-rich triazoles afforded 2-fluoroalkylated oxazoles.

First total synthesis of ent-asperparaline C and assignment of the absolute configuration of asperparaline C.

The first asymmetric total synthesis of a member of the asperparaline family was accomplished and the unknown absolute configuration of asperparaline C has been determined to be all-(S). The key steps of the synthesis are an oxidative radical cyclization, a selective reduction of one of the tertiary amides, a singlet oxygen Diels-Alder reaction and a reductive spirocyclization.