Use of 19F NMR spectroscopy to screen chemical libraries for ligands that bind to proteins

Identification of compounds from chemical libraries that bind to macromolecules by use of NMR spectroscopy has gained increasing importance during recent years. A simple methodology based on (19)F NMR spectroscopy for the screening of ligands that bind to proteins, which also provides qualitative information about relative binding strengths and the presence of multiple binding sites, is presented here. A library of fluorinated compounds was assembled and investigated for binding to the two bacterial chaperones PapD and FimC, and also to human serum albumin (HSA). It was found that library members which are bound to a target protein could be identified directly from line broadening and/or induced chemical shifts in a single, one-dimensional (19)F NMR spectrum. The results obtained for binding to PapD using (19)F NMR spectroscopy agreed well with independent studies based on surface plasmon resonance, providing support for the versatility and accuracy of the technique. When the library was titrated to a solution of PapD chemical shift and linewidth changes were observed with increasing ligand concentration, which indicated the presence of several binding sites on PapD and enabled the assessment of relative binding strengths for the different ligands. Screening by (19)F NMR spectroscopy should thus be a valuable addition to existing NMR techniques for evaluation of chemical libraries in bioorganic and medicinal chemistry.     

Application of the 19F NMR technique to observe binding of the general anesthetic halothane to human serum albumin.

19F NMR techniques were employed to characterize the binding property of the widely used general anesthetic halothane with human serum albumin (HSA). It was found that 19F(1H) NOE and 2D 1H-19F HOESY experiments detected intermolecular NOEs between halothane 19F and HSA protons. Measurements of the diffusion coefficients for halothane were also carried out by 1H and 19F NMR, indicating the interaction of halothane with HSA. The present results indicate that these techniques are very suitable to identify a fluorine-containing ligand binding with a protein receptor in the drug-discovery process.     

Polymer-supported tetrafluorophenol: a new activated resin for chemical library synthesis

A new tetrafluorophenol activated resin that facilitates the use of 19F NMR to quantitate loading is presented. This new resin provides a useful tool for acylation, and a novel activated polymeric sulfonate ester to generate sulfonamides. This activated resin reacts with a wide scope of N-nucleophiles including primary and secondary amines, and anilines. This new activated resin methodology provides a powerful tool for pure single-compound library synthesis.     

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.     

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.     

一种新的离子液体负载的双(三氟乙酰氧基)碘苯试剂的合成

以氯乙酰氯和对碘苯胺为原料,经酰化合成了4-碘-氯乙酰苯胺,接着与1-甲基咪唑反应得到氯化1-甲基-3-(4-碘苯氨基甲酰甲基)咪唑钅翁,随后在水溶液中发生阴离子交换,合成了1-甲基-3-(4-碘苯氨基甲酰甲基)咪唑四氟硼酸盐;四氟硼酸盐在过氧化氢/三氟乙酸酐体系中氧化得到一种新的离子液体负载的双(三氟乙酰氧基)碘苯试剂1-甲基-3-[4-双(三氟乙酰氧基)碘苯氨基甲酰甲基]咪唑四氟硼酸盐。反应总收率62.3%。试剂没有吸湿性,在空气中长期放置不变质。化学结构用IR、1H NMR、13C NMR、19F NMR和元素分析表征。     

Design and parallel solid-phase synthesis of ring-fused 2-pyridinones that target pilus biogenesis in pathogenic bacteria

A new method for the solid-phase synthesis of enantiomerically enriched highly substituted ring-fused 2-pyridinones 13 has been developed. The synthesis mediates introduction of substituents at two positions in the 2-pyridinone ring in a diverse manner and is suitable for parallel synthesis. (19)F NMR spectroscopy was used as a tool to monitor each of the five steps in the reaction sequence. The optimized conditions thus obtained were then used to prepare a library of 20 2-pyridinones with high yields. The library members were chosen from a statistical multivariate design to ensure diversity and reliable data for structure-activity relationships. Screening of the library against the bacterial periplasmic chaperone PapD was performed using surface plasmon resonance. Three new 2-pyridinones with a higher affinity for the chaperone PapD than the previous best 13[10,1] were found, and important structural features could be deduced.     

Solid-state NMR (19F and 13C) study of graphite monofluoride (CF)n: 19F spin-lattice magnetic relaxation and 19F/13C distance determination by Hartmann-Hahn cross polarization

Graphite monofluoride (CF)(n) was studied by solid-state NMR. (19)F spin-lattice relaxation time T(1) and second moment measurements of the (19)F line are presented. A "chair" conformation structure is found to be compatible with the experimental data. Relaxation is shown to be mainly due to paramagnetic oxygen. The presence of a molecular motion with an activation energy of 1.685 kJ.mol(-1) (202.7 K) is also evidenced. (19)F magic angle spinning (MAS) NMR and (13)C MAS NMR with (19)F to (13)C cross-polarization allows the determination of CF and CF(2) groups. Reintroduction of dipolar coupling by cross-polarization is used for C-F bond length determination (0.138 +/- 0.001 nm).     

Synthesis and spectroscopic analysis of a stereoisomer library of the phytophthora mating hormone α1 and derived bis-Mosher esters

Fluorous mixture synthesis provided all eight diastereomers of the phytophthora hormone α1 with the R configuration at C11 as individual samples after demixing and detagging. The library of all possible bis-Mosher esters (16) was then made by esterification. Complete sets of (1)H, (13)C, and (for the Mosher esters) (19)F NMR spectra were recorded, assigned, and compared with each other and with published spectra. Not all of the spectra are unique, and the (1)H NMR spectra of the Mosher esters provided the most information. The previous assignment of the natural sample as an "all-R" stereoisomer mixed with its 3S-epimer was confirmed.     

High-resolution (19)F MAS NMR spectroscopy: structural disorder and unusual J couplings in a fluorinated hydroxy-silicate

High-resolution (19)F magic angle spinning (MAS) NMR spectroscopy is used to study disorder and bonding in a crystalline solid. (19)F MAS NMR reveals four distinct F sites in a 50% fluorine-substituted deuterated hydrous magnesium silicate (clinohumite, 4Mg(2)SiO(4)·Mg(OD(1-x)F(x))(2) with x = 0.5), indicating extensive structural disorder. The four (19)F peaks can be assigned using density functional theory (DFT) calculations of NMR parameters for a number of structural models with a range of possible local F environments generated by F(-)/OH(-) substitution. These assignments are supported by two-dimensional (19)F double-quantum MAS NMR experiments that correlate F sites based on either spatial proximity (via dipolar couplings) or through-bond connectivity (via scalar, or J, couplings). The observation of (19)F-(19)F J couplings is unexpected as the fluorines coordinate Mg atoms and the Mg-F interaction is normally considered to be ionic in character (i.e., there is no formal F-Mg-F covalent bonding arrangement). However, DFT calculations predict significant (19)F-(19)F J couplings, and these are in good agreement with the splittings observed in a (19)F J-resolved MAS NMR experiment. The existence of these J couplings is discussed in relation to both the nature of bonding in the solid state and the occurrence of so-called "through-space" (19)F-(19)F J couplings in solution. Finally, we note that we have found similar structural disorder and spin-spin interactions in both synthetic and naturally occurring clinohumite samples.     

Application of fluorine NMR for structure identification of steroids

Fluorinated steroids were examined using 1D and 2D homo- and heteronuclear (19)F NMR, such as (19)F-(1) H and (19)F-(13)C. The utilization of fluorine NMR accounted for spectral simplification and resulted in a straightforward pathway for the determination of structures including the configuration of these compounds; these steroids present an illustrative example for other types of fluorinated compounds, which are increasingly encountered in drug discovery. The potential of (19)F NMR is elaborated on in detail for two compounds containing diastereotopic fluorines with different coupling patterns. The analysis of the coupling patterns and the through-space interactions resulted in the determination of the structure and configuration. Heteronuclear correlation experiments, i.e. (19)F-(1)H HETCOR, (19)F-(13)C HMQC and HMBC, and (19)F-(1)H HOESY, were applied to determine first the relative stereochemistry and then the molecular configuration at C4 and C5 of a steroidal compound bearing a fused three-membered ring with two fluorine substituents. These examples proved (19)F NMR to be a useful addition to the extensively used (1)H and (13)C NMR within structure elucidation and configuration determination of small molecules.     

Fluorine-NMR competition binding experiments for high-throughput screening of large compound mixtures

High-throughput ligand-based NMR screening with competition binding experiments is extended to (19)F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the (19)F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the (19)F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented.     

Synthesis and characterization of Cu(II) paddlewheel complexes possessing fluorinated carboxylate ligands

The goal of this study was to establish the relationship between the ¹⁹F NMR line broadening and the varying distance between the ¹⁹F nucleus and copper(II) ion, with the aim of gathering data that can be used to interpret ¹⁹F NMR spectra of subsequent fluorine-labeled, copper-binding proteins. Fluorinated alkyl and aryl copper(II) carboxylates were synthesized from fluorinated carboxylic acids and Cu(OH)₂. The copper(II) carboxylates were characterized using ¹⁹F NMR, IR, and single crystal X-ray diffraction. In the alkyl carboxylate compounds, the line broadening and chemical shift lessened with increased distance between the fluorine atom and the copper ions; however, in the aryl carboxylate derivatives, increased distance was not a factor in the amount of line broadening or change in chemical shift between the acid and metal salt. The compound, bis(3-(trifluoromethyl)butyrate) copper(II) (5) was found to possess the optimum combination of decreased line broadening and increased chemical shift sensitivity in ¹⁹F NMR. The crystal structures obtained for compounds 1, 2, 4, and 6 were analogous to previous copper(II) carboxylate complexes, though it is noted that compound 6, bis(5,5,5-trifluoropentanoate) copper(II) assumes a tetrameric structure lacking apical ligands, and thus enables the formation of an extended network of near-neighbor copper(II) ions.     

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.     

19F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis

Ligand‐based ¹⁹F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the ¹⁹F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the ¹⁹F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the ¹⁹F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment‐based screening. Copyright © 2016 John Wiley & Sons, Ltd.     

19F‐NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo‐β‐Lactamase

Resistance to β‐lactam antibiotics mediated by metallo‐β‐lactamases (MBLs) is a growing problem. We describe the use of protein‐observe ¹⁹F‐NMR (PrOF NMR) to study the dynamics of the São Paulo MBL (SPM‐1) from β‐lactam‐resistant Pseudomonas aeruginosa . Cysteinyl variants on the α3 and L3 regions, which flank the di‐Zn^II active site, were selectively ¹⁹F‐labeled using 3‐bromo‐1,1,1‐trifluoroacetone. The PrOF NMR results reveal roles for the mobile α3 and L3 regions in the binding of both inhibitors and hydrolyzed β‐lactam products to SPM‐1. These results have implications for the mechanisms and inhibition of MBLs by β‐lactams and non‐β‐lactams and illustrate the utility of PrOF NMR for efficiently analyzing metal chelation, identifying new binding modes, and studying protein binding from a mixture of equilibrating isomers.     

Systematic study of protein detection mechanism of self-assembling 19F NMR/MRI nanoprobes toward rational design and improved sensitivity

(19)F NMR/MRI probe is expected to be a powerful tool for selective sensing of biologically active agents owing to its high sensitivity and no background signals in live bodies. We have recently reported a unique supramolecular strategy for specific protein detection using a protein ligand-tethered self-assembling (19)F probe. This method is based on a recognition-driven disassembly of the nanoprobes, which induced a clear turn-on signal of (19)F NMR/MRI. In the present study, we conducted a systematic investigation of the relationship between structure and properties of the probe to elucidate the mechanism of this turn-on (19)F NMR sensing in detail. Newly synthesized (19)F probes showed three distinct behaviors in response to the target protein: off/on, always-on, and always-off modes. We clearly demonstrated that these differences in protein response could be explained by differences in the stability of the probe aggregates and that "moderate stability" of the aggregates produced an ideal turn-on response in protein detection. We also successfully controlled the aggregate stability by changing the hydrophobicity/hydrophilicity balance of the probes. The detailed understanding of the detection mechanism allowed us to rationally design a turn-on (19)F NMR probe with improved sensitivity, giving a higher image intensity for the target protein in (19)F MRI.     

19F single-quantum and 19F-33S heteronuclear multiple-quantum coherence NMR of SF6 in thermotropic nematogens and in the gas phase

(19)F single-quantum (SQC) and (19)F-(33)S heteronuclear multiple-quantum coherence (HMQC) NMR spectroscopy of sulfur hexafluoride (SF(6)) dissolved in thermotropic liquid crystals (TLCs) were used to investigate the properties of TLCs. On one hand, environmental effects on the NMR parameters of SF(6), (19)F nuclear shielding, (19)F-(33)S spin-spin coupling, secondary isotope effects of sulfur on (19)F shielding, and the self-diffusion coefficient in the direction of the external magnetic field were studied as well. The temperature dependence of the (19)F shielding of SF(6) in TLCs was modeled with a function that takes into account the properties of both TLC and SF(6). It appears that the TLC environment deforms the electronic system of SF(6) so that the (19)F shielding tensor becomes slightly anisotropic, with the anisotropy being from -0.5 to -1.4 ppm, depending upon the TLC solvent. On the contrary, no sign of residual dipolar coupling between (19)F and (33)S was found, meaning that the so-called deformational effects, which arise from the interaction between vibrational and reorientational motions of the molecule, on the geometry of the molecule are insignificant. Diffusion activation energies, E(a), were determined from the temperature dependence of the self-diffusion coefficients. In each TLC, E(a) increases when moving from an isotropic phase to a nematic phase. The spin-spin coupling constant, J((19)F,(33)S), increases by ca. 10 Hz when moving from the gas phase to TLC solutions. The secondary isotope shifts of (19)F shielding are practically independent of TLC solvent and temperature. For the first time, (19)F-(33)S heteronuclear multiple-quantum NMR spectra were recorded for SF(6) in the gas phase and in a liquid-crystalline solution.     

Selection of enantioselective acyl transfer catalysts from a pooled peptide library through a fluorescence-based activity assay: an approach to kinetic resolution of secondary alcohols of broad structural scope.

An assay employing a fluorescently labeled split and pool peptide library has been applied to the discovery of a new class of octapeptide catalysts for the kinetic resolution of secondary alcohols. A highly diverse library of peptide-based catalysts was synthesized on solid-phase synthesis beads such that each individual bead was co-functionalized with (i) a uniform loading of a pH-sensitive fluorophore and (ii) a unique peptide-based catalyst. The library was then screened for activity in acylation reactions employing (+/-)-sec-phenylethanol as the substrate and acetic anhydride as the acylation agent. From the most active catalysts, a lead peptide (4) was identified that provides a selectivity-factor (k(rel)) of 8.2 upon resynthesis and evaluation under homogeneous conditions. A "directed" second-generation split and pool peptide library was synthesized such that the new peptide sequences in the library were biased toward the lead structure. Random samples of the second generation library were screened in single bead assays that revealed several new peptide-based catalysts that afford improved selectivities in kinetic resolutions. Peptide catalyst 13 proves effective for the kinetic resolution of sec-phenylethanol (k(rel) = 20), as well as eight other secondary alcohols of a broad substrate scope (k(rel) = 4 to >50).     

Gel-phase 19F NMR spectral quality for resins commonly used in solid-phase organic synthesis; a study of peptide solid-phase glycosylations

The spectroscopic properties for seven different commercial resins used in solid-phase synthesis were investigated with (19)F NMR spectroscopy. A fluorine-labeled dipeptide was synthesized on each resin, and the resolution of the (19)F resonances in CDCl(3), DMSO-d(6), benzene-d(6) and CD(3)OD were measured with a conventional NMR spectrometer, i.e. without using magic angle spinning. In general, resins containing poly(ethylene glycol) chains (ArgoGel, TentaGel and PEGA) were found to be favorable for the (19)F NMR spectral quality. Three serine containing tri-, penta-, and heptapeptides were then prepared on an ArgoGel resin functionalized with a fluorine-labeled linker. The resin bound peptides were glycosylated utilizing a thiogalactoside glycosyl donor carrying fluorine-labeled protective groups. Monitoring of the glycosylations with gel-phase (19)F NMR spectroscopy allowed each glycopeptide to be formed in similar 80% yield, using a minimal amount of glycosyl donor (3 x 2 equivalents). In addition, it was found that the glycosylation yields were independent of peptide length.