NOE Experiments Research Articles

Synthesis of novel isoxazolidine analogues of homonucleosides

A general method for the synthesis of nucleobase-derived nitrones 4a–e by treatment of N-(2-oxoethyl)nucleobases with N-methylhydroxylamine is reported. The nitrones 4a–e were applied in the synthesis of isoxazolidine homonucleosides. Moderate diastereoselectivities (de 28–82%) were observed for cycloadditions between nitrones 4a–e and allyl alcohol with cis-isoxazolidines predominating. The stereochemistry of the substituted isoxazolidines was established based on an analysis of 2D NOE experiments for uracil-containing cycloadducts 6a and 7a. Cycloadditions of uracil-based nitrone 4a with vinyl-, allyl-, vinyloxymethyl- and allyloxymethylphosphonates gave the respective phosphonylated cis-isoxazolidines as the major adducts.

2-Acylamino- and 2,4-Bis(acylamino)pyrimidines as Supramolecular Synthons Analyzed by Multiple Noncovalent Interactions. DFT, X-ray Diffraction, and NMR Spectral Studies

Intermolecular interactions of ten 2-acylamino and 2,4-bis(acylamino)pyrimidines (7 of which are previously unknown) have been investigated by X-ray structural, quantum chemical (DFT), and NMR spectral methods. Especially the concentration dependencies of the (1)H NMR chemical shifts and titrations with other molecules capable of multiple hydrogen bonding provided useful information regarding their association via triple or quadruple hydrogen bonding, which is controlled by the conformational preferences of 2-acylamino- and 2,4-bis(acylamino)pyrimidines. On comparison of the properties of 2-acylamino- and 2,4-bis(acylamino)pyrimidines with the corresponding pyridines, an additional nitrogen in the heterocyclic ring is the crucial factor in explaining the stability of various conformers and dimers of pyrimidines. Computational modeling of their dimerization (self-association) and heteroassociation supports the experimental findings. The substituent effects in 2-acylamino- and 2,4-bis(acylamino)pyrimidines are discussed via inter- and intramolecular terms. The subtle balance between several structural factors and their influence on the aggregation of studied pyrimidines was confirmed also by variable-temperature NMR and NOE experiments. X-ray structures of 2-methyl- and 2-adamantyl-CONH-pyrimidines revealed very different intermolecular interactions, showing the importance of the substituent size on the self-assembly process. As a whole NMR spectral, X-ray structural, and computational data of 2-acylamino- and 2,4-bis(acylamino)pyrimidines can be interpreted in terms of multiple intra-/intermolecular interactions.

Conformational Analysis of Fluorinated Pyrrolidines Using 19F–1H Scalar Couplings and Heteronuclear NOEs

A series of 3-fluoropyrrolidines have been studied to investigate the influence of the stereoelectronic fluorine gauche effect on ring conformations in the solid state by single-crystal X-ray analysis and in solution phase by NMR spectroscopy. As part of these studies 1D (19)F-(1)H heteronuclear NOE (HOESY) experiments have been optimised for applications to small molecules and are described in detail. These have been employed to estimate (19)F-(1)H internuclear distances and were combined with vicinal (3)J(F,H) and (3)J(H,H) scalar coupling constants to analyse the ring conformations. Where possible the derived solution-phase structural data have been compared with those of the crystalline state. The results demonstrate the influence of the gauche effect in stabilising C(γ)-exo conformations of the fluorinated pyrrolidines. It was further shown that when steric interactions were also present, this conformational bias was diminished and the contribution of the alternative C(γ)-endo conformation was seen to increase in solution at lower sample temperatures.

NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir

Xenotropic murine leukemia virus-related virus (XMRV) is a virus created through recombination of two murine leukemia proviruses under artificial conditions during the passage of human prostate cancer cells in athymic nude mice. The homodimeric protease (PR) of XMRV plays a critical role in the production of functional viral proteins and is a prerequisite for viral replication. We synthesized XMRV PR using the wheat germ cell-free expression system and carried out structural analysis of XMRV PR in a complex with an inhibitor, amprenavir (APV), by means of NMR. Five different combinatorially 15N-labeled samples were prepared and backbone resonance assignments were made by applying Otting’s method, with which the amino acid types of the [1H, 15N] HSQC resonances were automatically identified using the five samples (Wu et al., 2006) [14]. A titration experiment involving APV revealed that one APV molecule binds to one XMRV PR dimer. For many residues, two distinct resonances were observed, which is thought to be due to the structural heterogeneity between the two protomers in the APV:XMRV PR=1:2 complex. PR residues at the interface with APV have been identified on the basis of chemical shift perturbation and identification of the intermolecular NOEs by means of filtered NOE experiments. Interestingly, chemical shift heterogeneity between the two protomers of XMRV PR has been observed not only at the interface with APV but also in regions apart from the interface. This indicates that the structural heterogeneity induced by the asymmetry of the binding of APV to the XMRV PR dimer is transmitted to distant regions. This is in contrast to the case of the APV:HIV-1 PR complex, in which the structural heterogeneity is only localized at the interface. Long-range transmission of the structural change identified for the XMRV PR complex might be utilized for the discovery of a new type of drug.

The Dynamic Structure of Thrombin in Solution

The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R1, R2, and heteronuclear NOE experiments, variable temperature TROSY 2D [1H-15N] correlation spectra, and Rex measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na+ binding site have order parameters below 0.8. Significant Rex was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales.

ChemInform Abstract: Turtschamide, a Cytotoxic Putrescine Bisamide from Corydalis turtschaninovii.

Abstract A putrescine bisamide with a unique cyclic structure derived from l -tyrosine, turtschamide ( 1 ), was isolated from the tubers of Corydalis turtschaninovii . The structure of 1 was established by extensive spectroscopic study, and its absolute configuration was determined by a combination of NOE experiment and application of the Marfey’s method. Turtschamide ( 1 ) exhibited cytotoxicity against the A549, SK-OV-3, SK-MEL-2, and HCT-15 cells.

Structures and absolute stereochemistry of dinapinones A1 and A2, inhibitors of triacylglycerol synthesis, produced by penicillium pinophilum FKI-3864

During our screening program for microbial inhibitors of triacylglycerol synthesis in mammalian cells, four structurally related new compounds, dinapinones A1 (1) and A2 (2) and monapinones A (3) and B (4), were isolated from the culture broth of Penicillium pinophilum FKI-3864. Compounds 3 and 4 were produced by the fungus only when fermented in seawater-supplemented medium. The structures of 1 to 4 were elucidated by spectroscopic studies including various NMR experiments. Compounds 1 and 2 were atropisomers consisting of two monomers with the same planar structure of dihydronaphthopyranone as 3. The absolute stereochemistry of 3 was elucidated by NOE experiment and circular dichroism spectra. Furthermore, the stereochemistry of 1 and 2 was elucidated by in vitro conversion from the structure-defined 3 to its dimers 1 and 2.

One new antitumour cassane-type diterpene from Caesalpinia crista

1α-acetoxy-5α, 7β-dihydroxycassa-11,13(15)-diene-16,12-lactone, a new cassane-type diterpene was isolated from Caesalpinia crista. The structure of this compound was elucidated by analysis of NMR spectra, and the relative configuration was established by NOE experiment. The new compound was evaluated for antitumour activity against T47D, DU145 and showed significant inhibitory activities.

Cichorins B and C: two new benzo-isochromenes from Cichorium intybus

Two new benzo-isochromenes, named cichorins B (1) and C (2), were isolated from Cichorium intybus. The structures of the new compounds were elucidated by detailed spectroscopic analysis such as 1H, 13C NMR, COSY, HMQC, HMBC, and HR-EI-MS. Relative configurations of asymmetric centers of cichorins B and C were determined by the analysis of the 1H NMR coupling constants together with the 2D NOESY and 1D NOE experiments as well as from value.

Atropisomers of Hindered Triarylisocyanurates: Structure, Conformation, Stereodynamics, and Absolute Configuration

The syn and anti diastereoisomers of some 1,3,5-triarylisocyanurate derivatives were isolated and their configuration assigned by NOE experiments and by X-ray diffraction. The kinetics of the syn/anti interconversion were determined, and the experimental activation energies matched satisfactorily the values predicted by DFT computations. Low-temperature NMR spectra were employed to determine the rotation barrier of N-bonded unhindered aryl substituents: these barriers, too, are satisfactorily reproduced by DFT computations. In the case of racemic diastereoisomers, the two expected enantiomers (atropisomers) were isolated by enantioselective HPLC and the absolute configuration established by DFT simulation of the electronic and vibrational circular dichroism spectra.

Oliveridepsidones A–D, antioxidant depsidones from Garcinia oliveri

Four new prenylated depsidones, oliveridepsidones A-D, were isolated from the bark of Garcinia oliveri collected in Vietnam. Their structures were elucidated using mainly NMR techniques ((1)H and (13)C NMR, HMQC, HMBC and NOE experiments).

Direct Evidence for CH···π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs

Although weak interactions play subtle but important roles in dictating protein structures, their experimental detection is nontrivial. From NOE experiments we provide direct evidence for the presence of CH···π interaction, operational between the C(α)-H of the first Pro and the aromatic (Aro) side chain of Xaa, in a peptide series with the general sequence Ac-Pro-Pro-Xaa-NH(2). Indirect evidence of CH···π interaction is provided from ring current-induced upfield displacement of Pro(1) C(α)-H chemical shifts and restriction of side-chain (χ1) rotation of Xaa. A consequence of this interaction is the enhanced stability of the Pro-cisPro conformer in Ac-Pro-Pro-Xaa-NH(2) when Xaa is aromatic. The free energies associated with trans to cis transformation of the Pro-Pro moiety are 0.35, 0.59, 0.64, and 0.82 kcal/mol when Xaa is Tyr, Trp, Phe, and His (pH of 8.4), respectively. In comparison, the corresponding free energy is ∼1.55 kcal/mol when Xaa is nonaromatic. The observed population of Pro-cisPro-His and the pH-induced perturbation of electron density of the His side chain were correlated, providing further evidence for a direct role of CH···π interaction in modulating the stability of Pro-cisPro population in Ac-Pro-Pro-Aro-NH(2). Our study establishes Pro-Pro-Aro to be a new sequence motif that can stabilize Pro-cisPro peptide bonds. This study not only identifies a new structurally biased sequence motif but also directly demonstrates the role played by CH···π interactions in subtly altering conformational preferences of three-residue peptide sequences with implications on the role played by cis-peptide bonds in unfolded proteins.

Novel isoxazole polycyclic aromatic hydrocarbons as DNA-intercalating agents

The third generation of isoxazole polycyclic aromatic hydrocarbons, acting as DNA-intercalator agents and possessing the binding constants in the range 104–105 M−1, in order to easily diffuse targeting remotely implanted tumors, has been synthesized in good yields according to the 1,3-dipolar cycloaddition methodology. The structure of the obtained cycloadducts has been determined by NOE experiments and supported by computational studies at PM3 level. All the obtained compounds have been tested for their in vitro cytotoxic activity and the most potent of them, (3RS,5SR)-2-benzyl-N,N-dimethyl-3-(pyren-1-yl)isoxazolidine-5-carboxamide (7d), showed an IC50 of 4 μM upon the human lung cancer (A-549) cells. Moreover, compound 7d showed binding constant for the intercalation with calf thymus DNA, poly-d(AT)2 and poly-d(GC)2 of 1.7 × 105 M−1, 1.6 × 105 M−1 and 0.3 × 105 M−1, respectively. Biological and docking studies showed that, in vitro, these compounds complex by intercalation between base pairs, approaching the DNA from its minor groove with a preference for the AT nucleobases pairs.

Microbial β-glycosylation of entacapone by Cunninghamella echinulata ATCC 9245

The purpose of this paper is to describe the glycosylation of entacapone by cultures of Cunninghamella echinulata ATCC 9245. This method is then applied in toxicological and pharmacological studies. The cultures were grown in a fluid PDSM medium for 7 days at 28°C. After purification by silica gel flash column chromatography, the (E)-2-cyano-N,N-diethyl-3-(4-hydroxy-3-nitro-5-(3,4,5-trihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxy)phenyl) acrylamide was identified by IR, mass spectroscopy and (1)H and (13)C NMR. The correct position and β-configuration of the glucose was determined through HSQC, HMBC and NOE experiments.

Turtschamide, a cytotoxic putrescine bisamide from Corydalis turtschaninovii

A putrescine bisamide with a unique cyclic structure derived from l-tyrosine, turtschamide (1), was isolated from the tubers of Corydalis turtschaninovii. The structure of 1 was established by extensive spectroscopic study, and its absolute configuration was determined by a combination of NOE experiment and application of the Marfey’s method. Turtschamide (1) exhibited cytotoxicity against the A549, SK-OV-3, SK-MEL-2, and HCT-15 cells.

Core-modified hexaphyrin: synthesis and characterization of 31,34-disilahexaphyrinoid

Condensation of 16-silatripyrrane with pentafluorobenzaldehyde under catalytic conditions followed by DDQ oxidation leads to 31,34-disilahexaphyrinoid--a four times reduced derivative of 31,34-disilahexaphyrin which contains two built-in silole units flanked by four tetrahedrally hybridized meso carbons. In the preferred folded macrocyclic conformation the silole rings remain perpendicular to each other. The steric hindrance of bulky substituents at silicon atoms and β-positions of siloles prevented aromatization. Only one meso diastereomer (5S, 15S, 20R, 30R) has been isolated and subsequently identified by 1D and 2D NMR techniques. The density functional theory (DFT) has been applied to model the molecular structure of 31,34-disilahexaphyrinoid consistent with constraints imposed by NOE experiments. The total energies calculated at the B3LYP/6-31G**//B3LYP/6-31G** level for four feasible meso diastereomers clearly demonstrated the energetic preference for the meso diastereomer (5S, 15S, 20R, 30R).

Complete ¹H and 13C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. ¹H NMR, 13C NMR {¹H}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables.

NMR Structure of a Heterodimeric SAM:SAM Complex: Characterization and Manipulation of EphA2 Binding Reveal New Cellular Functions of SHIP2

The sterile alpha motif (SAM) for protein-protein interactions is encountered in over 200 proteins, but the structural basis for its interactions is just becoming clear. Here we solved the structure of theEphA2-SHIP2 SAM:SAM heterodimeric complex by use of NMR restraints from chemical shift perturbations, NOE and RDC experiments. Specific contacts between the protein surfaces differ significantly from a previous model and other SAM:SAM complexes. Molecular dynamics and docking simulations indicate fluctuations in the complex toward alternate, higher energy conformations. The interface suggests that EphA family members bind to SHIP2 SAM, whereas EphB members may not; correspondingly, we demonstrate binding of EphA1, but not of EphB2, to SHIP2. A variant of EphB2 SAM was designed that binds SHIP2. Functional characterization of a mutant EphA2 compromised in SHIP2 binding reveals two previously unrecognized functions of SHIP2 in suppressing ligand-induced activation of EphA2 and in promoting receptor coordinated chemotactic cell migration.

Rapid One-pot, Four Component Synthesis of Pyranopyrazoles Using Heteropolyacid Under Solvent-free Condition

A series of pyranopyrazoles, was efficiently synthesized via one-pot, four component reaction of ethyl acetoacetate, hydrazine hydrate, aldehydes and malononitrile in the presence of catalytic amount silicotungstic acid under solvent free condition. NOE experiments confirmed that the product exist exclusively in the 2H form. The present protocol offers the advantages of clean reaction, short reaction time, high yield, easy purification and economic availability of the catalyst.

A Kiyooka Aldol Approach for the Synthesis of the C(14)–C(23) Segment of the Diastereomeric Analog of Tedanolide C

The challenging synthesis of a quaternary center within the highly oxygenated setting of tedanolide C can be performed via a Kiyooka aldol reaction. Here, the diastereomeric analog of tedanolide C with the configurations between C10 and C20 opposite compared to the proposed structure was chosen as the synthetic target. The tetra-substituted silyl ketene acetal provides the southern hemisphere of tedanolide C in useful selectivities, and the absolute configuration of the newly generated quaternary center was determined by NOE experiments of the corresponding acetonide.