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At least 883 records · Page 49Linked to original sources
PubMed1986

The conformational analysis of substance P analogs using high-field NMR techniques.

High-field nuclear magnetic resonance measurements were carried out on substance P fragments SP4-11' [pGlu5]-SP5-11 and [pGlu6]SP6-11 both at 400 and at 500 MHz. A spectral simulation was carried out on two of these peptides and the coupling constants were interpreted in terms of the conformations. The JNH-CHa coupling constants are all approximately 8 Hz, with the exception of glycine, indicating no preferred conformation for the backbone. For the amino acids other than p-Glu, a comparison of the coupling constant data suggests the same relative rotamer populations for the side chains. Proton longitudinal relaxation time data were measured for all three peptides and support the above conclusions.

Magnetic Resonance Spectroscopy↗
PubMed1986

A PCILO study of the pharmacologically active conformation of local anesthetics of the procaine type. Conformational analysis and complex formation of protonated 2-diethylaminoethyl-acetate with formate anion.

To rationalize and improve receptor selectivity of local anesthetics of the procaine type a dynamic two-center model of the pharmacon-receptor interaction is suggested. A quantum chemical study within the Perturbation Configuration Interaction using Localized Orbitals (PCILO) approximations is carried out to find indications for a conformational change of this flexible drug from its thermodynamically preferred conformation to its pharmacologically active one. For this purpose, the pharmacon-receptor interaction is simulated quantum chemically by the interaction of the local anesthetic model compound 2-diethylaminoethyl-acetate (acetylcaine) with the one-center receptor model formate anion and the two-center receptor model gamma-aminobutyric acid in its zwitterionic form. In the present study, the conformational behaviour of acetylcaine is investigated in detail, confirming this molecule to be an appropriate model for procaine. In its formate complex the preferred conformation of acetylcaine is still retained with regard to the torsional angle of the [OCCN] fragment. Artefacts of the in-vacuo condition of the calculation are discussed. In view of the proposed interaction model, the importance of the first interaction of acetylcaine with the anionic receptor site is found to be in the fixation of the local anesthetic at the receptor surface, due to the long-range character of this interaction. Furthermore, an increased polarity of the carbonyl group of acetylcaine due to this interaction may enhance the proposed second interaction with the receptor.

Anesthetics, Local↗
PubMed1985

Conformational analysis and active site modelling of angiotensin-converting enzyme inhibitors.

The discovery of captopril as a potent, orally active inhibitor of angiotensin-converting enzyme (ACE) led to the recent development of many series of novel structures with similar biological activity. To date, however, all of these inhibitors are flexible or semiflexible molecules, and there is therefore no clear definition of the conformational requirements for ACE inhibition. In an effort to solve this problem, we have carried out conformational energy calculations on a series of eight structurally diverse ACE inhibitors. Comparison of the low-energy conformations available to these molecules leads to the conclusion that there is a common low-energy conformation throughout the series. The calculations thus define the structural and conformational requirements for ACE inhibition. Expansion of this model to the receptor level has been achieved by considering possible alternative receptor sites for each of the molecules in its proposed biologically active conformation and leads to an active-site model for ACE which may be useful for the design of further inhibitors.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2005

Conformational analysis of ochratoxin a by NMR spectroscopy and computational molecular modeling.

Two-dimensional NMR spectroscopy has been used for a complete assignment of the proton and carbon-13 spectra of the metabolite from Aspergillus ochraceus, ochratoxin A. In addition, phase-sensitive nuclear Overhauser effect spectrometry experiments and computational molecular modeling (MM2 and MMFF force field programs) have been employed to examine the conformational properties of ochratoxin A in chloroform solutions. Particular attention has been given to intramolecular hydrogen-bonding formation involving the phenolic group on dihydroisocoumarin, which may be responsible for the toxic mechanism of ochratoxin A.

Magnetic Resonance Spectroscopy↗
PubMed1992

Conformational analysis of p53 in resting and concanavalin A-stimulated mouse lymphocytes.

We report that p53 in resting and concanavalin A-stimulated Balb/c mouse lymphocytes cannot be distinguished on the basis of different reactivity with various epitope-specific monoclonal antibodies, regardless of whether the lymphocytes are stimulated with concanavalin A in the presence or absence of serum. Our results thus question the 'conformational hypothesis' put forward by Milner [Milner, J. (1991). Curr. Op. Cell Biol., 3, 282-286], according to which wild-type p53, depending on its conformational status, can act as a negative or a positive growth regulator.

Animals↗
PubMed2002

NMR conformational analysis of antide, a potent antagonist of the gonadotropin releasing hormone.

Antide is a decapeptide [(N-Ac-D-Nal(1)-D-Cpa(2)-D-Pal(3)-Ser(4)-Lys(Nic)(5)-D-Lys(Nic)(6)-Leu(7)-Ilys(8)-Pro(9)-D-Ala(10)-NH(2)] that acts in vivo as an antagonist of GnRH (gonadotropin-releasing hormone). The conformational behavior of antide has been studied in water, TFE, DMF, and DMSO solutions by means of 2D-NMR spectroscopy and molecular dynamics calculations. Antide adopts in aqueous solution a delta-shaped backbone conformation, which is characterized by an irregular turn around residues D-Pal(3)-Ser(4) and by the close spatial proximity of the side chains belonging to D-Nal(1) and Ilys(8) (as many as 17 NOE peaks were detected between these side chains). The side-chain protons of Ilys(8) (especially the H(gamma) ones) present remarkably upfield shifted resonances, because of ring current effects induced by the naphthyl moiety. The upfield shifted resonances of the Ilys(8) H(gamma) hydrogen atoms are strictly characteristic of the water delta-shaped conformation and can be considered as structure markers. The observation of ring current shifted Ilys(8) H(gamma) resonances under different conditions (temperature, pH, solvent) indicates a remarkable stability of the water delta-shaped conformation. Such a conformation is at least partially disrupted in solvent mixtures containing high percentages of organic solvents. TFE can induce a well-defined conformation, which is characterized by an S-shaped backbone conformation. In DMF and DMSO solution, the molecule is basically endowed with a random coil conformation and high fluxionality. Antide fulfills the conformational requirements that are known to play a crucial role in receptor recognition, namely (i) the presence of a turn in the backbone and (ii) the all-trans nature of peptide bonds. In addition, the structural rigidity of antide likely adds a further contribution to the receptor binding affinity.

Dimethyl Sulfoxide↗
PubMed1983

Conformational analysis of a ribopentanucleoside tetraphosphate in aqueous solution. A two-dimensional NMR study at 500 MHz.

The 30 ribose proton resonances of the pentaribonucleoside tetraphosphate m6(2)AUm6(2)AUm6(2)A have been assigned unequivocally by means of spin-echo-correlated spectroscopy, 2D J-resolved spectroscopy and Nuclear Overhauser difference spectroscopy, carried out at 500 MHz. A detailed comparison of the conformational properties of the title compound with its constituent fragments m6(2)AUm6(2)AU, m6(2)AUm6(2)A, m6(2)AU and the relevant monomers is given. Chemical shift data indicate the existence of a doubly "bulged out" conformer, in which the two interior U-fragments are not involved in regular nearest neighbour stacking interactions. The coupling constants of the ribose-ring are interpreted in terms of the N/S equilibrium, and population distributions along the backbone angles beta and gamma are presented. The combined data suggest a strong similarity between the 5'-terminal triplets in m6(2)AUm6(2)AUm6(2)A, m6(2)AUm6(2)AU and m6(2)AUm6(2)A2.

Adenine↗
PubMed2004

1H and 13C NMR spectral assignments and conformational analysis of 14 19-nor-neoclerodane diterpenoids.

Unambiguous and complete assignments of 1H and 13C NMR chemical shifts for 14 19-nor-neoclerodane diterpenoids, nine of them isolated from natural sources and five other synthetic derivatives, are presented. The assignments are based on 2D shift-correlated (1H,1H-COSY, 1H,13C-gHSQC and 1H,13C-gHMBC) and NOE experiments. The conformations of rings A and B of these compounds are supported by the 3J(H,H) values and they agree with the low-energy conformations obtained by semi-empirical calculations. Moreover, the data obtained in this work for 2-acetoxyteucvidin and a semisynthetic 18-aldehyde derivative indicate that the configuration at C-2 of the former and at C-10 of the latter must be reversed with respect to those reported previously.

Benzofurans↗
PubMed2004

Synthesis, conformational analysis, and cytotoxicity of new analogues of the natural cyclodepsipeptide jaspamide.

Three analogues of the natural bioactive cyclodepsipeptide jaspamide (3-5) were efficiently synthesized using a combination of solid and solution phase techniques. The preliminary design of the molecules has involved the rational substitution and/or simplification of the most critical structural features of the lead compound. The synthetic products were subjected to pharmacological assays, and the conformational properties were investigated by MM (molecular mechanics) and MD (molecular dynamics) calculations, to describe the potential pharmacophoric core responsible for the observed activities.

Antineoplastic Agents↗
PubMedDate not supplied

Conformational analysis of neuropeptide Y segments by CD, NMR spectroscopy and restrained molecular dynamics.

Neuropeptide Y (NPY), a peptide amide comprising 36 residue has been shown to act as a potent vasoconstrictor. In order to shed light on the structural requirements for the biological activities with respect to the different prerequisites for affinity to the NPY receptor subtypes Y1 and Y2, in the present study the syntheses and conformational analyses of two C-terminal segments, NPY(18-36) and NPY(13-36), are described. The results obtained by CD measurements, two-dimensional NMR spectroscopy and a conformational refinement of the NMR-derived structure by molecular mechanics stimulations support the findings of previously published structure-activity relationship studies for biologically active and selective compounds. In particular, the alpha-helical conformation as well as an appropriate exposure of the side chains of the critical C-terminal dipeptide within NPY(18-36) are in agreement with the prerequisites proposed for Y2 receptor binding of that segment.

Amino Acid Sequence↗