Conformational Preferences In Solution Research Articles

Enantiodiscrimination of Inherently Chiral Thiacalixarenes by Residual Dipolar Couplings.

Inherently chiral compounds, such as calixarenes, are chiral due to a nonplanar three-dimensional (3D) structure. Determining their conformation is essential to understand their properties, with nuclear magnetic resonance (NMR) spectroscopy being one applicable method. Using alignment media to measure residual dipolar couplings (RDCs) to obtain structural information is advantageous when classical NMR parameters like the nuclear Overhauser effect (NOE) or J-couplings fail. Besides providing more accurate structural information, the alignment media can induce different orientations of enantiomers. In this study, we examined the ability of polyglutamates with different side-chain moieties─poly-γ-benzyl-l-glutamate (PBLG) and poly-γ-p-biphenylmethyl-l-glutamate (PBPMLG) ─to enantiodifferentiate the inherently chiral phenoxathiin-based thiacalix[4]arenes. Both media, in combination with two solvents, allowed for enantiodiscrimination, which was, to the best of our knowledge, proved for the first time on inherently chiral compounds. Moreover, using the experimental RDCs, we investigated the calix[4]arenes conformational preferences in solution, quantitatively analyzed the differences in the alignment of the enantiomers, and discussed the pitfalls of the use of the RDC analysis.

Synthesis and conformational analysis of N-aryl-N-(6-azulenyl)acetamides

We synthesized a series of N-(6-azulenyl)-N-arylacetamides, and investigated their conformational preferences in solution and in the crystalline state by means of NMR and X-ray analyses. The results indicated that the conformational preferences of these amides are dependent on both the relative π-electron densities of the N-aromatic parts and the three-dimensional relationship of the carbonyl group to the aryl groups. The N-(6-azulenyl) group has a very different effect from the previously reported N-(2-azulenyl) group on the conformational preferences of aromatic amides.

Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution.

Conformational control in peptoids, N-substituted glycines, is crucial for the design and synthesis of biologically-active compounds and atomically-defined nanomaterials. While there are a growing number of structural studies in solution, most have been performed with conformationally-constrained short sequences (e.g., sterically-hindered sidechains or macrocyclization). Thus, the inherent degree of heterogeneity of unconstrained peptoids in solution remains largely unstudied. Here, we explored the folding landscape of a series of simple peptoid tetramers in aqueous solution by NMR spectroscopy. By incorporating specific 13 C-probes into the backbone using bromoacetic acid-2-13 C as a submonomer, we developed a new technique for sequential backbone assignment of peptoids based on the 1,n-Adequate pulse sequence. Unexpectedly, two of the tetramers, containing an N-(2-aminoethyl)glycine residue (Nae), had preferred conformations. NMR and molecular dynamics studies on one of the tetramers showed that the preferred conformer (52%) had a trans-cis-trans configuration about the three amide bonds. Moreover, >80% of the ensemble contained a cis amide bond at the central amide. The backbone dihedral angles observed fall directly within the expected minima in the peptoid Ramachandran plot. Analysis of this compound against similar peptoid analogs suggests that the commonly used Nae monomer plays a key role in the stabilization of peptoid structure via a side-chain-to-main-chain interaction. This discovery may offer a simple, synthetically high-yielding approach to control peptoid structure, and suggests that peptoids have strong intrinsic conformational preferences in solution. These findings should facilitate the predictive design of folded peptoid structures, and accelerate application in areas ranging from drug discovery to biomimetic nanoscience.

Conformational Properties of Aromatic Oligoamides Bearing Pyrrole Rings.

N-Alkylbenzanilides generally exist in cis conformation both in the crystalline state and in various solvents, and this cis conformational preference can be utilized to construct dynamic helical oligoamides. Here, we synthesized the pyrrole-containing amides 2-5 and their oligomers 6-8 and examined their conformations in the crystalline state and in solution. All the N-methylated amides showed cis conformational preference in solution, but the ratio of the cis isomer was decreased when the amide bond was attached at the 4-position of the pyrrole ring, probably because the destabilization of the trans conformer due to electronic repulsion between the pyrrole π electrons and the amide carbonyl lone-pair electrons is reduced due to the small torsion angle between the 5-membered N-pyrrole and the amide bond. In the crystalline state, N-methylated amides showed cis structure, except for compound 5, and cis conformational preference was observed for the pyrrole amides. The CD spectra of oligoamides 15-18 bearing chiral N-substituents were consistent with the presence of dynamic and well-defined chiral foldamers, which were structurally distinct from N-alkylated poly( p-benzamide)s 1.

DFT calculations and NMR measurements applied to the conformational analysis of cis and trans-3-phenylaminocyclohexyl N,N-dimethylcarbamates

The three-dimensional structure of a potential drug molecule is of critical importance. Factors that determine its conformational stability and, consequently, corresponding biological/physicochemical properties of interest must therefore be carefully analyzed. Conformational properties and molecular structures of cis and trans-3-phenylaminocyclohexyl N,N-dimethylcarbamates were studied by low temperature 1H and 13C NMR spectroscopy and electronic structure calculations. B3LYP and M06-2X methods associated with the 6-311++G(2df,2p) basis set, and the integral-equation-formalism polarizable continuum model were used to study the conformational preferences in dichloromethane, acetone and methanol. NMR measurements indicated that for the cis isomer, the conformer with both substituents in equatorial position is the most stable, while for the trans isomer, the conformer with the carbamate group in the axial position and the arylamine in the equatorial position is favored in all solvents. B3LYP/6-311++G(2df,2p) theory level associated with IEF-PCM described properly the conformational preference in solution. NBO analyses were applied to determine the importance of hyperconjugative interactions in the conformational equilibrium.

Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study.

Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 μs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the μs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.

Correlation between Solid-State and Solution Conformational Ratios in a Series of N-(o-Tolyl)Succinimide Molecular Rotors

The syn-anti conformational equilibrium of a library of 30 N-(o-tolyl)succinimide molecular rotors was measured in solution via 1H NMR and in the solid-state via X-ray crystallography. A strong correlation was observed between the solution and solid-state mole fractions of syn-conformers (χsyn). All rotors, even those with a small conformational preference in solution (±0.15 kcal/mol), displayed the same conformation in their crystal structures. The conformational preferences in the crystals tended to be more pronounced with a predominance of all syn- or anti-structures. However, when the rotors had no conformational preference in solution, the conformational preferences in the crystal structures varied widely.

Structure and conformational dynamics of an aromatic sulfonamide: NMR, X-Ray and computational studies

Two conformational diastereoisomers due to the hindered Aryl-NSO 2 rotation were observed by NMR in the model compound N,N’-bis-tosyl-N,N’-dipropargyl-1,4-diamine-2,3-dimethyl benzene 1. X-Ray analysis showed that only the syn conformation is present in the solid state. The conformational preference in solution was evalu ated by DFT calculations and experimentally determined by low-temperature NMR experiments. It was found that the anti conformation is the more populated in low-polarity solvents whereas the syn is the favored one in polar solvents.

Complete analysis of the 1H and 13C NMR spectra of diastereomeric mixtures of (R,S‐ and S,S‐)‐3,6‐dimethoxy‐2,5‐dihydropyrazine‐substituted indoles and their conformational preference in solution

Complete analysis of the (1)H and (13)C NMR spectra obtained with and without a chemical shift reagent (Eu(fod)(3)), of bis-lactim ether 1 (Schöllkopf auxiliary) and monosubstituted 3- or 2-{(2R,5S or 2S,5S)-5-isopropyl-3,6-dimethoxy-2,5-dihydropyrazin-2-yl]methyl}-1H-indoles is presented using gradient-selected one-dimensional (1D) and two-dimensional NMR techniques, such as 1D TOCSY, 1D NOESY (DPFGSE NOE), gCOSY, NOESY, ROESY gHETCOR, gHSQC and gHMBC. The contour plot of the gCOSY spectrum of 1-10 revealed cross peaks arising from the five-bond coupling between the H2 and H5 resonances of the dihydropyrazine ring for syn- ((5)J(H2, H5) = 4-5.7 Hz) and for anti-isomers ((5)J(H2, H5) = 3.4-3.8 Hz). The magnitude of the coupling constant was utilized to distinguish between the syn- and the anti-isomers (diastereomers). The precise values of (n)J(HH) (n = 3, 4, 5, 6) coupling constants for the indole and 2,5-dihydropyrazine moieties deduced from the calculated NMR spectra were supported by 1D TOCSY and gCOSY experiments and gauge invariant atomic orbital (GIAO) calculations. The magnitude of the coupling constants ((5)J(H2, H5)) indicates that the dihydropyrazine ring exists in a boat conformation. In both isomers, the indole group adopts a 'folded' conformation in which one diastereotopic face is effectively shielded by the aromatic benzene ring of the indole. This is supported by gradient-selected 1D NOESY and 2D NOESY experiments. Theoretical calculations of the conformation were performed to support the through-space shielding effect of the aromatic indole moiety based on the DFT/GIAO calculated (1)H NMR data (chemical shifts and coupling constants) for 2-syn- and 2-anti-diastereomers in CDCl(3).

Conformational analysis of phorboxazole bis‐oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.

From the gas phase to aqueous solution: Vibrational spectroscopy, Raman optical activity and conformational structure of carbohydrates

Structural investigations of isolated and hydrated glucose, galactose and lactose structures in the gas phase based upon infra-red ion dip (IRID) spectroscopy conducted at low temperatures, are linked with parallel investigations conducted in aqueous solution at 298 K based upon measurements of their vibrational Raman and Raman optical activity (ROA) spectra. ‘Basis sets’ of computed (gas phase) Raman and ROA spectra associated with their low-lying conformational structures are used to construct ‘weighted sums’ which can approximate their experimental Raman and ROA spectra recorded in solution and provide estimates of their conformational population distributions in aqueous solution at 298 K; they are compared with estimates based upon analysis of NMR measurements and molecular mechanics and molecular dynamics calculations. The altered conformational preferences in the singly hydrated complexes of glucose and galactose isolated in the gas phase, appear to be sustained in aqueous solution, supporting the view that explicit hydration provides a key influence on their conformational preferences in solution. On the other hand, the conformational preference of the isolated β(1 → 4) disaccharide, lactose which resists conformational alteration when singly hydrated, is altered when it is transferred to aqueous solution at 298 K. The computational evidence suggests the control is exerted by entropic effects associated with a loosening of the structure around the glycosidic linkage.

Synthesis and Conformational Analysis of 6-C-Methyl-Substituted 2-Acetamido-2-deoxy-β-d-glucopyranosyl Mono- and Disaccharides

Several 6-C-substituted 2-acetamido-2-deoxy-beta-D-glucopyranosides (beta-D-GlcNAc monosaccharides 1a-3a and 1,4-linked disaccharides 1b-3b) were studied by solution NMR spectroscopy. Conformational analysis of the (6S)- and (6R)-C-methyl-substituted beta-d-GlcNAc monosaccharides indicates that the stereodefined methyl groups impose predictable conformational biases on the exocyclic C-5-C-6 bond, as determined by (1)H-(1)H and (13)C-(1)H coupling constants. Variable-temperature NMR experiments in methanol-d(4) were performed to determine DeltaDeltaH and DeltaDeltaS values derived from the two lowest energy conformers. These indicate that while the influence of 6-C-methyl substitution on conformational enthalpy is in accord with the classic principles of steric interactions, conformational preference in solution can also be strongly affected by other factors such as solvent-solute interactions and solvent reorganization.

Peptide analogs containing the pentacyclo[5,4,0,02,6,03,6,05,9]undecane scaffold: conformational analysis in solution

In order to evaluate the conformational preferences of depsipeptides attached to polycyclic compounds, we have investigated conformational preferences in solution by NMR spectroscopy and in the theoretical domain by dynamic simulation, semi-empirical and ab initio calculations. In CDCl 3 solution, the polycyclic scaffolds 8 and 10 displayed different types of turn conformation while compounds 9, 11, (±)- 12 and (±)- 13 displayed a well-defined turn structure, characterized, respectively, by a eight-membered hydrogen-bonded ring and by a γ-like strand hydrogen-bonded ring for each peptide chain. In a strong solvating medium such as DMSO-d6 the depsipeptide (±)- 12 adopts a γ-like strand hydrogen-bonded ring for one peptide chain and, for the other one, a bifurcated H-bond formed by a γ-like strand and a non-classical C5-structure. Theoretical calculations, supported by the experimental data, made it possible to identify these conformations and were of great importance in the discussion of the observed results.

Aminopyrazole Oligomers for β-SheetStabilization of Peptides

A general concept for the stabilization of β-sheets by designed artificial ligands is introduced. The ligands have two key features: they contain acylated 3-aminopyrazoles with a DAD hydrogen bond donor and acceptor pattern, and they were synthesized as oligomers in order to multiply their hydrogen bond interactions with peptides in the β-sheet conformation. Dimeric aminopyrazoles were accessible by reaction of the N1-Boc-protected aminopyrazole derivative 1 with several acid dichlorides followed by a standard deprotection procedure with trifluoroacetic acid. For the oligomers, Nl-PMB protection of new pyrazole amino acids followed by an iterative extension protocol with peptide coupling using PyClop or Mukaiyama's reagent led to the target compounds. All protecting groups were subsequently removed in a final deprotection step with warm trifluoroacetic acid. Two dimeric key compounds 3b and 3f were examined by NMR at various temperatures, in NOESY experiments as well as by X-ray crystallography in order to elucidate their conformational preference in solution and the solid state. The emerging picture was the same for all methods: both ligands adopt a flat conformation with a high degree of pre-orientation and the correct DAD pattern for optimal interaction with peptides in their extended conformation. Aggregation assays with the Prion protein and the Alzheimer's peptide Aβ (1-40) show highly promising results for some of the dimeric and oligomeric ligands at very low concentrations.

China: Chongqing YuGang — TiO 2

The activity of five glutamic acid analogues substituted in position 3 or 4 by a methyl (3T, 3E, 4T, and 4E) or a methylene group (4M) has been examined at one cloned Glu receptor subtype, MGluR1. These analogues interact with glutamate receptors of the central nervous system, especially the ligand 4T [(2S,4S)-4-methylglutamic acid] at the metabotropic glutamate receptor mGluR1. It was observed that only the 4T isomer is as potent an agonist as glutamic acid, whereas other isomers are less active. Furthermore, 4E [(2S,4R)-4-methylglutamic acid] exhibited an exceptional selectivity for the KA ionotropic receptor subtype while 4M [(2S)-4-methyleneglutamic acid] was active at the NMDA receptors. These molecules represent suitable tools among a population of similar glutamate analogues for a classical structure-function relationship study. We have undertaken a conformational analysis by 1H and 13C NMR spectroscopy and molecular modelling of these molecules. Hetero- and homonuclear coupling constants were measured in order to assign the diastereotopic methylene protons at C(3) or C(4), and used for comparison in molecular dynamics (MD) simulations. The hydrogen-bonding possibility, steric effects or electrostatic interactions may be a considerable influence in stabilizing a conformational population in D2O solution. The conformations may be grouped by the two backbone torsion angles, χ1 [α-CO−2-C(2)-C(3)-C(4)] and χ2 [+NC(2)-C(3)-C(4)-γCO−2] and by the two characteristic distances between the potentially active functional groups, αN???—γCO−2 (d2) and αCO−2—γCO−2 (d2). The conformational preferences in solution of 4T, 4E and (3T, 3E, 4M) are discussed in the light of the physical features known for a specific metabotropic agonist (ACPD) and specific ionotropic agonists (KA) and (NMDA), respectively.

Synthesis and conformational preferences in solution and crystalline states of an aza-tripeptide

The aza-tripeptide Boc-Ala-AzPip-Ala-NHiPr (AzPip: 2-aza pipecolyl residue) was synthesized in seven steps using preferentially the diisopropylcarbodiimide/1-hydroxy-7-aza-benzotriazole (DIPCDI/AtOH) coupling method and via the Boc-AzPip-OBzl pivotal intermediate. Its crystal molecular structure is characterized by the presence of a βVI-like turn around the N-terminal Ala-AzPip sequence and stabilized by two intramolecular hydrogen bonds sharing the same (Boc)CO carbonyl acceptor. In solution (chloroform, DMSO), two isomers are in equilibrium, one of them resembling the stereoisomer found in the crystal, the other being unfolded, but keeping the cis-isomerism of the Ala-AzPip bond and the pronounced degree of pyramidicity of the axial 2-amide Nα nitrogen atom.

Torsion angle based design of peptidomimetics: A dipeptidic template adopting β-I Turn (Ac-Aib-AzGly–NH 2)

We have attempted to design a model dipeptide (acetyl dipeptide amide, Ac-CA1-CA2–NH 2) that can adopt specifically typical torsion angles of the β-I turn (φ i+1 , ψ i+1 , φ i+2 , ψ i+2 =−60°, −30°, −90°, 0°). The key of the design is the combination of constrained amino acids that prefer to adopt the desired torsion angles. We chose Aib (aminoisobutyric acid) as the first residue of which φ and ψ angles must be −60° and −30°, respectively. Then, we selected an azaamino acid as the second residue since previous studies have indicated that they prefer to adopt ±90° of φ angle and 0° or 180° of ψ angle. The conformational preference of the resulting Ac-Aib-AzGly–NH 2 is investigated using ab initio methods. The conformations implying β-I and β-I′ turns are energetically most favorable, as we expected. Thus, we synthesized the designed molecule on the solid phase considering the future generation of combinatorial libraries using an automatic peptide synthesizer. Then, NMR spectroscopy was carried out to confirm their conformational preference in solution was carried out. The results indicated that the Ac-Aib-AzGly–NH 2 adopt β-I or β-I′ turns in solution forming an intramolecular hydrogen bonding between Ac–C(O) and terminal NH 2. We believe that such a small peptidomimetic template is highly useful for the design of drug candidates and molecular devices.

Human p8 Is a HMG-I/Y-like Protein with DNA Binding Activity Enhanced by Phosphorylation

We have studied the biochemical features, the conformational preferences in solution, and the DNA binding properties of human p8 (hp8), a nucleoprotein whose expression is affected during acute pancreatitis. Biochemical studies show that hp8 has properties of the high mobility group proteins, HMG-I/Y. Structural studies have been carried out by using circular dichroism (near- and far-ultraviolet), Fourier transform infrared, and NMR spectroscopies. All the biophysical probes indicate that hp8 is monomeric (up to 1 mm concentration) and partially unfolded in solution. The protein seems to bind DNA weakly, as shown by electrophoretic gel shift studies. On the other hand, hp8 is a substrate for protein kinase A (PKA). The phosphorylated hp8 (PKAhp8) has a higher content of secondary structure than the nonphosphorylated protein, as concluded by Fourier transform infrared studies. PKAhp8 binds DNA strongly, as shown by the changes in circular dichroism spectra, and gel shift analysis. Thus, although there is not a high sequence homology with HMG-I/Y proteins, hp8 can be considered as a HMG-I/Y-like protein.

Configurational1H NMR study of optically active 7-(1-phenylethyl)-2-oxa-7-azabicyclo[3.2.0]heptan-6-one derivatives using Pirkle’s alcohols and a chiral shift reagent

Four novel stereoisomers of 7-(1-phenylethyl)-2-oxa-7-azabicyclo[3.2.0]heptan-6-one were prepared under high pressure from [2+2] cycloaddition of the pure enantiomers of 1-phenylethyl isocyanate and 2,3-dihydrofuran. Their conformational preferences in solution and the absolute configurations of the bridgehead carbon atoms were unambiguously determined by 1H NMR spectroscopy using tris[3-(2,2,2-trifluoro-1-hydroxyethylidene)-d-camphorato]europium(III) and (R)- or (S)-1-(9-anthryl)-2,2,2-trifluoroethanol (Pirkle’s alcohols). MM2 single-point energy calculations were consistent with the experimentally determined stereochemistry. ©1998 John Wiley & Sons, Ltd.

Conformational Preferences of a Peptide Corresponding to the Major Antigenic Determinant of Foot-and- Mouth Disease Virus: Implications for Peptide-Vaccine Approaches

The conformational preferences in solution of a peptide corresponding to the GH loop of the VP1 capsid protein from the foot-and-mouth disease virus were examined by proton nuclear magnetic resonance and circular dichroism. The GH loop is the major antigenic determinant of the virus and participates in cell attachment through an integrin-like Arg-Gly-Asp sequence. The synthetic peptide, corresponding to residues Gly132 to Ser162 of the VP1 capsid protein of the serotype O, is largely disordered in aqueous solution as shown by the absence of long- and medium-range NOE contacts and by random-like chemical shifts values. Helical contents in aqueous solution were estimated to be less than 10%, as determined by extrapolation of trifluoroethanol titration from CD measurements, in good agreement with estimations from NMR experiments. In the presence of 40% trifluoroethanol an α-helix, flanked by two proline residues between Asn12 (Asn143 in the intact protein) and Leu28 (159), is induced. This contrasts with the 310helix observed between residues Leu148 and Val155 in the crystal structure of the dithiothreitol-reduced virus, indicating that the cosolvent does not stabilize a residual, low-populated structure, similar to that in the intact virus. Several algorithms also fail to predict the structure found in the intact virus because these are based mainly on local sequence information. The lack of structure of the peptide in aqueous solution strongly suggests that the conformational determinants sufficient for the structure stabilization of this highly immunogenic antigen are mostly dictated by interactions of the loop with other regions of the virus structure, and do not arise from local amino acid sequence information. The ability of designed GH-VP1 peptides to neutralize anti-virus antibodies is likely to arise from antibody-induced conformation of the peptide and its application as peptide vaccines is not straightforward. Similarly, insertion of these peptides in carriers or macromolecular assemblies as vaccine vectors would depend on the conformation adopted at the insertion site and its success cannot be predicted.