A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

Summary The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: -mercapto-,-dimethyl)propionic acid (Dmp), (-mercapto-,-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (,-dimethyl--mercapto)propionic acid (-Dmp), forming analogs of strongly reduced biological activity, with the -mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of -turn at residues 3 and 4: 1/III, II, and I/III, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle C-S-S-C. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa¹]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa¹]-oxytocin. An analysis of the effect of -substitution on relative energies showed that the conformations with the N-C-CH₂-CH₂ (₁) and C-CH₂-CH₂-S (₁) angles of the first residue around (–100°, 60°) and (100°, –60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of -substitution the allowed values of ₁ are close to ± 60°. This requirement, being in contradiction to the one concerning -substitution, could explain the very low biological activity of the -substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and -substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both I/III and II types of backbone structure, while the second one is allowed only for the II type of backbone. No conformation of the I/III type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.     

Experimental and Theoretical Studies of Bromination of Diethyl 2,4,6‐Trimethyl‐1,4‐dihydropyridine‐3,5‐dicarboxylate

A reaction of diethyl 2,4,6‐trimethyl‐1,4‐dihydropyridine‐3,5‐dicarboxylate with 1, 2, and more equivalents of N‐bromosuccinimide (NBS) in methanol was investigated by NMR spectroscopy at a temperature interval ranging from 25 to 40°C. The reaction was found to proceed through several steps. The structures of the intermediates diethyl 3‐bromo‐2,4,6‐trimethyl‐3,4‐dihydropyridine‐3,5‐dicarboxylate, diethyl 3‐bromo‐2‐methoxy‐2,4,6‐trimethyl‐1,2,3,4‐tetrahydropyridine‐3,5‐dicarboxylate, and diethyl 3,5‐dibromo‐2‐methoxy‐2,4,6‐trimethyl‐2,3,4,5‐tetrahydropyridine‐3,5‐dicarboxylate were identified by multinuclear (¹H, ¹³C, and ¹⁵N) NMR spectral data. The optimal structures of all species participating in the reaction as well as changes in their relative energies along with the proposed pathway of the reaction were analyzed by quantum‐chemical calculations. The mechanism of bromination of diethyl 2,4,6‐trimethyl‐1,4‐dihydropyridine‐3,5‐dicarboxylate with NBS in methanol was found to favor the bromination in the 2,6‐methyl side chains as the only products in full agreement with experimental observations.     

Natural‐Antioxidant‐Inspired Benzo[b]selenophenes: Synthesis,Redox Properties,and Antiproliferative Activity

The cyclization of arylalkynes under selenobromination conditions, combined with an acid‐induced 3,2‐aryl shift, was elaborated as a general synthetic pathway for the preparation of polyhydroxy‐2‐ and ‐3‐arylbenzo[b]selenophenes from the same starting materials. The redox properties, free‐radical‐scavenging ability, and cytotoxicity against malignant cell lines (MCF‐7, MDA‐MB‐231, HepG2, and 4T1) of the synthesized compounds were explored, and the obtained results were used to consider the structure–activity relationships (SARs) in these compounds. Consequently, the structural features that were responsible for the highly potent peroxyl‐radical‐scavenging activity were established.     

Asymmetric Synthesis of 1,3-Diamines. II: Diastereoselective reduction of atropisomeric N-tert-butanesulfinylketimines

Chiral, nonracemic o-aminobenzylamines were prepared in a highly diastereoselective reduction of atropisomeric N-tert-butanesulfinylketimines. The ortho-substituent ensures the distinct reactivity of atropisomers 4d-f. The free energy of activation for atropisomerization of sulfinylimines 4d-f in THF-d(8) was determined by NMR methods to range from 70.8 to 97.9 kJ/mol.     

Serial Polarization Transfer by Combination of Cross-Relaxation and Rotational Resonance for Sensitivity-Enhanced Solid-State NMR

Methods which induce site-specificity and sensitivity enhancement in solid-state magic-angle spinning NMR spectroscopy become more important for structural biology due to the increasing size of molecules under investigation. Recently, several strategies have been developed to increase site specificity and thus reduce signal overlap. Under dynamic nuclear polarization (DNP) for NMR signal enhancement, it is possible to use cross-relaxation transfer induced by select dynamic groups within the molecules which is exploited by SCREAM-DNP (Specific Cross Relaxation Enhancement by Active Motions under DNP). Here, we present an approach where we additionally reintroduce the homonuclear dipolar coupling with rotational resonance (R²) during SCREAM-DNP to further boost the selectivity of the experiment. Detailed analysis of the polarization buildup dynamics of ¹³C-methyl polarization source and ¹³C-carbonyl target in 2-¹³C-ethyl 1-¹³C-acetate provides information about the sought-after and spurious transfer pathways. We show that dipolar-recoupled transfer rates greatly exceed the DNP buildup dynamics in our model system, indicating that significantly larger distances can be selectively and efficiently hyperpolarized.     

Intramolecular C-H···O hydrogen bonding in 1,4-dihydropyridine derivatives

The diastereotopy of the methylene protons at positions 2 and 6 in 1,4-dihydropiridine derivatives with various substituents has been investigated. NMR spectroscopy and quantum chemistry calculations show that the CH···O intramolecular hydrogen bond is one of the factors amplifying the chemical shift differences in the 1H-NMR spectra.     

15N NMR of 1,4‐dihydropyridine derivatives

In this article, we describe the characteristic ¹⁵N and ¹H_N NMR chemical shifts and ¹J(¹⁵N–¹H) coupling constants of various symmetrically and unsymmetrically substituted 1,4‐dihydropyridine derivatives. The NMR chemical shifts and coupling constants are discussed in terms of their relationship to structural features such as character and position of the substituent in heterocycle, N‐alkyl substitution, nitrogen lone pair delocalization within the conjugated system, and steric effects. Copyright © 2013 John Wiley & Sons, Ltd.     

Dynamics of protein and peptide hydration

Biological processes often involve the surfaces of proteins, where the structural and dynamic properties of the aqueous solvent are modified. Information about the dynamics of protein hydration can be obtained by measuring the magnetic relaxation dispersion (MRD) of the water (2)H and (17)O nuclei or by recording the nuclear Overhauser effect (NOE) between water and protein protons. Here, we use the MRD method to study the hydration of the cyclic peptide oxytocin and the globular protein BPTI in deeply supercooled solutions. The results provide a detailed characterization of water dynamics in the hydration layer at the surface of these biomolecules. More than 95% of the water molecules in contact with the biomolecular surface are found to be no more than two-fold motionally retarded as compared to bulk water. In contrast to small nonpolar molecules, the retardation factor for BPTI showed little or no temperature dependence, suggesting that the exposed nonpolar residues do not induce clathrate-like hydrophobic hydration structures. New NOE data for oxytocin and published NOE data for BPTI were analyzed, and a mutually consistent interpretation of MRD and NOE results was achieved with the aid of a new theory of intermolecular dipolar relaxation that accounts explicitly for the dynamic perturbation at the biomolecular surface. The analysis indicates that water-protein NOEs are dominated by long-range dipolar couplings to bulk water, unless the monitored protein proton is near a partly or fully buried hydration site where the water molecule has a long residence time.