Simultaneous 19F NMR Screening of Prolyl Oligopeptidase and Dipeptidyl Peptidase IV Inhibitors

Prolyl oligopeptidase (POP) and dipeptidyl peptidase IV (DPP IV) are serine proteases that belong to the same family of enzymes. These peptidases are relevant because of their association with the pathophysiology of serious illnesses, such as type 2 diabetes (DPP IV), and those related to cognitive disorders (POP). Several NMR‐based screening methods are being used to find and validate new hit scaffolds. In particular, ¹⁹F NMR‐based screening methods have proven to be powerful tools for the discovery and development of new inhibitors. Here we present an accurate and reliable ¹⁹F NMR‐based simultaneous assay that is used to screen for new selective POP and DPP IV inhibitors in compound mixtures. This activity assay consists of the simultaneous performance of POP and DPP‐IV ¹⁹F NMR activity assays in the presence of their fluorine‐containing substrates. Furthermore, the assays were conducted in the presence of 0.01 % v/v of Triton X‐100, which is a detergent that disrupts micelle formation, thereby preventing unspecific aggregate‐based inhibition. Finally, this ¹⁹F NMR methodology was applied to screen for ligands in plant extracts. Our results indicate that this method allows the simultaneous and accurate identification of selective POP and DPP IV inhibitors in these compound mixtures.     

Design and Generation of Highly Diverse Fluorinated Fragment Libraries and their Efficient Screening with Improved 19F NMR Methodology

Fragment screening performed with ¹⁹F NMR spectroscopy is becoming increasingly popular in drug discovery projects. With this approach, libraries of fluorinated fragments are first screened using the direct‐mode format of the assay. The choice of fluorinated motifs present in the library is fundamental in order to ensure a large coverage of chemical space and local environment of fluorine (LEF). Mono‐ and poly‐fluorinated fragments to be included in the libraries for screening are selected from both in‐house and commercial collections, and those that are ad hoc designed and synthesized. Additional fluorinated motifs to be included in the libraries derive from the fragmentation of compounds in development and launched on the market, and compounds contained in other databases (such as Integrity, PDB and ChEMBL). Complex mixtures of highly diverse fluorine motifs can be rapidly screened and deconvoluted in the same NMR tube with a novel on the fly combined procedure for the identification of the active molecule(s). Issues and problems encountered in the design, generation and screening of diverse fragment libraries of fluorinated compounds with ¹⁹F NMR spectroscopy are analyzed and technical solutions are provided to overcome them. The versatile screening methodology described here can be efficiently applied in laboratories with limited NMR setup and could potentially lead to the increasing role of ¹⁹F NMR in the hit identification and lead optimization phases of drug discovery projects.     

Development of Fragment‐Based n‐FABS NMR Screening Applied to the Membrane Enzyme FAAH

Despite the recognized importance of membrane proteins as pharmaceutical targets, the reliable identification of fragment hits that are able to bind these proteins is still a major challenge. Among different ¹⁹F NMR spectroscopic methods, n‐fluorine atoms for biochemical screening (n‐FABS) is a highly sensitive technique that has been used efficiently for fragment screening, but its application for membrane enzymes has not been reported yet. Herein, we present the first successful application of n‐FABS to the discovery of novel fragment hits, targeting the membrane‐bound enzyme fatty acid amide hydrolase (FAAH), using a library of fluorinated fragments generated based on the different local environment of fluorine concept. The use of the recombinant fusion protein MBP‐FAAH and the design of compound 11 as a suitable novel fluorinated substrate analogue allowed n‐FABS screening to be efficiently performed using a very small amount of enzyme. Notably, we have identified 19 novel fragment hits that inhibit FAAH with a median effective concentration (IC₅₀) in the low mM –μM range. To the best of our knowledge, these results represent the first application of a ¹⁹F NMR fragment‐based functional assay to a membrane protein.     

Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate

The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution ¹⁹F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.     

High-resolution F and H NMR of a vinylidenefluoride telomer

The reaction products of vinylidenefluoride (VDF) with methanol as a telogen have been analysed in the solution state by ¹H and ¹⁹F nuclear magnetic resonance (NMR) spectroscopy. High-resolution ¹⁹F and ¹H NMR spectra were achieved using high-power ¹H and ¹⁹F decoupling, respectively, giving superior resolution and revealing previously unresolved signals of the vinylidenefluoride telomer (VDFT). ¹H and ¹⁹F homo- and hetero-nuclear scalar coupling constants are presented and the spectra of functional groups and reverse units (including the identification of short-chain structures) are discussed. Furthermore, the application of ¹⁹F or ¹H decoupling for the correct assessment of reverse-unit content and degree of polymerisation is demonstrated. This work highlights the need for high-resolution NMR spectroscopy to determine both the chemical structure and the composition of these important fluoropolymers.     

19F NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens

We report here the nuclear magnetic resonance ¹⁹F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter-screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow-up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low-micromolar binding affinity without losing binding specificity between two different terminator structures.     

Insights into Protein Stability in Cell Lysate by 19F NMR Spectroscopy

In living organisms, protein folding and function take place in an inhomogeneous, highly crowded environment possessing a concentration of diverse macromolecules of up to 400 g/L. It has been shown that the intracellular environment has a pronounced effect on the stability, dynamics and function of the protein under study, and has for this reason to be considered. However, most protein studies neglect the presence of these macromolecules. Consequently, we probe here the overall thermodynamic stability of cold shock protein B from Bacillus subtilis (BsCspB) in cell lysate. We found that an increase in cell lysate concentration causes a monotonic increase in the thermodynamic stability of BsCspB. This result strongly underlines the importance of considering the biological environment when inherent protein parameters are quantitatively determined. Moreover, we demonstrate that targeted application of ¹⁹F NMR spectroscopy operates as an ideal tool for protein studies performed in complex cellular surroundings.     

Fluorine NMR‐Based Screening on Cell Membrane Extracts

The possibility of measuring the action of inhibitors of specific enzymatic reactions in intact cells, cell lysates or membrane preparations represents a major advance in the lead discovery process. Despite the relevance of assaying in physiological conditions, only a small number of biophysical techniques, often requiring complex set‐up, are applicable to these sample types. Here, we demonstrate the first application of n‐fluorine atoms for biochemical screening (n‐FABS), a homogeneous and versatile assay based on ¹⁹F NMR spectroscopy, to the detection of high‐ and low‐affinity inhibitors of a membrane enzyme in cell extracts and determination of their IC₅₀ values. Our approach can allow the discovery of novel binding fragments against targets known to be difficult to purify or where membrane‐association is required for activity. These results pave the way for future applications of the methodology to these relevant and complex biological systems.     

Monitoring Binding of HIV‐1 Capsid Assembly Inhibitors Using 19F Ligand‐and 15N Protein‐Based NMR and X‐ray Crystallography: Early Hit Validation of a Benzodiazepine Series

The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)‐1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identified via high‐throughput screening using an in vitro capsid assembly assay (CAA). Here, we demonstrate how a combination of NMR and X‐ray co‐crystallography allowed for the rapid characterization of the early hits from this inhibitor series. Ligand‐based ¹⁹F NMR was used to confirm inhibitor binding specificity and reversibility as well as to identify the N‐terminal domain of the capsid (CA_NTD) as its molecular target. Protein‐based NMR (¹H and ¹⁵N chemical shift perturbation analysis) identified key residues within the CA_NTD involved in inhibitor binding, while X‐ray co‐crystallography confirmed the inhibitor binding site and its binding mode. Based on these results, two conformationally restricted cyclic inhibitors were designed to further validate the possible binding modes. These studies were crucial to early hit confirmation and subsequent lead optimization.     

Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design

An empirical correlation between the fluorine isotropic chemical shifts, measured by ¹⁹F NMR spectroscopy, and the type of fluorine–protein interactions observed in crystal structures is presented. The CF, CF₂, and CF₃ groups present in fluorinated ligands found in the Protein Data Bank were classified according to their ¹⁹F NMR chemical shifts and their close intermolecular contacts with the protein atoms. Shielded fluorine atoms, i.e., those with increased electron density, are observed primarily in close contact to hydrogen bond donors within the protein structure, suggesting the possibility of intermolecular hydrogen bond formation. Deshielded fluorines are predominantly found in close contact with hydrophobic side chains and with the carbon of carbonyl groups of the protein backbone. Correlation between the ¹⁹F NMR chemical shift and hydrogen bond distance, both derived experimentally and computed through quantum chemical methods, is also presented. The proposed “rule of shielding” provides some insight into and guidelines for the judicious selection of appropriate fluorinated moieties to be inserted into a molecule for making the most favorable interactions with the receptor.     

19F NMR chemical shifts induced by a helical peptide

(19)F NMR spectra of two neutral, organic-soluble helical peptide octamers, each labeled at its N terminus with either 4-fluorobenzamide or 4-trifluoromethylbenzamide, in solvents with widely varying dielectric constants have been observed. The peptides are oligomers of alpha-aminoisobutyric acid (Aib), which is a residue known to form stable 3(10) helices in organic solution. In relation to the (19)F NMR spectra of a control molecule, the peptide terminating in 4-fluorobenzamide shows a solvent-dependent downfield chemical shift of between approximately 1.5 and approximately 4 ppm, whilst the peptide terminating in 4-trifluoromethylbenzamide shows only an approximately 0.2 ppm chemical shift dependence on the solvent dielectric constant. The experimental observations were compared to calculated values of the electric field generated by the correlation of dipolar amide units through the peptide's helical conformation. We find the chemical-shift response of the 4-fluorobenzamide group to the peptide's calculated electric field is consistent with the magnitude of (19)F chemical shift dispersion observed in proteins.     

Design and preparation of polyphenyl distance markers for solid-state 19F NMR

With ¹³C-labeled samples, it is possible to measure internuclear distances up to 7 Å by solid-state NMR, thus providing a powerful tool for probing ligand—receptor interactions. However, limitations in measurable distances and appreciable natural abundant ¹³C background signals present problems in solid-state ¹³C NMR. In order to overcome these disadvantages, a set of reference compounds with known F—F distances, namely, quinolinol, p-biphenyl, and p-terphenyl-bearing trifluoromethyl and trifluoromethylthio groups, have been synthesized. The preparation of these reference compounds and means for diluting these references in solid-state NMR are described.     

1H{19F} NOE NMR Structural Signatures of the Insulin R6 Hexamer: Evidence of a Capped HisB10 Site in Aryl‐ and Arylacryloyl‐carboxylate Complexes

New and improved insulin : ¹H{¹⁹F} NOE NMR difference spectra for CF₃‐substituted aromatic carboxylates bound at the HisB10 sites of the R₆ human insulin (HI) hexamer show strong NOEs between the CF₃ groups and the LeuB6, AsnB3, and PheB1 sidechains. The NOEs and structural modeling establish that these carboxylates form closed complexes with the HisB10 site capped by the PheB1 rings.

     

Perfluoro-tert-butyl Group-Derived Capmatinib: Synthesis,Biological Evaluation and Its Application in 19F Magnetic Resonance Imaging

Capmatinib is an FDA-approved drug to treat metastatic non-small cell lung cancer with MET-exon 14 skipping. Herein, the perfluoro-tert-butyl group, which possesses nine chemically identical fluorine atoms, was introduced on Capmatinib to afford a targeted ¹⁹F magnetic resonance imaging (MRI) probe, perfluoro-tert-butyl group-derived Capmatinib ( 9F-CAP ). The ¹⁹F MRI concentration limit was found to be 25 mM in FLASH sequence. Molecular docking simulation, surface plasmon resonance (SPR) (with a K_d of 40.7 μM), half-inhibitory concentration (with a IC₅₀ of 168 nM), Annexin V, and cytotoxicity assays jointly demonstrated that the 9F-CAP targeted cMET protein specifically. Therefore, the targeted imaging capability of 9F-CAP is of great significance for the preoperative diagnosis of specific cancers.     

A Morphological Study of Poly[Bis(Trifluoroethoxy)Phosphazene] Using Solid-State NMR: Introducing Domain Selective 1H and 19F Decoupled 13C MAS NMR

Using solid-state NMR methods the morphological behavior of poly[bis(trifluoroethoxy)phosphazene] was studied, employing four nuclei of interest – ¹H, ¹⁹F, ³¹P and ¹³C. Measurements on all four nuclei support that at ambient temperature the crystalline and amorphous phases coexist. Variable temperature studies showed that above T(1) = 90° only a single highly mobile phase exists, which is presumed to be the 2D mesophase. All four nuclei showed that when heat cycling the polymer, repeatedly above T(1), an increase in crystallinity occurs with each cycle. For the first time ¹³C MAS NMR spectra, using high power ¹⁹F and ¹H decoupling, were obtained, which exhibited the same behaviour domain. Filtered ¹³C{¹H,¹⁹F} MAS spectra containing signal from the crystalline domain using the discrimination induced by variable amplitude minipulses (DIVAM) sequence were measured. Heat treated and solvent cast material showed differences in these ¹³C spectra, that were consistent with a decrease in backbone conformations upon heating, suggesting an increase in the extended chain form corresponding to the γ form. Analogous sensitivity to variations in crystal phase composition has not been seen previously using ¹H, ¹⁹F and ³¹P methods, emphasizing the importance of ¹³C MAS methods to morphological studies of phosphazenes. This paper is dedicated to Professor Harry R. Allcock     

19F MRI Nanotheranostics for Cancer Management: Progress and Prospects

Fluorine magnetic resonance imaging (¹⁹F MRI) is a promising imaging technique for cancer diagnosis because of its excellent soft tissue resolution and deep tissue penetration, as well as the inherent high natural abundance, almost no endogenous interference, quantitative analysis, and wide chemical shift range of the ¹⁹F nucleus. In recent years, scientists have synthesized various ¹⁹F MRI contrast agents. By further integrating a wide variety of nanomaterials and cutting-edge construction strategies, magnetically equivalent ¹⁹F atoms are super-loaded and maintain satisfactory relaxation efficiency to obtain high-intensity ¹⁹F MRI signals. In this review, the nuclear magnetic resonance principle underlying ¹⁹F MRI is first described. Then, the construction and performance of various fluorinated contrast agents are summarized. Finally, challenges and future prospects regarding the clinical translation of ¹⁹F MRI nanoprobes are considered. This review will provide strategic guidance and panoramic expectations for designing new cancer theranostic regimens and realizing their clinical translation.     

Structure and dynamics of a vinylidene fluoride oligomer and its cyclodextrin inclusion compounds as studied by solid-state F MAS and H → F CP/MAS NMR spectroscopy

The molecular structure and dynamics of a vinylidene fluoride oligomer telomerized by carbon tetrachloride (Cl-OVDF) and its inclusion compound (IC) with β-cyclodextrin (β-CD) have been investigated using solid-state ¹⁹F magic angle spinning (MAS) and ¹H → ¹⁹F cross-polarization (CP)/MAS NMR spectroscopy. The preferential IC formation of the lower-molecular-weight components with β-CD was used to refine as-received Cl-OVDF. The refined Cl-OVDF with larger molecular weight readily takes γ-form (tttg⁺tttg⁻) conformation, and it also forms ICs with β-CD (Cl-OVDF/β-CD IC) under a certain condition. ¹⁹F MAS NMR indicates that Cl-OVDF chains virtually isolated in the β-CD cavities take no specific conformations even at −40 °C. The temperature dependence of the magnetic relaxation times (T₁^F, T_1ρ^F) indicates that the Cl-OVDF chains in ICs undergo molecular motions similar to the amorphous phase in the bulk, although the intramolecular spin diffusion among ¹⁹F nuclei is more significant in the former because of the one-dimensional confinement.     

Solid-state F MAS and H→F CP/MAS NMR study of the phase transition behavior of vinylidene fluoride-trifluoroethylene copolymers: 1. Uniaxially drawn films of VDF 75% copolymer

The changes in the phase structures and molecular mobility caused by the ferroelectric-paraelectric phase transition of vinylidene fluoride (VDF) and trifluoroethylene (TrFE) copolymer, P(VDF₇₅/TrFE₂₅), were analyzed using variable temperature (VT) solid-state ¹⁹F MAS and ¹H→¹⁹F CP/MAS NMR spectroscopy. The CF₂ signal of the VDF chain sequence and the CHF signal at the head-to-head linkage of VDF-TrFE sequence showed higher frequency shift in the temperature range 43-92 °C, whereas no change was found for the CHF signal at the head-to-tail linkage of VDF-TrFE up to 92 °C. Hence, VT ¹⁹F MAS spectra revealed that the VDF-TrFE head-to-tail sequence is the most stable part in polymer chains against trans-gauche conformational exchange motions below the phase transition temperature (Curie temperature, T_c) on heating. However, all chain sequences including TrFE units undergo conformational exchange at around T_c. The phase transition behavior is clearly recognized in the ¹⁹F spectral shapes, in which the broad signals of the ferroelectric immobile phase disappeared between 115 and 119 °C. In addition, T_1ρ^F for all peaks decreased to a unique value (ca. 20 ms) at 119 °C, indicating that uniform molecular motion accompanied by a full chain rotation occurred at the temperature. The significantly longer T_1ρ^F for all peaks (ca. 20 ms) in the paraelectric phase (119 °C) than that in the amorphous domain (<4 ms) at ambient temperature supports the conclusion that there is restricted rotational motion of polymer chains around the chain axis in the paraelectric phase. On cooling from 119 to 85 °C, a gradual decrease in gauche conformers in the paraelectric phase was confirmed by the low-frequency displacement of CF₂ signals in VDF sequences accompanied by slight decreases in T₁^F and T_1ρ^F. The phase transition was observed between 85 and 77 °C on cooling, in which the characteristic signals of the paraelectric phase disappeared, the T_1ρ^F values of all peaks quickly increased, and the broad crystalline signals abruptly appeared at 77 °C.