Palladium-Catalyzed Carbonylative Four-Component Synthesis of β-Perfluoroalkyl Amides

Transition-metal-catalyzed multicomponent carbonylation is one of the most efficient strategies to construct carbonyl-containing compounds. Herein, a palladium-catalyzed four-component perfluoroalkylation/aminocarbonylation of unactivated alkenes with perfluoroalkyl halides, and amines was developed. A wide range of substrates, including anilines, alkylamines, sulfonamides, and hydrazines are all suitable reaction partners for this catalyst system, resulting in various β-perfluoroalkyl amides with good functional-group tolerance and excellent chemoselectivity. Furthermore, not only alkyl olefins, but also aliphatic alkynes, and even alkyl allenes can all be employed. Notably, several medical and bioactive related molecules are compatible here as well.

Efficient Synthesis of Trifluoromethylated Purine Ribonucleosides and Ribonucleotides

The protocols presented in this article describe highly detailed synthesis of trifluoromethylated purine nucleotides and nucleosides (G and A). The procedure involves trifluoromethylation of properly protected (acetylated) nucleosides, followed by deprotection leading to key CF₃ -containing nucleosides. This gives synthetic access to 8-CF₃ -substituted guanosine derivatives and three adenosine derivatives (8-CF₃ , 2-CF₃ , and 2,8-diCF₃ ). In further steps, phosphorylation and phosphate elongation (for selected examples) result in respective trifluoromethylated nucleoside mono-, di-, and triphosphates. Support protocols are included for compound handling, purification procedures, analytical sample preparation, and analytical techniques used throughout the performance of the basic protocols. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of trifluoromethylated guanosine and adenosine derivatives Basic Protocol 2: Synthesis of trifluoromethylated guanosine and adenosine monophosphates Basic Protocol 3: Synthesis of phosphorimidazolides of ^8-CF3 GMP and ^8-CF3 AMP Basic Protocol 4: Synthesis of trifluoromethylated guanosine and adenosine oligophosphates Support Protocol 1: TLC sample preparation and analysis Support Protocol 2: Purification protocol for Basic Protocol 1 Support Protocol 3: HPLC analysis and preparative HPLC Support Protocol 4: Ion-exchange chromatography.

Automated Glycan Assembly of 19 F-labeled Glycan Probes Enables High-Throughput NMR Studies of Protein-Glycan Interactions

Protein-glycan interactions mediate important biological processes, including pathogen host invasion and cellular communication. Herein, we showcase an expedite approach that integrates automated glycan assembly (AGA) of 19 F-labeled probes and high-throughput NMR methods, enabling the study of protein-glycan interactions. Synthetic Lewis type 2 antigens were screened against seven glycan binding proteins (GBPs), including DC-SIGN and BambL, respectively involved in HIV-1 and lung infections in immunocompromised patients, confirming the preference for fucosylated glycans (Lex , H type 2, Ley ). Previously unknown glycan-lectin weak interactions were detected, and thermodynamic data were obtained. Enzymatic reactions were monitored in real-time, delivering kinetic parameters. These results demonstrate the utility of AGA combined with 19 F NMR for the discovery and characterization of glycan-protein interactions, opening up new perspectives for 19 F-labeled complex glycans.

Synthesis and application of a 19F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs

Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (FPdC) that displays an unprecedented quantum yield and highly sensitive 19F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19F NMR spectroscopic DNA analysis. FPdC and FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19F chemical shift in response to i-motif formation. The utility of FPdC was exemplified through reversible fluorescence switching of an FPdC-containing i-motif oligonucleotide in the presence of Ag(i) and cysteine.

A Bisboronic Acid Sensor for Ultra-High Selective Glucose Assay by 19F NMR Spectroscopy

Glucose is a significant analyte both in biology and biomedical science, it is of great importance to selectively detect glucose both in body fluids and complex mixture. In this study, a simple ¹⁹F NMR based sensor was synthesized easily, which exhibited a high selectivity and robust anti-interference ability toward glucose detection both in a mixture containing up to 10 saccharides and human urine samples without any pretreatment. Combined with this sensor system, glucose could be well detected in human urine samples and the limit of detection was 0.41 mM by using a 400 MHz NMR spectrometer with 128 scans (ca. 4 min). This method had a potential for specific detection of glucose in complex mixture and diagnosis of diabetes mellitus related diseases in body fluid.

From medium to endoplasmic reticulum: Tracing anticancer phenolato titanium(IV) complex by 19F NMR detection

Titanium(IV) complexes of diaminobis(phenolato)-bis(alkoxo) ligands are promising anticancer drugs, showing marked in-vivo efficacy with no toxic side-effects in mice, hence, it is of interest to elucidate their mechanism of action. Herein, we employed a fluoro-substituted derivative, FenolaTi, for mechanistic analysis of the active species and its cellular target by quantitative ¹⁹F NMR detection to reveal its biodistribution and reactivity in extracellular and intracellular matrices. Upon administration to the serum-containing medium, FenolaTi interacted with bovine serum albumin. 20 h post administration, the cellular accumulation of FenolaTi derivatives was estimated as 37% of the administered compound, in a concentration three orders-of-magnitude higher than the administered dose, implying that active membrane transportation facilitates cellular penetration. An additional 19% of the administered dose that was detected in the extracellular environment had originated from post-apoptotic cells. In the cell, interaction with cellular proteins was detected. Although some intact Ti(IV) complex localized in the nucleus, no signals for isolated DNA fractions were detected and no reactivity with nuclear proteins was observed. Interestingly, higher accumulation of FenolaTi-derived compounds in the endoplasmic reticulum (ER) and interaction with proteins therein were detected, supporting the role of the ER as a possible target for cytotoxic bis(phenolato)-bis(alkoxo) Ti(IV) complexes.

Molecular Boronic Acid-Based Saccharide Sensors

Boronic acids can reversibly bind diols, a molecular feature that is ubiquitous within saccharides, leading to their use in the design and implementation of sensors for numerous saccharide species. There is a growing understanding of the importance of saccharides in many biological processes and systems; while saccharide or carbohydrate sensing in medicine is most often associated with detection of glucose in diabetes patients, saccharides have proven to be relevant in a range of disease states. Herein the relevance of carbohydrate sensing for biomedical applications is explored, and this review seeks to outline how the complexity of saccharides presents a challenge for the development of selective sensors and describes efforts that have been made to understand the underpinning fluorescence and binding mechanisms of these systems, before outlining examples of how researchers have used this knowledge to develop ever more selective receptors.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

Suzuki–Miyaura Coupling Reactions of Fluorohalobenzenes

Organofluorine compounds have gained interest in the fields of pharmaceuticals, agrochemicals, diagnostics, materials, and catalysis. Suzuki–Miyaura coupling reactions of fluorinated arenes made a tremendous impact in chemical and biological research and made organofluorinated molecules more readily available. This review gives a brief summary of Suzuki–Miyaura coupling reactions of fluorinated benzene derivatives. In this context, various aspects, such as regio­selectivity, efficiency, and applications, are discussed.

1 Introduction

2 Organofluorine Compounds

3 Suzuki–Miyaura Reactions of Fluorohalobenzenes

3.1 Fluorophthalates

3.2 Reactions of Pentafluorohalobenzenes

3.3 Tetrafluorohalobenzenes

3.4 Trifluorohalobenzenes

3.5 Difluorohalobenzenes

3.6 Monofluorohalobenzenes

3.7 Halo(trifluoromethyl)benzenes

3.8 Trifluoromethyl Pyridines

4 S Summary

Amyloid binding and beyond: a new approach for Alzheimer's disease drug discovery targeting Aβo-PrPC binding and downstream pathways

Amyloid β oligomers (Aβo) are the main toxic species in Alzheimer's disease, which have been targeted for single drug treatment with very little success. In this work we report a new approach for identifying functional Aβo binding compounds. A tailored library of 971 fluorine containing compounds was selected by a computational method, developed to generate molecular diversity. These compounds were screened for Aβo binding by a combined 19F and STD NMR technique. Six hits were evaluated in three parallel biochemical and functional assays. Two compounds disrupted Aβo binding to its receptor PrPC in HEK293 cells. They reduced the pFyn levels triggered by Aβo treatment in neuroprogenitor cells derived from human induced pluripotent stem cells (hiPSC). Inhibitory effects on pTau production in cortical neurons derived from hiPSC were also observed. These drug-like compounds connect three of the pillars in Alzheimer's disease pathology, i.e. prion, Aβ and Tau, affecting three different pathways through specific binding to Aβo and are, indeed, promising candidates for further development.

Perfluoro-tert-butanol: a cornerstone for high performance fluorine-19 magnetic resonance imaging

As a versatile quantification and tracking technology, 19F magnetic resonance imaging (19F MRI) provides quantitative "hot-spot" images without ionizing radiation, tissue depth limit, and background interference. However, the lack of suitable imaging agents severely hampers its clinical application. First, because the 19F signals are solely originated from imaging agents, the relatively low sensitivity of MRI technology requires high local 19F concentrations to generate images, which are often beyond the reach of many 19F MRI agents. Second, the peculiar physicochemical properties of many fluorinated compounds usually lead to low 19F signal intensity, tedious formulation, severe organ retention, etc. Therefore, the development of 19F MRI agents with high sensitivity and with suitable physicochemical and biological properties is of great importance. To this end, perfluoro-tert-butanol (PFTB), containing nine equivalent 19F and a modifiable hydroxyl group, has outperformed most perfluorocarbons as a valuable building block for high performance 19F MRI agents. Herein, we summarize the development and application of PFTB-based 19F MRI agents and analyze the strategies to improve their sensitivity and physicochemical and biological properties. In the context of PFC-based 19F MRI agents, we also discuss the challenges and prospects of PFTB-based 19F MRI agents.

Perfluorocarbons in Chemical Biology

Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.

Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex

G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.

Self-organization Properties of a GPCR-Binding Peptide with a Fluorinated Tail Studied by Fluorine NMR Spectroscopy

Conjugation of the bioactive apelin-17 peptide with a fluorocarbon chain results in self-organization of the peptide into micelles. Fluorine NMR spectroscopy studies show that the fluoropeptide's micelles are monodisperse, while proton NMR indicates that the peptide moiety remains largely disordered despite micellization. A very fast exchange rate is measured between the free and micellar states of the peptide which enables the number of molecules present in the micelle to be estimated as 200, in agreement with values found by dynamic light scattering measurements.

Fluorine NMR functional screening: from purified enzymes to human intact living cells

The substrate- or cofactor-based fluorine NMR screening, also known as n-FABS (n fluorine atoms for biochemical screening), represents a powerful method for performing a direct functional assay in the search of inhibitors or enhancers of an enzymatic reaction. Although it suffers from the intrinsic low sensitivity compared to other biophysical techniques usually applied in functional assays, it has some distinctive features that makes it appealing for tackling complex chemical and biological systems. Its strengths are represented by the easy set-up, robustness, flexibility, lack of signal interference and rich information content resulting in the identification of bona fide inhibitors and reliable determination of their inhibitory strength. The versatility of the n-FABS allows its application to either purified enzymes, cell lysates or intact living cells. The principles, along with theoretical, technical and practical aspects, of the methodology are discussed. Furthermore, several applications of the technique to pharmaceutical projects are presented.

Synthesis of complex unnatural fluorine-containing amino acids

The area of fluorinated amino acid synthesis has seen rapid growth over the past decade. As reports of singly fluorinated natural amino acid derivatives have grown, researchers have turned their attention to develop methodology to access complex proteinogenic examples. A variety of reaction conditions have been employed in this area, exploiting new advances in the wider synthetic community such as photocatalysis and palladium cross-coupling. In addition, novel fluorinated functional groups have also been incorporated into amino acids, with SFX and perfluoro moieties now appearing with more frequency in the literature. This review focuses on synthetic methodology for accessing complex non-proteinogenic amino acids, along with amino acids containing multiple fluorine atoms such as CF3, SF5 and perfluoroaromatic groups.

Selective Nuclear Magnetic Resonance Experiments for Sign-Sensitive Determination of Heteronuclear Couplings: Expanding the Analysis of Crude Reaction Mixtures

State-of-the-art nuclear magnetic resonance (NMR) selective experiments are capable of directly analyzing crude reaction mixtures. A new experiment named HD-HAPPY-FESTA yields ultrahigh-resolution total correlation subspectra, which are suitable for sign-sensitive determination of heteronuclear couplings, as demonstrated here by measuring the sign and magnitude for proton-fluorine couplings (J_HF) from major and minor isomer products of a two-step reaction without any purification. Proton-fluorine couplings ranging from 51.5 to -2.6 Hz could be measured using HD-HAPPY-FESTA, with the smallest measured magnitude of 0.8 Hz. Experimental J_HF values were used to identify the two fluoroketone intermediates and the four fluoroalcohol products. Results were rationalized and compared with the density functional theory (DFT) calculations. Experimental data were further compared with the couplings reported in the literature, where pure samples were analyzed.

Versatile Nickel(II) Scaffolds as Coordination-Induced Spin-State Switches for 19 F Magnetic Resonance-Based Detection

¹⁹ F magnetic resonance (MR) based detection coupled with well-designed inorganic systems shows promise in biological investigations. Two proof-of-concept inorganic probes that exploit a novel mechanism for ¹⁹ F MR sensing based on converting from low-spin (S=0) to high-spin (S=1) Ni²⁺ are reported. Activation of diamagnetic NiL₁ and NiL₂ by light or β-galactosidase, respectively, converts them into paramagnetic NiL₀ , which displays a single ¹⁹ F NMR peak shifted by >35 ppm with accelerated relaxation rates. This spin-state switch is effective for sensing light or enzyme expression in live cells using ¹⁹ F MR spectroscopy and imaging that differentiate signals based on chemical shift and relaxation times. This general inorganic scaffold has potential for developing agents that can sense analytes ranging from ions to enzymes, opening up diverse possibilities for ¹⁹ F MR based biosensing.

Oligonucleotides DNA containing 8-trifluoromethyl-2'-deoxyguanosine for observing Z-DNA structure

Z-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (^FG). 2D NMR strongly suggested that ^FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by¹⁹F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.

Pauson-Khand reaction of fluorinated compounds

The Pauson-Khand reaction (PKR) is one of the key methods for the construction of cyclopentenone derivatives, which can in turn undergo diverse chemical transformations to yield more complex biologically active molecules. Despite the increasing availability of fluorinated building blocks and methodologies to incorporate fluorine in compounds with biological interest, there have been few significant advances focused on the fluoro-Pauson-Khand reaction, both in the inter- and intramolecular versions. Furthermore, the use of vinyl fluorides as olefinic counterparts had been completely overlooked. In this review, we collect the advances both on the stoichiometric and catalytic intermolecular and intramolecular fluoro-Pauson-Khand reaction, with special attention to the PKR of enynes containing a fluoride moiety.

Telomeric DNA-RNA-hybrid G-quadruplex exists in environmental conditions of HeLa cells

In the present study, we employed a ¹⁹F NMR approach to study the association of telomere RNA and DNA in vitro and in living human cells. We successfully characterized the DNA-RNA hybrid G-quadruplex (HQ) structure formed by telomeric DNA and RNA. We further demonstrated for the first time that an HQ conformation can exist in the environmental conditions of HeLa cells.

Kitamura Electrophilic Fluorination Using HF as a Source of Fluorine

This review article focused on the innovative procedure for electrophilic fluorination using HF and in situ generation of the required electrophilic species derived from hypervalent iodine compounds. The areas of synthetic application of this approach include fluorination of 1,3-dicarbonyl compounds, aryl-alkyl ketones, styrene derivatives, α,β-unsaturated ketones and alcohols, homoallyl amine and homoallyl alcohol derivatives, 3-butenoic acids and alkynes.

Perfluoro-tert-Butyl Hydroxyprolines as Sensitive, Conformationally Responsive Molecular Probes: Detection of Protein Kinase Activity by 19F NMR

¹⁹F NMR spectroscopy provides the ability to quantitatively analyze single species in complex solutions but is often limited by the modest sensitivity inherent to NMR. 4R- and 4S-Perfluoro-tert-buyl hydroxyproline contain 9 equivalent fluorines, in amino acids with strong conformational preferences. In order to test the ability to use these amino acids as sensitive probes of protein modifications, the perfluoro-tert-buyl hydroxyprolines were incorporated into substrate peptides of the protein kinases PKA and Akt. Peptides containing each diastereomeric proline were rapidly phosphorylated by each protein kinase and exhibited ¹⁹F chemical shift changes as a result of phosphorylation. The sensitivity of the perfluoro-tert-butyl group allowed quantitative analysis of the kinetics of phosphorylation over three half-lives at single-digit micromolar concentrations of each species. The distinct conformational preferences of these amino acids allowed the optimization of the substrate with a conformationally matched amino acid, in order to maximize the rate of phosphorylation. PKA preferred the 4R-amino acid at the -1 position, whereas the closely related AGC kinase Akt preferred the 4S-amino acid. These data, combined with analysis of structures of the Michaelis complexes of these kinases in the PDB, suggest that PKA recognizes the PPII conformation at the P-1 position relative to the phosphorylation site, while Akt/PKB recognizes an extended conformation at this position. These results suggest that conformational targeting may be employed to increase specificity in recognition by protein kinases. Perfluoro-tert-butyl hydroxyprolines were applied to the real-time detection and quantification of PKA activity and inhibition of PKA activity in HeLa cell extracts via ¹⁹F NMR spectroscopy. The coupling of proline ring pucker with main chain conformation suggests broad application of perfluoro-tert-butyl hydroxyprolines in molecular sensing and imaging.

Halogen-directed chemical sialylation: pseudo-stereodivergent access to marine ganglioside epitopes

Sialic acids are conspicuous structural components of the complex gangliosides that regulate cellular processes. Their importance in molecular recognition manifests itself in drug design (e.g. Tamiflu®) and continues to stimulate the development of effective chemical sialylation strategies to complement chemoenzymatic technologies. Stereodivergent approaches that enable the α- or β-anomer to be generated at will are particularly powerful to attenuate hydrogen bond networks and interrogate function. Herein, we demonstrate that site-selective halogenation (F and Br) at C3 of the N-glycolyl units common to marine Neu2,6Glu epitopes enables pseudo-stereodivergent sialylation. α-Selective sialylation results from fluorination, whereas traceless bromine-guided sialylation generates the β-adduct. This concept is validated in the synthesis of HLG-1 and Hp-s1 analogues.

Sialic acids are conspicuous structural components of the complex gangliosides that regulate cellular processes.

8-Fluoro-N-2-isobutyryl-2′-deoxyguanosine: Synthesis and Reactivity

3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2′-deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2′-deoxyguanosine and C8:5′-O-cyclo-2′-deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis.

Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-β-lactamase 1

19F NMR protein observed spectroscopy is evaluated as a method for analysing protein metal binding using the New Delhi metallo-β-lactamase 1. The results imply 19F NMR is useful for analysis of different metallated protein states and investigations on equilibrium states in the presence of inhibitors. One limitation is that 19F labelling may affect metal ion binding. The sensitive readout of changes in protein behaviour observed by 19F NMR spectra coupled with the broad scope of tolerated conditions (e.g. buffer variations) means 19F NMR should be further investigated for studying metal ion interactions and the inhibition of metallo-enzymes during drug discovery.

Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes

Protected guanosine and adenosine ribonucleosides and guanine nucleotides are readily functionalized with CF₃ substituents within the nucleobase. Protected guanosine is trifluoromethylated at the C8 position under radical-generating conditions in up to 95% yield and guanosine 5'-oligophosphates in up to 35% yield. In the case of adenosine, the selectivity of trifluoromethylation depends heavily on the functional group protection strategy and leads to a set of CF₃-modified nucleosides with different substitution patterns (C8, C2, or both) in up to 37% yield. Further transformations based on phosphorimidazolide chemistry afford various CF₃-substituted mono- and dinucleoside oligophosphates in good yields. The utility of the trifluoromethylated nucleotides as probes for ¹⁹F NMR-based real-time enzymatic reaction monitoring is demonstrated with three different human nucleotide hydrolases (Fhit, DcpS, and cNIIIB). Substrate and product(s) resonances were sufficiently separated to enable effective tracking of each enzymatic activity of interest.

NMR spectral analysis of strongly second-order 6-, 8-, 9- and 10- spin-systems (1 H─19 F, 19 F─19 F, and 13 C─19 F) in perfluorotoluyl- and tetrafluoro-pyridyl-aromatics using the lineshape method ANATOLIA

A simple to use nuclear magnetic resonance analysis method has been tested on complex ¹ H, ¹⁹ F, and ¹³ C multiplets. This open-source line-shape analysis method analysis of total lineshape (ANATOLIA)¹ provides some significant advantages over traditional assign-iterate methods of NMR spectral analysis by avoiding false minima and progressing optimisation to the global minimum. The target molecules are 1-perfluorotol-4-yl-2-perfluorotol-4-yl-oxymethyl-1H-benzimidazole (molecule-I) and 1-tetrafluoropyrid-4-yl-2-tetrafluoropyrid-4-yl-thio-1H-benzimidazole (molecule-II) which were produced as part of a family of fluorinated drug scaffolds prepared for anticancer and antiparasitic screening. Spectra display significant second-order effects with ¹ H Δδ = 3.68 and 4.67 Hz for the aromatic hydrogen "triplets", with ¹⁹ F ⁴ J_AA' , ⁴ J_BB' , ⁴ J_XX' , and ⁴ J_YY' coupling constants range from +4.8 to -14.0 Hz and for ¹³ C-isotopomers ¹⁹ F Δδ of up to 111.56 Hz. A spin-system of six coupling nuclei (H_a H_b H_c H_d F_Y F_Y' ) was analysed in 12 s, a spin-system of nine coupling fluorine nuclei (AA'BB'CCC-YY') was analysed within 2 min, and 10 coupling nuclei (XX'YY'ZZZ-BB'-H_d ) was optimised in 6 min using a laptop computer. ANATOLIA was also robust enough to be able to yield accurate spectral values from inaccurate input values. In both compounds, a fluorine-fluorine coupling constant was identified between the two fluoro-aromatic rings (F_BB' and F_YY' ) of +4.05 and +4.67 Hz and attributed to a through-space interaction. Ab initio structure optimisations and coupling constant calculations provided useful input data for spectral analysis. A modern ¹⁹ F nuclear magnetic resonance spectrum of perfluorotoluene (octafluorotoluene) and analysis from 1975 was used as a test data set to assess ANATOLIA.

Monofluoroalkene-Isostere as a 19 F NMR Label for the Peptide Backbone: Synthesis and Evaluation in Membrane-Bound PGLa and (KIGAKI)3

Solid-state ¹⁹ F NMR is a powerful method to study the interactions of biologically active peptides with membranes. So far, in labelled peptides, the ¹⁹ F-reporter group has always been installed on the side chain of an amino acid. Given the fact that monofluoroalkenes are non-hydrolyzable peptide bond mimics, we have synthesized a monofluoroalkene-based dipeptide isostere, Val-Ψ[(Z)-CF=CH]-Gly, and inserted it in the sequence of two well-studied antimicrobial peptides: PGLa and (KIGAKI)₃ are representatives of an α-helix and a β-sheet. The conformations and biological activities of these labeled peptides were studied to assess the suitability of monofluoroalkenes for ¹⁹ F NMR structure analysis.

19F Magnetic Resonance Activity-Based Sensing Using Paramagnetic Metals

Fluorine magnetic resonance imaging (¹⁹F MRI) is a promising bioimaging technique due to the favorable magnetic resonance properties of the ¹⁹F nucleus and the lack of detectable biological background signal. A range of imaging agents have been developed for this imaging modality including small molecule perfluorocarbons, fluorine-rich macromolecules and nanoparticles, and paramagnetic metal-containing agents. Incorporation of paramagnetic metals into fluorinated agents provides a unique opportunity to manipulate relaxation and chemical shift properties of ¹⁹F nuclei. Paramagnetic centers will enhance relaxation rates of nearby ¹⁹F nuclei through paramagnetic relaxation enhancement (PRE). Further, metals with anisotropic unpaired electrons can induce changes in ¹⁹F chemical shift through pseudocontact shift (PCS) effects. PRE and PCS are dependent on the nature of the metal center itself, the molecular scaffold surrounding it, and the position of the ¹⁹F nucleus relative to the metal center. One intriguing prospect in ¹⁹F magnetic resonance molecular imaging is to design responsive agents that can serve to provide a read out biological activity, including the activity of enzymes, redox activity, the activity of ions, etc. Paramagnetic agents are well suited for this activity-based sensing as metal complexes can be designed to respond to specific biological activities and give a corresponding ¹⁹F response that results from changes in the metal complex structure and subsequently PRE/PCS. Broadly speaking, when designing paramagnetic ¹⁹F MR biosensors, one can envision that in response to changes in analyte activity, the number of unpaired electrons of the metal changes or the ligand conformation/chemical composition changes. This Account highlights activity-based probes from the Que lab that harness paramagnetic metals to modulate ¹⁹F signal. We discuss probes that use conversion from Cu²⁺ to Cu⁺ in response to reducing environments to dequench the ¹⁹F MR signal. Probes in which oxidants convert Co²⁺ to Co³⁺, resulting in chemical shift responses, are also described. Finally, we explore our foray into using Ni²⁺ coordination switching to furnish probes with different ¹⁹F signals when they are converted between 4-coordinate square planar and higher coordination numbers. A major barrier for ¹⁹F MR molecular imaging is in vivo application, as signal sensitivity is relatively low, requiring long imaging times to detect imaging agents. Nanoparticle and macromolecular agents show promise due to their higher fluorine density and longer circulation times; however, their analyte scope is limited to analytes that induce cleavage events. A grand challenge for researchers in this area is adapting lessons learned from small molecule paramagnetic probes with promising in vitro activities for the development of probes with enhanced in vivo utility for basic biological and clinical applications.

Synthesis, Characterization, and Dynamic Behavior of Well-defined Dithiomaleimide-functionalized Maltodextrins

:

Maltodextrins have an increasing number of biomedical and industrial applications due to their attractive physicochemical properties such as biodegradability and biocompatibility. Herein, we describe the development of a synthetic pathway and characterization of thiol-responsive maltodextrin conjugates with dithiomaleimide linkages. 19F NMR studies were also conducted to demonstrate the exchange dynamics of the dithiomaleimide-functionalized sugar end groups.

Site-Specific Isotopic Labeling (SSIL): Access to High-Resolution Structural and Dynamic Information in Low-Complexity Proteins

Remarkable technical progress in the area of structural biology has paved the way to study previously inaccessible targets. For example, large protein complexes can now be easily investigated by cryo-electron microscopy, and modern high-field NMR magnets have challenged the limits of high-resolution characterization of proteins in solution. However, the structural and dynamic characteristics of certain proteins with important functions still cannot be probed by conventional methods. These proteins in question contain low-complexity regions (LCRs), compositionally biased sequences where only a limited number of amino acids is repeated multiple times, which hamper their characterization. This Concept article describes a site-specific isotopic labeling (SSIL) strategy, which combines nonsense suppression and cell-free protein synthesis to overcome these limitations. An overview on how poly-glutamine tracts were made amenable to high-resolution structural studies is used to illustrate the usefulness of SSIL. Furthermore, we discuss the potential of this methodology to give further insights into the roles of LCRs in human pathologies and liquid-liquid phase separation, as well as the challenges that must be addressed in the future for the popularization of SSIL.

Divergent synthesis of 5',7'-difluorinated dihydroxanthene-hemicyanine fused near-infrared fluorophores

We describe an expedient access to a 5',6',7'-trifluoro dihydroxanthene-hemicyanine fused scaffold in 2 steps and 54% overall yield from the corresponding salicylic aldehyde. A 6'-regioselective nucleophilic aromatic substitution (SNAr) reaction with a wide range of nitrogen, sulfur or selenium nucleophiles then gives access to 16 near-infrared (NIR) fluorophores emitting in the 710-750 nm range. We also report the experimental and theoretical photophysical investigations of these unique optical agents that include the first series of 6'-heavy atom substituted dihydroxanthenes, extending the pool of polyfluorinated markers for biomedical and material applications.

Improving the accuracy of 1 H-19 F internuclear distance measurement using 2D 1 H-19 F HOESY

With the rise in fluorinated pharmaceuticals, it is becoming increasingly important to develop new ¹⁹ F NMR-based methods to assist in their analysis. Crucially, obtaining information regarding the conformational dynamics of a molecule in solution can aid the design of strongly binding therapeutics. Herein, we report the development of a 2D ¹ H-¹⁹ F Heteronuclear Overhauser Spectroscopy (HOESY) experiment to measure ¹ H-¹⁹ F internuclear distances, with accuracies of ~5% when compared with ¹ H-¹⁹ F internuclear distances calculated by quantum chemical methods. We demonstrate that correcting for cross-relaxation of ¹ H, using the diagonal peaks from the 2D ¹ H-¹ H Nuclear Overhauser Enhancement Spectroscopy (NOESY), is critical in obtaining accurate values for ¹ H-¹⁹ F internuclear distances. Finally, we show that by using the proposed method to measure ¹ H-¹⁹ F internuclear distances, we are able to determine the relative stereochemistry of two fluorinated pharmaceuticals.

5-Fluoro-2'-deoxycytidine as a Probe for the Study of B/Z-DNA Transition by 19F NMR Spectroscopy

5-Fluoro-2'-deoxycytidine was synthesized by treating 5-fluoro-2'-deoxyuridine with 2,4,6-trimethylphenol in the presence of 1-methylpyrrolidine and trifluoroacetic anhydride, followed by aminolysis. Among N-acetyl, pivaloyl, and benzoyl, N-acetyl was found to be suitable for the protection of the exocyclic amine of 5-fluoro-2'-deoxycytidine because of the stability of the N ⁴-protected nucleoside under acidic conditions and its ease of removal after solid-phase synthesis. This modified nucleoside was incorporated into d(CG)₆ sequences through the phosphoramidite chemistry-based solid-phase synthesis. Circular dichroism experiments suggest that replacement of 2'-deoxycytidine with 5-fluoro-2'-deoxycytidine does not lead to detectable conformational changes, either in the B- or Z-form. ¹⁹F NMR spectroscopy of d(CG)₆ containing 5-fluoro-2'-deoxycytidine revealed that B/Z-DNA transition induced by sodium chloride is likely initiated at terminal ends, leading to unwinding at the middle of duplexes, and eventual switch of handedness when sodium chloride concentration reaches a threshold value.

Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells

Although the telomeric sequence has been reported to form various G-quadruplex topologies in vitro and in Xenopus laevis oocytes, in living human cells, the topology of telomeric DNA G-quadruplex remains a challenge. To investigate the human telomeric DNA G-quadruplex in a more realistic human cell environment, in the present study, we demonstrated that the telomeric DNA sequence can form two hybrid-type and two-tetrad antiparallel G-quadruplex structures by in-cell 19F NMR in living human cells (HELA CELLS). This result provides valuable information for understanding the structures of human telomeric DNA in living human cells and for the design of new drugs that target telomeric DNA.

Approaches to Obtaining Fluorinated α-Amino Acids

Fluorine does not belong to the pool of chemical elements that nature uses to build organic matter. However, chemists have exploited the unique properties of fluorine and produced countless fluoro-organic compounds without which our everyday lives would be unimaginable. The incorporation of fluorine into amino acids established a completely new class of amino acids and their properties, and those of the biopolymers constructed from them are extremely interesting. Increasing interest in this class of amino acids caused the demand for robust and stereoselective synthetic protocols that enable straightforward access to these building blocks. Herein, we present a comprehensive account of the literature in this field going back to 1995. We place special emphasis on a particular fluorination strategy. The four main sections describe fluorinated versions of alkyl, cyclic, aromatic amino acids, and also nickel-complexes to access them. We progress by one carbon unit increments. Special cases of amino acids for which there is no natural counterpart are described at the end of each section. Synthetic access to each of the amino acids is summarized in form of a table at the end of this article with the aim to make the information easily accessible to the reader.