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Spatial arrangement of 2-hydroxy-2',5'-diazachalcones was studied by means of infrared and NMR spectral data and molecular models calculations. The models were calculated in vacuum using semi-empirical AM1 method (software HyperChem 5.1). The initial geometries of the molecules were built by means of standard parameters and then optimized by Polak-Ribiere geometrical optimization. It was found that (E)-s-cis-conformers with synperiplanar arrangement of C-alpha and C-6 have the lowest heats of formation (standard heat of formation).
Full geometry optimizations were carried out at the HF/6-31G** and B3LYP/6-31G** levels for methylcyclohexane, 2-, 3-, and 4-methyltetrahydropyran, 2-, 3-, and 4-methylpiperidine, 2-, 3-, and 4-methylthiane, 2-, 4-, and 5-methyl-1,3-dioxane, and 2-, 4-, and 5-methyl-1,3-dithiane and also for S-methyl thianium. Constrained geometry optimizations were carried out for methylcyclohexane, 2-methyl-1,3-dioxane, and the axial conformers of 2- and 3-methyltetrahydropyran and 2- and 3-methylpiperidine. The steric repulsion model, which is believed to account for the conformational energies of the cited compounds, was tested by stretching bonds and bending angles so that the axial methyl group is either forced to approach the ring gamma methylenes or get farther away from them. The calculated energies show that the energy costs of these perturbations are not dependent on the distances between the axial methyl group and the ring gamma methylenes and are not dependent on whether the methyl is axial or equatorial. It is shown that, besides the steric repulsion model, the conformational energies of the compounds studied are dictated by hyperconjugative interactions involving mainly the methine hydrogen. The C[bond]C lengths of the axial and equatorial conformers of methylcyclohexane are shown to be related to hyperconjugation.
Irradiation of dTpdT with 300 kJ/m2 of 254 nm produces numerous photo-products, one of which labeled dT6pd4T[1] was purified by HPLC. dT6pd4T has a UV spectrum (H20, pH 7) with lambda max = 326 nm and lambda min = 265 nm, and a P-31 NMR resonance at -3.46 ppm (normal dTpdT occurs at -4.01 ppm; TMP, 30 degrees C). 2-D COSY NMR spectra facilitated proton resonance assignments and 2-D NOESY spectra aided analysis of spatial orientation. Carbon-13 and proton-coupled P-31 NMR spectra of dT6pd4T were also obtained. These analyses indicate: C5=C6 of dT6p- is saturated and the -pd4T base is more aromatic; the dT6p- base possesses a configuration of 5R, 6S; dT6p- and -pd4T have anti-type glycosidic conformations; furanose conformation of dT6p- is mainly C3'-endo and that of -pd4T exists in a C3'-endo in equilibrium C3'-exo; exocyclic bonds gamma (C5'-C4'), beta (05'-C5') and epsilon (C3'-03') are non-classical rotamers; dihedral angle about epsilon (C3'-03') is smaller relative to dTpdT.
A screened electrostatic potential model of hydration which could avoid the time consuming Monte-Carlo procedures is derived from the study of the dielectric effect of a water molecule in the vicinity of two charges. It is shown that the molecular dielectric constant depends on the distance, sizes and signs of the interacting charges. The model is used to evaluate the hydration energy of the tetrapeptide (TYR-GLY-GLY-PHE) conformations. Results are in good agreement with Monte-Carlo calculations.
Complete 1H and 13C NMR assignments, determined by one- and two-dimensional homo- and hetero-nuclear experiments, are reported for the antigenic capsular polysaccharide (CPS) from Streptococcus pneumoniae serotype 9N (S9 in American nomenclature). Distance constraints derived from 1D NOE difference experiments were combined with energy minimisation (simulated annealing) and molecular dynamics (MD) calculations to determine the most favoured conformation of S9 in aqueous solution at 70 degrees C. NOE values simulated for several static conformational models using the NOEMOL program did not correlate well with experimental values, whereas time averaged interproton distances calculated from 500 ps of restrained MD (using the Tropp formalism to account for rapid internal mobility) were in close agreement with experimentally derived distance estimates.
Some linear truncated analogs of endothelin-1 display potent agonistic activity at the ET(B) receptor, especially when the side chain of Trp21 is N-formylated. Then, the three-dimensional arrangements of six structurally reduced linear analogs, three formylated and three nonformylated, have been investigated by high resolution NMR spectroscopy and molecular modeling, in order to pinpoint the conformational features related to the biological activity. Two-dimensional double-quantum-filtered correlation spectroscopy (DQFCOSY), total correlation spectroscopy (TOCSY) and nuclear Overhauser enhancement spectroscopy (NOESY) were recorded and analyzed for each molecule. Interspatial distance constraints were derived from the intensity of the NOESY connectivities. The formation of hydrogen bonding was monitored from the temperature dependence of the NH chemical shifts. Molecular models calculated by means of distance geometry, simulated annealing and energy minimization, using the NMR constraints, strongly suggested a global elongated structure for the formylated analogs exhibiting biological activity, and a folded arrangement for the unformylated derivatives. Homology comparisons allowed the identification of a beta-turn-like folding of the C-terminal segment Asp18-Trp21 as a probable key-factor for activity.
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Solid state NMR sample preparation and resonance assignments of the U-[13C,15N] 2x10.4 kDa dimeric form of the regulatory protein Crh in microcrystalline, PEG precipitated form are presented. Intra- and interresidue correlations using dipolar polarization transfer methods led to nearly complete sequential assignments of the protein, and to 88% of all 15N, 13C chemical shifts. For several residues, the resonance assignments differ significantly from those reported for the monomeric form analyzed by solution state NMR. Dihedral angles obtained from a TALOS-based statistical analysis suggest that the microcrystalline arrangement of Crh must be similar to the domain-swapped dimeric structure of a single crystal form recently solved using X-ray crystallography. For a limited number of protein residues, a remarkable doubling of the observed NMR resonances is observed indicative of local static or dynamic conformational disorder. Our study reports resonance assignments for the largest protein investigated by solid state NMR so far and describes the conformational dimeric variant of Crh with previously unknown chemical shifts.
Bicyclonucleosides bearing a 5-deoxy-5-N-hydroxyamino-3,N5-(1,1-ethano)-beta-D-furanosyl sugar moiety (15-18) have been prepared by glycosidation of the corresponding bicyclosugars obtained via an intramolecular reverse Cope elimination. The configuration of the asymmetric carbon of the 1,1-ethano bridge is the most important factor directing the conformation of the N-hydroxypyrrolidine ring and its invertomers ratio as shown by variable temperature H NMR experiments.
A 500 MHz and 300 MHz NMR study of the trinucleoside diphosphate 3'd(A2'-5'A2'-5'A) is presented. In addition, circular dichroism is used to study base stacking in the title compound. The complete 1H-NMR spectral assignment of the sugar ring proton signals is given. Information about the sugar ring (N- or S-type conformation) and about the backbone geometry along C4'-C5' and C5'-O5' bonds is obtained from the NMR coupling constants. It is shown that the trimer mainly occurs in the N-N-N stacked state at low temperatures; the presence of a minor amount of N-N-S conformational sequence is indicated.
Magnetic resonance peaks have been assigned to individual protons of the constituent amino acids in the neurohypophyseal hormone, oxytocin, and in related peptides. The assignments were made possible by operation at 220 MHz with the use of variable temperature studies, proton homonuclear spin-decoupling, and comparison of spectra of oxytocin analogs. Some of the observed chemical shifts, and NH-CH(alpha) coupling constants were studied in relation to the conformation of the hormone.
One-dimensional transient NOE build-up curves were measured for the synthetic disaccharide alpha-D-Fuc-(1-->4)-beta-D-GlcNAc 1 utilizing Gaussian shaped pulses. Simulated build-up curves from Metropolis Monte Carlo simulations were compared to the experimental data. Disaccharide 1 is structurally related to methyl beta-D-maltoside in that it also contains an alpha-(1-->4) linkage, and it has the same configuration of groups around the glycosidic linkage. Analysis of NOEs in methyl beta-D-maltoside is restricted to those observed upon selective excitation of H1' because of severe spectral overlap. The situation is different in 1 where 1H-NMR signals are well separated. Several interglycosidic NOEs were observed. The corresponding build-up curves allowed an accurate determination of the conformational preferences at the glycosidic linkage in 1. Comparison of experimental and theoretical NOE build-up curves showed clearly that rigid minimum-energy models cannot account for the experimental data. The best fit of experimental NOE build-up curves was obtained with theoretical curves from a 2 x 10(6) step Metropolis Monte Carlo simulation with the temperature parameter set at 1000 K. Finally, it was observed that only the interglycosidic NOE H5'/H6-pro-S significantly depends upon varying conformation distributions at the alpha-(1-->4)-glycosidic linkage, induced by choosing different temperature parameters for the Metropolis Monte Carlo simulations.
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The asymmetric syntheses of heteroaromatic 3-[(tert-butyldimethylsilyl)oxy]-2-azetidinones 12-16 via chiral ester enolate-imine cyclocondensation chemistry are described. The azetidinones contain heteroaromatic moieties which, in certain cases, contribute to a decrease in enantioselectivity due to possible alternate coordinations in the transition states. The (3R,4S)-3-[(tert-butyldimethylsilyl)oxy]-4-heteroaryl-2-azetidinones were subsequently converted to the heteroaromatic taxanes 31-36 and 43-45. Conformational analyses of the 3'-(2-pyridyl) analogue 31 and 3'-(2-furyl) analogue 43 indicate they have solution conformational preferences virtually identical to paclitaxel and docetaxel. Heteroaromatic N-acyl paclitaxel analogues 47-51 were prepared from N-debenzoylpaclitaxel via Schotten-Baumann acylation. The majority of the 14 analogues displayed good to excellent activity in a microtubule assembly assay in comparison to paclitaxel. The analogues were also tested for cytotoxicity against B16 melanoma cells. 3'-Dephenyl-3'-(2-pyridyl)paclitaxel (31), 3'-dephenyl-3'-(2-furyl)paclitaxel (34), N-BOC-3'-dephenyl-3'-(2-furyl)paclitaxel (43), 3'-dephenyl-3'-(2-furyl)-N-(hexanoyl)paclitaxel (44), and N-debenzoyl-N-(3-furoyl)paclitaxel (51) were found to be more cytotoxic than paclitaxel against this cell line. 3'-Dephenyl-3'-(4-pyridyl)paclitaxel (33) and N-debenzoyl-N-(2-furoyl)paclitaxel (50) displayed cytotoxicity against B16 melanoma cells similar to paclitaxel.
Many microorganisms produce biologically important polysaccharides containing galactofuranosyl, arabinofuranosyl and/or fructofuranosyl residues. Recent interest in identifying antibiotics that act by inhibiting the biosynthesis of these glycans has resulted in the development of new and efficient methods for the assembly of oligosaccharides containing furanose residues. In general, it is now possible to synthesize any furanose-containing oligosaccharide with reasonable efficiency. In conjunction with these synthetic investigations, an increasing number of studies have probed the conformation of furanose rings, and a solid appreciation of the conformational preferences of key furanoside ring systems is now available.
A backbone bridged and disulfide bridged bicyclic somatostatin analogue, compound 1 (PTR-3205), was designed and synthesized by solid-phase methodology. The binding of compound 1 to the five different somatostatin receptors, expressed in CHO or COS-7 cells, indicate a high degree of selectivity towards hsstr2. The three-dimensional structure of this compound has been determined in DMSO-d(6) and in water by 1H NMR and by molecular dynamics simulations. Similar backbone conformations were observed in both solvents. We have established direct evidence that the backbone of this bicyclic somatostatin analogue assumes a 'folded' conformation in solution, where the lactam ring extends roughly in the plane of the beta-turn. The pharmacophoric region Phe-(D)-Trp-Lys-Thr of compound 1 is in accord with that of both the Veber compound L-363,301 (Merck) and sandostatin. We believe that the enhanced selectivity towards the hsst2 receptor, in comparison with other analogues, is due to its large hydrophobic region, composed of the lactam ring and the Phe side chains at positions 1 and 8.