A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase

¹⁹F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of ¹⁹F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The ¹⁹F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining ¹⁹F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments.     

多核19F磁共振成像研究进展

~(19)氟(~(19)F)的磁共振成像(MRI)研究可追溯到35年以上。在这段时间里,~1H磁共振成像的蓬勃发展使磁共振成为影像医学的支柱,但~(19)F磁共振成像研究的进展却较为缓慢。然而最近几年,~(19)F磁共振成像的研究受到了广泛的关注。在某种程度上,这是由于MR成像中软件与硬件的发展,更因为分子影像学的概念的提出与发展。本文将对~(19)F多核磁共振成像的应用,特别是使用全氟化碳纳米成像探针的19F多核磁共振成像进行综述。     

Investigation of the Ca2+-dependent interaction of trifluoperazine with S100a: A19F NMR and circular dichroism study

S100a is a heterodimeric, acidic calcium-binding protein that interacts with calmodulin antagonists in a Ca²⁺-dependent manner. In order to study the behavior of the hydrophobic domain on S100a when bound to Ca²⁺, its interaction with trifluoperazine (TFP) was investigated using¹⁶F nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. The dissociation constant (K _d) values of TFP, as estimated from the chemical shifts of¹⁹F NMR, were 191 and 29 m in the absence and presence of Ca²⁺, respectively, and were similar to those previously reported for S100b. However, the TFP linewidth in the presence of Ca²⁺-bound S100a was 65 Hz greater than in the presence of Ca²⁺-bound S100b. This suggests a slower TFP exchange rate for S100a than for S100b. Thus, the TFP linewidths observed for each isoform may reflect differences in structural and modulatory properties of the Ca²⁺-dependent hydrophobic domains on S100a and S100b. Additionally, the presence of magnesium had no effect on the observed Ca²⁺-induced TFP spectral changes in S100a solutions. Circular dichroism studies indicate that Ca²⁺ induces a small transition from -helix to random coil in S100a; in contrast, the opposite transition is reported for calmodulin (Hennesseyet al., 1987). However, TFP did not significantly alter the secondary structure of Ca²⁺-bound S100a; this observation is similar to the effect of TFP on Ca²⁺-bound calmodulin and troponin C (Shimizu and Hatano, 1984; Gariépy and Hodges, 1983). It is, therefore, proposed that TFP binds to a hydrophobic domain on S100a in a fashion similar to other calcium-modulated proteins.     

13C NMR analysis of aporphine alkaloids

The ¹³C NMR spectra of some tertiary and quaternary aporphine alkaloids are recorded and the signals assigned. The substituent shielding effects together with the effects of N- and O-methylation, and the twisting of the biphenyl system, are analysed and utilized in the spectral interpretation.     

19F nuclear magnetic resonance observations of aldehyde dismutation catalyzed by horse liver alcohol dehydrogenase

We have examined aspects of the second catalytic activity of alcohol dehydrogenase from horse liver (LADH), which involves an apparent dismutation of an aldehyde substrate into alcohol and acid in the presence of LADH and NAD. Using the substrate p-trifluoromethylbenzaldehyde, we have observed various bound complexes by ¹⁹F NMR in an effort to further characterize the mechanism of the reaction. The mechanism appears to involve the catalytic activity of LADH · NAD · aldehyde complex which reacts to form an enzyme · NADH · acid complex. The affinity of the acid product for LADH · NADH is weak and the acid product readily desorbs from the ternary complex. The resulting LADH · NADH can then react with a second molecule of aldehyde to form NAD and the corresponding alcohol. The result is the conversion of two molecules of aldehyde to one each of acid and alcohol, with LADH and NAD acting catalytically. This sequence of reactions can also explain the slow formation of acid product observed when alcohol and NAD are incubated with the enzyme.     

Detection of site-specific binding and co-binding of ligands to macromolecules using 19F NMR

Study of ligand-macromolecular interactions by 19F nuclear magnetic resonance (NMR) spectroscopy affords many opportunities for obtaining molecular biochemical and pharmaceutical information. This is due to the absence of a background fluorine signal, as well as the relatively high sensitivity of 19F NMR. Use of fluorine-labeled ligands enables one to probe not only binding and co-binding phenomena to macromolecules, but also can provide data on binding constants, stoichiometries, kinetics, and conformational properties of these complexes. Under conditions of slow exchange and macromolecule-induced chemical shifts, multiple 19F NMR resonances can be observed for free and bound ligands. These shifted resonances are a direct correlate of the concentration of ligand bound in a specific state rather than the global concentrations of bound or free ligand which are usually determined using other techniques such as absorption spectroscopy or equilibrium dialysis. Examples of these interactions are demonstrated both from the literature and from interactions of 5-fluorotryptophan, 5-fluorosalicylic acid, flurbiprofen, and sulindac sulfide with human serum albumin. Other applications of 19F NMR to study of these interactions in vivo, as well for receptor binding and metabolic tracing of fluorinated drugs and proteins are discussed.     

The interaction of myosine S1 with phosphorothioates of ADP: An 18O exchange study by 31P NMR

The ¹⁸O exchange reaction which labeled P_i undergoes in the presence of complexes of myosin subfragment 1, MgCl₂, and the different phosphorothioates of ADP has been observed by ³¹P NMR. From these experiments it can be concluded that ADP and ADP (α-S) (A) on the one hand and ADP (β-S) and ADP (α-S) (B) on the other hand form similar complexes as far as the number of reversals of the nucleoside triphosphate formation step from the nucleoside diphosphate and P_i, is concerned. In addition, the same seems to hold for the rate constant k_?2, which describes the binding step of free P_i, to the subfragment 1 nucleoside diphosphate complex. These observations support former kinetic experiments which yielded the same similarities for the rate parameters describing association and dissociation of the subfragment 1 nucleotide complexes.     

13C NMR spectral analysis of some isoquinoline alkaloids

The ¹³C NMR spectra of some isoquinoline and tetrahydroisoquinoline alkaloids and their corresponding N-methosalts and of the bisbenzylisoquinoline alkaloid isochondodendrine were recorded and the signals assigned. The substituent shielding effects and the ¹³C¹H long range couplings were analysed and utilized in the spectral interpretation.     

13C NMR spectral analysis of grindelane diterpenoid acids

The ¹³C NMR spectra of methyl grindelate and some of its derivatives were recorded and the signals assigned. Based on these assignments and on a comparison with previously reported data, information regarding the structures and stereochemistry of the products under study was obtained.     

Dienoic acids,synthesis and 13C NMR spectral analysis

A preparation of E,E-2,4-dienoic acids, together with the assignments of their ¹³C NMR signals and the shifts observed after transformation into their sodium salts, is described. The stereochemistry of the double bonds of 3,5-dienoic esters, obtained from 2,4-dienoic acids, on the basis of ¹³C NMR data, is also presented.     

A high-resolution NMR study (1H, 13C, 31P) of the interaction of paramagnetic ions with phospholipids in aqueous dispersions

¹H-, ¹³C-and ³¹P-NMR spectra of egg-yolk phosphatidylcholine (PC), phosphatidylserine (PS) and phosphatidic acid (PA) and cosonicated mixtures of these phospholipids were obtained from ultrasonicatcd dispersions containing Pr³⁺, Eu³⁺, Gd³⁺ and Mn²⁺ ions.The differences in chemical shift values. °_n, between the “inner” and “outer” resonance signals for the different nuclei of the polar head group of egg-yolk phosphatidyl choline provide information about the average distances of the paramagnetic ion within the polar groups of the phospholipid molecules. In the Pr(²H₂O)³⁺_n/egg-yolk phosphatidylcholine system the ions are nearest to the phosphate and -CH₂CH₂ group, respectively but relatively far from the N(CH₃)₃ group of the polar head group of the lipid.The integral analysis of the¹ H-NMR spectra obtained from dispersions containing Pr³⁺ and Mn²⁺ ions enables us to calculate the number of the polar groups in both sides of the egg-yolk phosphatidylcholine bilayer, the size of the lipid vesicle and to give some features of the arrangement of the phospholipid molecules in cosonicated egg-yolk phosphatidylcliotine/ phosphatidytserine vesicles. At p²H 8.3 in PC/PS mixtures an extreme asymmetry is observed with PS preferentially in the outer side of the membrane. This side contains approximately three times more PS than PC molecules.Some comments are made concerning the quantitative integral analysis of proton-noise decoupled ³¹ P-NMR spectra as obtained from similar phospholipid mixtures by Michaelson et al. and Berden et at.     

13C NMR analysis of alkaloids from peschiera fuchsiaefolia

Fractionation of an ethereal extract of Peschiera fuchsiaefolia resulted in the isolation of decarbomethoxyvoacamine, demethylvoacamine, voacamidine, perivine, 16-epiaffinine and voacanginehydroxyindolenine, together with the previously reported alkaloids voacamine, voacangine, voachalotine and affinisine. Analysis of the ¹³C NMR spectra of the bisindole alkaloids and of 16-epiaffinine is reported.     

13C NMR analysis of podophyllotoxin and some of its derivatives

The ¹³C NMR spectra of podophyllotoxin and some of its derivatives were recorded and the signals assigned. Based on these assignments and on comparison with previously reported ¹H NMR data, information regarding the stereochemistry and conformations of the products under study was obtained.     

Selective incorporation of 14C-arachidonic acid into the phospholipids of intact tissues and subsequent metabolism to 14C-prostaglandins

A method is described for the efficient incorporation of radioactive arachidonic acid into the lipids of rabbit hearts and kidneys. Infusion of ¹⁴C-arachidonate through perfused tissues resulted in the quantitative removel of label from the media. Analysis of the lipids from tissues labeled by this procedure revealed that the majority of the ¹⁴C-arachidonate was incorporated into phospholipids. Essentially all of the radioactivity in phosphatidylcholine was found in the 2-position. Subsequent to the ¹⁴C-arachidonate infusion, stimulation of prostaglandin biosynthesis (e.g. by bradykinin) resulted in the release of radioactive prostaglandins. This suggests that the ¹⁴C-arachidonate is incorporated in a manner such that it is available for homone-stimulated prostaglandin biosynthesis. The method described allows both qualitative and quantitative analysis of arachidonate metabolism in intact tissues and offers significant advantages over other presently used methods.     

Measuring bacterial production via rate of incorporation of [3H]thymidine into DNA

Thymidine (TdR) incorporation into DNA as a measure of bacterial production in environmental samples relies on assumptions about what organisms incorporate exogenous thymidine, extent of dilution of labelled thymidine by internal and external pools, and analytical methods for recovery and purification of bacterial DNA. We have examined these assumptions with regard to the feasibility of using [³H]TdR incorporation in the water column and sediments of a blackwater river. The extent of dilution of added [³H]TdR may be determined with isotope dilution plots (Moriarty and Pollard, 1981 and 1982) and these indicate a wide range of degree of participation of added [³H]TdR. Previously described methods for extracting DNA from sediment bacteria may lead to underestimates and we described a more efficient recovery scheme.     

13C NMR spectral analysis of lignans from Araucaria angustifolia

Pinoresinol dimethyl ether, secoisolariciresinol, lariciresinol, isolariciresinol and isolariciresinol-4′-methyl ether were isolated from the knots of dead trees of Araucaria angustifolia. The ¹³C NMR spectra of these compounds, their methyl and acetyl derivatives, and the corresponding one of matairesinol, have been recorded and the signals assigned. On the basis of these assignments, the structure of the new monomethyl ether of isolariciresinol has been established.     

67Zn and 1H NMR studies of Zn2+-imidazole and carboxylate complexes

⁶⁷Zn NMR studies of naturally abundant Zn²⁺-imidazole and carboxylate ligands Complexes are shown. Thus, quadrupolar relaxation changes in ⁶⁷Zn NMR caused by adding imidazole ligands are more remarkable than those by carboxylate ligands. The changes caused by adding less bulky imidazole ligands are more prominent than those caused by a bulky imidazole ligan. Changes in Zn²⁺ quadrupolar relaxation rate caused by adding a cyclic hexapeptide consisting of L-histidine, L-cystein(Acm) and D-leucine are larger than those by a corresponding linear hexapeptide. Those changes in the quadrupolar relaxation rate of ⁶⁷Zn NMR among Zn²⁺ complexes can be reasonably interpreted in terms of the differences of equilibrium constants of those complexes to a first approximation.     

Measurement of intracellular pH in maize root tissue with α-methyl fluorinated alanines and in-vivo 19F NMR spectroscopy

Methods for the simultaneous measurement of vacuolar and cytoplasmic pH in plant tissues currently have significant limitations. This study demonstrates the usefulness of methyl difluoro alanine (F₂ALA) and methyl trifluoro alanine (F₃ALA) with in-vivo ¹⁹F NMR spectroscopy to measure vacuolar and cytoplasmic pH in maize root tissue. The pH dependence of the chemical shift of F₂ALA and F₃ALA is greater than either the commonly used ³¹P NMR signal of inorganic phosphate or the ¹³C NMR signals of trans-aconitic acid, which is also found in some plant cells. F₂ALA and F₃ALA were also able to detect changes over a greater range of pH. When maize root tissue was incubated in the presence of 0.35 m m F₂ALA or F₃ALA, these accumulated to significant concentrations in two compartments of different pH with no significant effect on growth rate of root tips. The time course of accumulation and the pH of the two compartments were consistent with one being the cytoplasm and the other the vacuole. The chemical shift of both C₂ of trans-aconitic acid and vacuolar F₃ALA indicated that the mean vacuolar pH of maize root cells was 4.6 and that the pH gradient across the tonoplast membrane was about 2.8 units. Under a variety of conditions, there was considerable heterogeneity in the pH of the vacuoles in maize root tissue as indicated by the peak width of the signal from F₃ALA. The significance of these values is discussed in terms of the bioenergetics of proton transport across the tonoplast membrane in vivo.