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At least 793 records · Page 44Linked to original sources
PubMed1996

Benzoxazines. II. Synthesis, conformational analysis, and structure--activity relationships of 3,4-dihydro-2H-1,4-benzoxazine-8-carboxamide derivatives as potent and long-acting serotonin-3 (5-HT3) receptor antagonists.

A series of 3,4-dihydro-2H-1,4-benzoxazine-8-carboxamide derivatives was synthesized and evaluated for serotonin-3 (5HT3) receptor antagonistic activities by means of assays of 5-HT3 receptor binding and the ability to antagonize the von Bezold-Jarisch reflex in rats. Replacement of the 1,4-benzoxazine ring with a 1,4-benzthiepine ring or seven-membered ring (i.e., 1,5-benzoxepine or 1,5-benzthiepine) resulted in decreased affinity for 5-HT3 receptor. Introduction of substituents at the 2 position of the 1,4-benzoxazine ring increased the antagonistic activities (dimethyl > methyl > dihydro > phenyl). The compounds bearing a 9-methyl-9-azabicyclo[3.3.1]non-3-yl moiety as the basic part of 3,4-dihydro-2H-1,4-benzoxazine-8-carboxamide derivatives were equipotent to those bearing 1-azabicyclo[2.2.2]oct-3-yl moiety. The 9-methyl-9-azabicyclo[3.3.1]non-3-yl moiety was confirmed to adopt a boat-chair conformation on the basis of both NMR studies and X-ray analysis. In this series, endo-6-chloro-3,4-dihydro-N-(9-methyl-9-azabicyclo[3.3.1]non-3-yl)-2,2, 4-trimethyl-2H-1,4-benzoxazine-8-carboxamide showed the highest affinity for 5-HT3 receptors (Ki = 0.019 nM), and a long-lasting 5-HT3 receptor antagonistic activity as evidenced by antagonism to the von Bezold--Jarisch reflex in rats. Such a long-lasting 5-HT3 receptor antagonism would be attributed to the introduction of both two methyl groups at the 2 position of the benzoxazine ring and the 9-methyl-9-azabicyclo[3.3.1]non-3-yl moiety, which adopts the boat-chair conformation.

Amides↗
PubMed2000

Oxazolopiperidin-2-ones as type II' beta-turn mimetics: synthesis and conformational analysis.

We describe a straightforward synthesis of 9-substituted 3-aminooxazolidinopiperidin-2-ones 4. Some derivatives were prepared for use in peptide synthesis as rigidified surrogates of the Ala-Pro dipeptide. Analysis of the amide derivatives 14 by NMR experiments and molecular mechanics/dynamics calculations shows that the major isomer 14a has a stronger propensity than the minor isomer 14b to adopt beta-turn conformations, and the calculations indicate that in water 14a adopts a stable betaII' turn conformation.

Magnetic Resonance Spectroscopy↗
PubMed2000

Conformational analysis and stability of collagen peptides by CD and by 1H- and 13C-NMR spectroscopies.

Four small type I collagen CNBr peptides containing complete natural sequences were purified from bovine skin and investigated by CD and 1H- and 13C-nmr spectroscopies to obtain information concerning their conformation and thermal stability. CD showed that a triple helix was formed at 10 degrees C in acidic aqueous solution by peptide alpha l(I) CB2 only, and to lesser extent, by alpha 1(I) CB4, whereas peptides alpha 1(I) CB5 and alpha 2(I) CB2 remained unstructured. Analytical gel filtration confirmed that peptides alpha 1(I) CB2 and alpha 1(I) CB4 only were able to form trimeric species at temperature between 14 and 20 degrees C, and indicated that the monomer = trimer equilibrium was influenced by the chaotropic nature of the salt present in the eluent, by its concentration, and by temperature variations. CD measurements at increasing temperatures showed that alpha 1(I) CB2 was less stable than its synthetic counterpart due to incomplete prolyl hydroxylation of the preparation from the natural source. 1H- and 13C-nmr spectra acquired in the temperature range 0-47 and 0-27 degrees C, respectively, indicated that with decreasing temperature the most abundant from of alpha 1(I) CB2 was in slow exchange with an assembled form, characterized by broad lines, as expected for the triple-helical conformation. A large number of trimer cross peaks was observed both in the proton and carbon spectra, and these were most likely due to the nonequivalence of the environments of the three chains in the triple helix. This nonequivalence may have implications for the aggregation of collagen molecules and for collagen binding to other molecules. The thermal transition from trimer to monomer was also monitored by 1H-nmr following the change in area of the signal belonging to one of the two beta protons of the C-terminal homoserine. The unfolding process was found to be fully reversible with a melting temperature of 13.4 degrees C, in agreement with CD results. The qualitative superposition of the melting curves obtained by CD for the peptide bond characteristics and by nmr for a side chain suggests that triple-helical backbone and side chains constitute a single unit.

Amino Acid Sequence↗
PubMed2001

Conformational analysis and kinetics of ring inversion for methylene- and dimethylsilyl-bridged dicyclooctatetraene.

Dicyclooctatetraenylmethane (1) and dicyclooctatetraenyldimethylsilane (2) in THF-d(8) at 272 K exist as mixtures of diastereomers in ratios of 1:0.8 and 1:1, respectively. Nine energy minima (four meso and five racemic conformers) were located for each compound by geometry optimization at the HF/6-31G level of theory. The effects of torsional strain, steric interactions and dynamic electron correlation were analyzed. The diastereomeric ratios for 1 and 2 were reproduced reasonably well from the total energy calculated for each conformer corrected for its conformational enthalpy and entropy contributions. The ratio of rate constants for bond shift (BS) (k(BS)(1)/k(BS)(2)) is three times greater than the corresponding ratio for ring inversion. This suggests that additional substituent effects, such as pi interactions, are operative in the transition state for BS.

Journal Article↗
PubMedDate not supplied

[Eight types of stacking interaction in dinucleotides. Conformational analysis of ApA, ApC, CpA, CpC, GpG].

On the basis of general stereochemical considerations the classification of the stacking state of dinucleoside phosphate (DNP) including eight types of stacks of nucleic bases has been suggested. With the use of the algorithm, which makes possible determination of the backbone conformation for the given nucleic bases arrangement, the stacking conformes of DNP were analysed by atom-atom potential method. For all compounds different types of stacking conformes were obtained with energy values lower than that for the unstacking state. It follows from the results of calculations that for description of the conformational situation of DNP in solution the "non-canonical" conformers should be born in mind. In particular the forms having different sugar conformations in Np- and in pN-parts of the dimers are of interest. The effect of choice of the atom-atom potential functions on optimal conformation of DNP is discussed. For single-stranded RNA several regular and non-regular structures are proposed.

Adenine Nucleotides↗
PubMed2006

Functional characterization and conformational analysis of the Herpesvirus saimiri Tip-C484 protein.

Tyrosine kinase interacting protein (Tip) of Herpesvirus saimiri (HVS) activates the lymphoid-specific member of the Src family kinase Lck. The Tip:Lck interaction is essential for transformation and oncogenesis in HVS-infected cells. As there are no structural data for Tip, hydrogen-exchange mass spectrometry was used to investigate the conformation of a nearly full-length form (residues 1-187) of Tip from HVS strain C484. Disorder predictions suggested that Tip would be mostly unstructured, so great care was taken to ascertain whether recombinant Tip was functional. Circular dichroism and gel-filtration analysis indicated an extended, unstructured protein. In vitro and in vivo binding and kinase assays confirmed that purified, recombinant Tip interacted with Lck, was capable of activating Lck kinase activity strongly and was multiply phosphorylated by Lck. Hydrogen-exchange mass spectrometry of Tip then showed that the majority of backbone amide hydrogen atoms became deuterated after only 10 s of labeling. Such a result suggested that Tip was almost totally unstructured in solution. Digestion of deuterium-labeled Tip revealed some regions with minor protection from exchange. Overall, it was found that, although recombinant Tip is still functional and capable of binding and activating its target Lck, it is largely unstructured.

Herpesvirus 2, Saimiriine↗
PubMed1992

Conformational analysis of the aromatase inhibitor 3-ethyl-3-(4-pyridyl)piperidine-2,6-dione (rogletimide) and discovery of potent 5-alkyl derivatives.

Analysis of the proton NMR spectra of 3-ethyl-3-(4-pyridyl)piperidine-2,6-dione (rogletimide, 1) shows that it exists in solution with the aromatic ring in an axial position; the same conformation was found for aminoglutethimide. Excess lithium diisopropylamide treatment of 1 formed a dianion which methylated at C-5. The major product with the methyl group trans to the pyridyl ring retained this ring in an axial position and had higher aromatase inhibitory potency than 1. The minor diastereoisomer with an equatorial pyridyl ring had low potency. Upon elongating the alkyl chain, particularly high inhibitory activity was found for the major product isomer having a C-5 octyl, coinciding with the high activity in C-3 and N-1 octyl derivatives of 1, but there was only a small difference in the activity between the enantiomers of 5-octyl-1 and activity was reduced rather than increased when octyl also replaced ethyl at C-3. The results partially support a previously described model comparing binding of androstenedione to aromatase in as much as an axial pyridyl ring is needed to mimic the axial C-19 methyl group of the steroid and bind to the heme component of the enzyme, but for the derivatives bearing a C-5 octyl, the function of the glutarimide ring seems to be simply as a spacer between the hydrophobic chain and the pyridyl ring.

Aminoglutethimide↗
PubMed2004

Conformational analysis of peptide analogues of silkmoth chorion protein segments using CD, NMR and molecular modelling.

Silkmoth proteins secreted from the follicular cells that surround the oocyte form a large extracellular assembly which is important for protecting and sustaining the structure of the oocyte and the developing embryo. These proteins have been classified into two major families (A and B). Sequence analysis showed conservation of a central domain containing long stretches of six amino acid residue repeats in both families, which have been suggested to be organized in beta-sheet structures. In this work NMR and CD spectra, as well as molecular calculations, have been used to investigate the conformational properties of two synthetic peptides (A and B), analogues of parts of the central domain of silkmoth chorion proteins of the A and B families, respectively. These peptides consist of three tandem repeats of the six-residue basic motif. Analysis of CD spectra of the two peptides in aqueous solutions and mixtures with organic solvents revealed beta-sheet and turn structural elements with a percentage higher than 40%. NOESY spectra at low temperatures (263-273 K) show sequential nOe connectivities (i, i + 1), indicative of a relative flexibility. The presence of HNi-HNi+1 cross-peaks and medium Halphai-HNi+1 connectivities, chemical shift deviations and temperature coefficient data provide, for the first time, experimental evidence that local folded structures around Gly residues occur in peptide segments of chorion proteins in solution. Simulated annealing calculations were used to examine the conformational space of the peptides and to probe the initial steps of amyloid fibril formation in the case of chorion proteins.

Amino Acid Sequence↗