PI by NMR: Probing CH–π Interactions in Protein–Ligand Complexes by NMR Spectroscopy

While CH–π interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH–π interactions in drug–protein complexes. Herein, we present a fast and reliable methodology called PI (π interactions) by NMR, which can differentiate the strength of protein–ligand CH–π interactions in solution. By combining selective amino‐acid side‐chain labeling with ¹H‐¹³C NMR, we are able to identify specific protein protons of side‐chains engaged in CH–π interactions with aromatic ring systems of a ligand, based solely on ¹H chemical‐shift values of the interacting protein aromatic ring protons. The information encoded in the chemical shifts induced by such interactions serves as a proxy for the strength of each individual CH–π interaction. PI by NMR changes the paradigm by which chemists can optimize the potency of drug candidates: direct determination of individual π interactions rather than averaged measures of all interactions.     

Flow injection analysis NMR (FIA–NMR): a novel flow NMR technique that complements LC–NMR and direct injection NMR (DI–NMR)

Details of a new flow NMR technique, flow injection analysis NMR (FIA–NMR), are presented for the first time. This method blends some aspects of both liquid chromatography–NMR and direct injection NMR, and complements both. FIA‐NMR is shown to be useful as an analytical technique, especially for repetitive analyses, and may also prove useful in the analysis of combinatorial chemistry libraries. The feasibility of FIA‐NMR is demonstrated by the quantitative analysis of an over‐the‐counter pharmaceutical. Copyright © 2003 John Wiley & Sons, Ltd.     

SEAL by NMR: Glyco‐Based Selenium‐Labeled Affinity Ligands Detected by NMR Spectroscopy

We report a method for the screening of interactions between proteins and selenium‐labeled carbohydrate ligands. SEAL by NMR is demonstrated with selenoglycosides binding to lectins where the selenium nucleus serves as an NMR‐active handle and reports on binding through ⁷⁷Se NMR spectroscopy. In terms of overall sensitivity, this nucleus is comparable to ¹³C NMR, while the NMR spectral width is ten times larger, yielding little overlap in ⁷⁷Se NMR spectroscopy, even for similar compounds. The studied ligands are singly selenated bioisosteres of methyl glycosides for which straightforward preparation methods are at hand and libraries can readily be generated. The strength of the approach lies in its simplicity, sensitivity to binding events, the tolerance to additives and the possibility of having several ligands in the assay. This study extends the increasing potential of selenium in structure biology and medicinal chemistry. We anticipate that SEAL by NMR will be a beneficial tool for the development of selenium‐based bioactive compounds, such as glycomimetic drug candidates.     

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.     

Solution and Solid‐State Studies on the Halide Binding Affinity of Perfluorophenyl‐Armed Uranyl–Salophen Receptors Enhanced by Anion–π Interactions

The enhancement of the binding between halide anions and a Lewis acidic uranyl–salophen receptor has been achieved by the introduction of pendant electron‐deficient arene units into the receptor skeleton. The association and the occurrence of the elusive anion–π interaction with halide anions (as tetrabutylammonium salts) have been demonstrated in solution and in the solid state, providing unambiguous evidence on the interplay of the concerted interactions responsible for the anion binding.     

Use of diffusion‐ordered NMR spectroscopy and HPLC–UV–SPE–NMR to identify undeclared synthetic drugs in medicines illegally sold as phytotherapies

The informal (and/or illegal) e‐commerce of pharmaceutical formulations causes problems that governmental health agencies find hard to control, one of which concerns formulas sold as natural products. The purpose of this work was to explore the advantages and limitations of DOSY and HPLC–UV–SPE–NMR. These techniques were used to identify the components of a formula illegally marketed in Brazil as an herbal medicine possessing anti‐inflammatory and analgesic properties. DOSY was able to detect the major components present at higher concentrations. Complete characterization was achieved using HPLC–UV–SPE–NMR, and 1D and 2D NMR analyses enabled the identification of known synthetic drugs. These were ranitidine and a mixture of orphenadrine citrate, piroxicam, and dexamethasone, which are co‐formulated in a remedy called Rheumazim that is used to relieve severe pain, but it is prohibited in Brazil because of a lack of sufficient pharmacokinetic and pharmacodynamic information. Copyright © 2013 John Wiley & Sons, Ltd.     

Non‐empirical calculations of NMR indirect carbon–carbon coupling constants. Part 4: Bicycloalkanes

A systematic study of the one‐bond and long‐range J(C,C), J(C,H) and J(H,H) in the series of nine bicycloalkanes was performed at the SOPPA level with special emphasis on the coupling transmission mechanisms at bridgeheads. Many unknown couplings were predicted with high reliability. Further refinement of SOPPA computational scheme adjusted for better performance was carried out using bicyclo[1.1.1]pentane as a benchmark to investigate the influence of geometry, basis set and electronic correlation. The calculations performed demonstrated that classical ab initio SOPPA applied with the locally dense Dunning's sets augmented with inner core s‐functions used for coupled carbons and Sauer's sets augmented with tight s‐functions used for coupled hydrogens performs perfectly well in reproducing experimental values of different types of coupling constants (the estimated reliability is ca 1–2 Hz) in relatively large organic molecules of up to 11 carbon atoms. Additive coupling increments were derived for J(C,C), J(C,H) and J(H,H) based on the calculated values of coupling constants within SOPPA in the model bicycloalkanes, in reasonably good agreement with the known values obtained earlier on pure empirical grounds. Most of the bridgehead couplings in all but one bicycloalkane appeared to be essentially additive within ca 2–3 Hz while bicyclo[1.1.1]pentane demonstrated dramatic non‐additivity of ?14.5 Hz for J(C,C), +16.6 Hz for J(H,H) and ?5.5 Hz for J(C,H), in line with previous findings. Non‐additivity effects in the latter compound established at the SOPPA level should be attributed to the through‐space non‐bonded interactions at bridgeheads due to the essential overlapping of the bridgehead rear lobes which provides an additional and effective non‐bonding coupling path for the bridgehead carbons and their protons in the bicyclopentane framework. Copyright © 2003 John Wiley & Sons, Ltd.     

Application of a Grubbs–Hoveyda Metathesis Catalyst Noncovalently Immobilized by Fluorous–Fluorous Interactions

A Grubbs–Hoveyda metathesis catalyst bearing a tris(perfluoroalkyl)silyl tag for efficient noncovalent attachment to fluorous silica gel (FSG) was synthesized and employed in ring‐closing metathesis (RCM) reactions in CH₂Cl₂. After the reaction, a solvent switch to a polar system allowed for recovery of the catalyst by filtration and its reuse. The approach was demonstrated for a number of different substrates. Furthermore, it was shown that the application of this catalytic system yielded products with low ruthenium content.     

Intermolecular Interactions and Protein Dynamics by Solid‐State NMR Spectroscopy

Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site‐specific ¹⁵N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small‐amplitude overall anisotropic motion sampling the interaction interface in the complex.     

Activation of – N=CH – bond in a Schiff base by divalent nickel monitored by NMR evidence

The Schiff base, 2–salicylidene–4–aminophenyl benzimidazole in ethanol undergoes activation of –N=CH– bond by Ni²⁺ in the presence of ammonia or primary alkyl amine to produce nickel complexes of the formula Ni{o–C₆H₄(O)CH NR}₂ . n H₂O [R = H, Me; n = 0; R = Et, n = 0.5] and 4–aminophenyl benzimidazole. The products have been identified by elemental analysis, magnetic susceptibility measurements and IR, ESR, mass and extensive NMR spectral studies. The possible mechanism for the activation of –N=CH – bond has also been proposed. Copyright © 2012 John Wiley & Sons, Ltd.     

Enhancement of Iodine–Hydride Interaction by Substitution and Cooperative Effects in NCX–NCI–HMY Complexes

The NCX‐NCI‐HMY (X=H, Cl, Br, I, Li; M=Be, Mg; Y=H, Li, Na) trimers are investigated to find ways to enhance the iodine–hydride interaction. The interaction energy in the NCI–HMH dimer is ?2.87 and ?5.87 kcal mol^?1 for M=Be and Mg, respectively. When the free H atom in the NCI–HMH dimer is replaced with an alkali atom, the interaction energy is enhanced greatly. When NCX is added into this dimer, the interaction energy of the iodine–hydride interaction is increased by 9–45 % and its increased percentage follows the order X=Cl<Br<H<I<Li and M=Be<Mg. The combination of the alkali substitution and the cooperativity results in a more prominent enhancing effect. The largest interaction energy is found for the NCLi–NCI–HMgLi trimer (?7.03 kcal mol^?1). The influence of the I???H interaction on the X???N interaction is also studied in the trimers. Both types of interactions are analyzed with NBO, AIM, and MEP. The interaction energy in the trimer is also unveiled by a many‐body analysis.