Parahydrogen‐Induced Polarization Transfer to 19F in Perfluorocarbons for 19F NMR Spectroscopy and MRI

Fluorinated substances are important in chemistry, industry, and the life sciences. In a new approach, parahydrogen‐induced polarization (PHIP) is applied to enhance ¹⁹F MR signals of (perfluoro‐n‐hexyl)ethene and (perfluoro‐n‐hexyl)ethane. Unexpectedly, the end‐standing CF₃ group exhibits the highest amount of polarization despite the negligible coupling to the added protons. To clarify this non‐intuitive distribution of polarization, signal enhancements in deuterated chloroform and acetone were compared and ¹⁹F–¹⁹F NOESY spectra, as well as ¹⁹F T₁ values were measured by NMR spectroscopy. By using the well separated and enhanced signal of the CF₃ group, first ¹⁹F MR images of hyperpolarized linear semifluorinated alkenes were recorded.     

Design,Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State 19F NMR Spectroscopy

A conformationally restricted monofluorinated α‐amino acid, (3‐fluorobicyclo[1.1.1]pentyl)glycine (F‐Bpg), was designed as a label for the structural analysis of membrane‐bound peptides by solid‐state ¹⁹F NMR spectroscopy. The compound was synthesized and validated as a ¹⁹F label for replacing natural aliphatic α‐amino acids. Calculations suggested that F‐Bpg is similar to Leu/Ile in terms of size and lipophilicity. The ¹⁹F NMR label was incorporated into the membrane‐active antimicrobial peptide PGLa and provided information on the structure of the peptide in a lipid bilayer.     

19F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells

Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein–protein interactions affect mobility, but examining viscosity and weak interaction effects is challenging. Herein, we demonstrate the use of ¹⁹F NMR spectroscopy to measure cytoplasmic viscosity and to characterize nonspecific protein–protein interactions in living Escherichia coli cells. The origins of resonance broadening in Escherichia coli cells were also investigated. We found that sample inhomogeneity has a negligible effect on resonance broadening, the cytoplasmic viscosity is only about 2–3 times that of water, and ubiquitous transient weak protein–protein interactions in the cytosol play a significant role in governing the detection of proteins by using in‐cell NMR spectroscopy.     

Direct Observation of Ca2+‐Induced Calmodulin Conformational Transitions in Intact Xenopus laevis Oocytes by 19F NMR Spectroscopy

The Ca²⁺‐mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by ¹⁹F NMR spectroscopy of the transition of the Ca²⁺‐free and ‐bound forms in Xenopus laevis oocytes at different Ca²⁺ levels. We find that the Ca²⁺‐bound CaM population increased greatly upon binding the target protein myosin light‐chain kinase (MLCK) at the same Ca²⁺ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long‐range structural constraints in cells. Our study shows that ¹⁹F NMR spectroscopy can be used to obtain long‐range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants.     

The 3F Library: Fluorinated Fsp3‐Rich Fragments for Expeditious 19F NMR Based Screening

Fragment‐based drug discovery (FBDD) is a popular method in academia and the pharmaceutical industry for the discovery of early lead candidates. Despite its wide‐spread use, the approach still suffers from laborious screening workflows and a limited diversity in the fragments applied. Presented here is the design, synthesis, and biological evaluation of the first fragment library specifically tailored to tackle both these challenges. The 3F library of 115 fluorinated, Fsp³‐rich fragments is shape diverse and natural‐product‐like with desirable physicochemical properties. The library is perfectly suited for rapid and efficient screening by NMR spectroscopy in a two‐stage workflow of ¹⁹F NMR and subsequent ¹H NMR methods. Hits against four diverse protein targets are widely distributed among the fragment scaffolds in the 3F library and a 67 % validation rate was achieved using secondary assays. This collection is the first synthetic fragment library tailor‐made for ¹⁹F NMR screening and the results demonstrate that the approach should find broad application in the FBDD community.     

Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan–Cyanovirin Interactions by Using 19F NMR Spectroscopy

NMR spectroscopy and isothermal titration calorimetry (ITC) are powerful methods to investigate ligand–protein interactions. Here, we present a versatile and sensitive fluorine NMR spectroscopic approach that exploits the ¹⁹F nucleus of ¹⁹F‐labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin‐N, a mannose binding anti‐HIV lectin. Two fluoro‐deoxy sugar derivatives, methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside and methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside were utilized. Binding was studied by ¹⁹F NMR spectroscopy of the ligand and ¹H–¹⁵N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that the strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding, as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin.     

Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside–RNA recognition, glucose‐nucleobase pairs have been examined. Deoxyoligonucleotides with a 6‐deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6‐Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6‐deoxyglucose‐guanine pair closely resembles a purine‐pyrimidine geometry. Quantum chemical calculations indicate that glucose‐purine pairs are as stable as a natural T‐A pair.     

Chemical‐Shift‐Resolved 19F NMR Spectroscopy between 13.5 and 135 MHz: Overhauser–DNP‐Enhanced Diagonal Suppressed Correlation Spectroscopy

Overhauser–DNP‐enhanced homonuclear 2D ¹⁹F correlation spectroscopy with diagonal suppression is presented for small molecules in the solution state at moderate fields. Multi‐frequency, multi‐radical studies demonstrate that these relatively low‐field experiments may be operated with sensitivity rivalling that of standard 200–1000 MHz NMR spectroscopy. Structural information is accessible without a sensitivity penalty, and diagonal suppressed 2D NMR correlations emerge despite the general lack of multiplet resolution in the 1D ODNP spectra. This powerful general approach avoids the rather stiff excitation, detection, and other special requirements of high‐field ¹⁹F NMR spectroscopy.     

Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband 19F NMR‐Based Screening

Fragment‐based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease‐relevant targets. Among the numerous screening techniques, fluorine‐detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high‐quality and diverse library containing nearly 4000 fragments and screening for target‐specific binders within days. At the core of the approach is a novel broadband relaxation‐edited NMR experiment that covers the entire chemical shift range of drug‐like ¹⁹F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.     

Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations

The antitumor drug cisplatin (cis‐[PtCl₂(NH₃)₂]) reacts with cellular DNA to form GG intrastrand adducts between adjacent guanines as predominant lesions. GGG sites have been shown to be hotspots of platination. To study the structural perturbation induced by binding of cisplatin to two adjacent guanines of a GGG trinucleotide, we examined here the decanucleotide duplex d[(G₁C₂C₃ G₆T₇‐ C₈G₉C₁₀) ? d(G₁₁C₁₂G₁₃A₁₄C₁₅C₁₆C₁₇G₁₈‐ G₁₉C₂₀)] ( dsCG*G*G ) intrastrand cross‐linked at the G* guanines by cis‐{Pt(NH₃)₂}²⁺ using NMR spectroscopy and molecular dynamics (MD) simulations. The NMR spectra of dsCG*G*G were found to be similar to those of previously characterized DNA duplexes cross‐linked by cisplatin at a pyG*G*X site (py=pyrimidine; X=C, T, A). This similarity of NMR spectra indicates that the base at the 3′‐side of the G*G*–Pt cross‐link does not affect the structure to a large extent. An unprecedented reversible isomerization between the duplex dsCG*G*G (bearing a –Pt chelate) and duplex dsGG*G*T (bearing a –Pt chelate) was observed, which yielded a 40:60 equilibrium between the two intrastrand GG–Pt cross‐links. No formation of interstrand cross‐links was observed. NMR spectroscopic data of dsCG*G*G indicated that the deoxyribose of the 5′‐G* adopts an N‐type conformation, and the cytidines C₃, C₁₅, and C₁₆ have average phase angles intermediate between S and N. The NMR spectroscopic chemical shifts of dsGG*G*T showed some fundamental differences to those of pyG*G*–platinum adducts but were in agreement with the NMR spectra reported previously for the DNA duplexes cross‐linked at an AG*G*C sequence by cisplatin or oxaliplatin. The presence of a purine instead of a pyrimidine at the 5′‐side of the G*G* cross‐link seems therefore to affect the structure of the XG* step significantly.     

Molecular Recognition of Rosmarinic Acid from Salvia sclareoides Extracts by Acetylcholinesterase: A New Binding Site Detected by NMR Spectroscopy

Acetylcholinesterase (AChE) inhibition is one of the most currently available therapies for the management of Alzheimer’s disease (AD) symptoms. In this context, NMR spectroscopy binding studies were accomplished to explain the inhibition of AChE activity by Salvia sclareoides extracts. HPLC‐MS analyses of the acetone, butanol and water extracts eluted with methanol and acidified water showed that rosmarinic acid is present in all the studied samples and is a major constituent of butanol and water extracts. Moreover, luteolin 4′‐O‐glucoside, luteolin 3′,7‐di‐O‐glucoside and luteolin 7‐O‐(6′′‐O‐acetylglucoside) were identified by MS² and MS³ data acquired during the LC‐MSⁿ runs. Quantification of rosmarinic acid by HPLC with diode‐array detection (DAD) showed that the butanol extract is the richest one in this component (134 μg mg^?1 extract). Saturation transfer difference (STD) NMR spectroscopy binding experiments of S. sclareoides crude extracts in the presence of AChE in buffer solution determined rosmarinic acid as the only explicit binder for AChE. Furthermore, the binding epitope and the AChE‐bound conformation of rosmarinic acid were further elucidated by STD and transferred NOE effect (trNOESY) experiments. As a control, NMR spectroscopy binding experiments were also carried out with pure rosmarinic acid, thus confirming the specific interaction and inhibition of this compound against AChE. The binding site of AChE for rosmarinic acid was also investigated by STD‐based competition binding experiments using Donepezil, a drug currently used to treat AD, as a reference. These competition experiments demonstrated that rosmarinic acid does not compete with Donepezil for the same binding site. A 3D model of the molecular complex has been proposed. Therefore, the combination of the NMR spectroscopy based data with molecular modelling has permitted us to detect a new binding site in AChE, which could be used for future drug development.