Conformational Studies Research Articles

Conformational studies and molecular characterization of the polysaccharide kefiran

Kefiran was produced from kefir grains, on a semi-industrial scale, using UHT skimmed milk as a raw material. The conformational characteristics of the polysaccharide were assessed by means of a series of techniques such as capillary viscometry, size-exclusion chromatography coupled to multi-angle laser light scattering, static light scattering, dynamic light scattering and zeta-potential measurements. The results indicated that kefiran behaved as a weakly charged polysaccharide with a having, possibly, a random coil conformation in aqueous solution. The weight average molecular weight was 6.71 × 105 Da, whereas the mean square radius of gyration was 43.2 nm. The effect of a series of solutes in various concentrations such as salts, organic acids, KOH, sugars, urea, ethanol, Na-caseinate and whey protein concentrates on the flow behavior of kefiran in aqueous dilute solutions was assessed by hydrodynamic, zeta potential and dynamic light scattering measurements. The results are discussed in the light of conformational changes observed.

The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study.

In the current study, we focused on the immune-checkpoints PD-1 pathway and in particular on the ligand PD-L1. We studied the conformational dynamics of PD-L1 through principal component analysis of existing crystal structures combined with classical and accelerated molecular dynamics simulations. We identified the maximum structural displacements that take place in all PD-L1 crystal structures and in the molecular dynamics trajectories. We found that these displacements are attributed to specific flexible regions in the protein. We also investigated the conformational preference for small molecule binding and highlighted a methionine residue at the binding site, which plays a key role in drug binding. The binding mechanism of PD-L1 to other binding partners is also discussed in detail from a computational perspective. We hope that the data presented here support the ongoing efforts to discover effective therapies targeting the PD-1 immune-checkpoint pathway.

Synthesis and structure elucidation of allyl Pd(II) complexes of NHC ligands derived from substituted imidazo[1,5-a]quinolin-1(2H)-ylidene

Nine Pd(II) complexes involving N-heterocyclic carbenes (NHCs) derived from 2-substituted and 2- and 7-substituted imidazo[1,5-a]quinolin-1(2H)-ylidene with auxiliary allylic ligands were synthesized and characterized. The structure and configuration of the complexes were elucidated on the basis of combination of dynamic NMR and DFT studies. Conformational studies in respect of hindered rotation around Pd-C bond and η3-η1-η3 pseudo allyl rotation were performed. The results from dynamic NMR and DFT studies confirmed the mechanism of selective η3-η1-η3 isomerization, whose energy barriers are affected by steric hindrance of substituents at nitrogen atom. Energy barriers of isomerization (16.7–18.8 kcal/mol) are slightly influenced by the electronic nature of substituents at seventh position in imidazo[1,5-a]quinolin-1(2H)-ylidene moiety. The results from DFT calculations were in good agreement with the experimental energy barriers.

Self-Organization Ability of Chiral Nα-Substituted, Nβ-Boc Protected α-Hydrazinoacetamides in the Crystal and Solution States.

The limitations of peptides have severely hampered their use in pharmacology, thus prompting the design of new peptidomimetic foldamers. This requires precise knowledge of the secondary structure of new compounds and the ability to predict their folding. Conformational studies of the basic units of these foldamers can be of invaluable assistance in designing new bioactive compounds. To this end, we investigated the conformation of three chiral Nα-substituted, Nβ-Boc protected α-hydrazinoacetamide model compounds containing various side chains both on the Nα- and Cα-atoms in both the crystal and solution states. On the basis of IR absorption spectroscopy, NMR, molecular dynamics calculations and X-ray diffraction experiments, we demonstrated that these three models adopt conformational preferences, relying on eight-, six- or five-membered H-bonded pseudocycles (C8, C6 or C5), depending on the steric bulk of both Nα- or Cα-side chains. This study sheds light onto the versatile folding ability of the specific class of α-Nα-hydrazinopeptides and emphasizes the key role of the Cα-side chain on the conformational preference of the folding.

Spectroscopic and theoretical studies of some 2-(2′-haloacetyl)-5-substituted: 1-Methylpyrrole, furan and thiophene

The conformational study of some 2-(2′-haloacetyl)-5-substituted five-membered heteroaromatic compounds Z-CH2C(O)(C4H2X)Y bearing a halogen (Z = Cl or Br) at the 2′-position and (Y = NO2, H, Me or Cl) substituents at the 5-position of the heteroaromatic ring for X = NMe, O and S was performed by IR carbonyl stretching band (νCO) analysis supported by the harmonic frequency, NBO and PCM calculations on the minima and saddle-point structures obtained at the M05-2X/aug-cc-pVTZ level. The computational results predicted the presence of four stable conformers, classified by the orientation of the Xring–CCO (syn/anti) and the OCC–Z (anticlinal/ synperiplanar) moieties as ac(syn), sp(syn), ac(anti) and sp(anti). The anti/syn equilibrium controls the relative stabilities of the conformers to a large extent while the anticlinal/synperiplanar accounts for the observed trend of the IR carbonyl band components. The computed νCO frequencies and the PCM trend of the relative abundance in solvents of increasing permittivity allowed the pairs of ac(syn)/ac(anti) and sp(syn)/sp(anti) conformers to be assigned to the lower and higher νCO frequency IR carbonyl doublet components, respectively. The PCM data failed to reproduce the experimental carbonyl triplet found in chloroform. However, the additional component could be justified by assuming the formation of complexes constituted by one chloroform molecule hydrogen bonded to the conformers in a PCM chloroform continuum.The NBO and short contact analysis suggested that the syn/anti conformational equilibrium is governed mainly by electrostatic interactions, while the anticlinal/synperiplanar depends to different extents on both orbital and electrostatic interactions.

Quantum chemical properties investigation and molecular docking analysis with DNA topoisomerase II of β-carboline indole alkaloids from Simaba guianensis: a combined experimental and theoretical DFT study

A theoretical and experimental DFT study of the vibrational, structural, and quantum properties of 9-methoxy-canthin-6-one (I) and 7-methoxy-(9H-β-carbolin-1-il)-(Z)-prop-2-enoic acid (II) alkaloids is presented using B3LYP exchange-correlation functional with 6-311G(2d,p) basis set. The theoretical geometry optimization data of both structures were compared with the X-ray data for a similar structure in the associated literature and a conformational study is presented for (II), providing a good comprehension of its conformers’ stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap, mapped molecular electrostatic potential surface (MEPS) calculations, and first- and second-order hyperpolarizabilities were also performed at the same calculation level. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. Calculated HOMO/LUMO energy gaps revealed the excitation energy of the structures, justifying their stability and kinetics reaction. IR studies showed that for structure II the intramolecular hydrogen bond of the conformations and the intermolecular hydrogen bonds of the dimeric form influence the results and also revealed several characteristic vibrations for both structures. Molecular docking studies with DNA topoisomerase II-DNA complex showed binding free energies of − 8.4 and − 9.6 kcal/mol for II and I, respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of − 9.9 kcal/mol, showing a good binding affinity of alkaloid I.

Self-Assembling Silk-Based Nanofibers with Hierarchical Structures.

Self-assembling fibrous supramolecular assemblies with sophisticated hierarchical structures at the mesoscale are of interest from both fundamental and applied engineering. In this paper, the relatively hydrophilic domains of silk fibroin (HSF) were extracted and used in studies of self-assembly. The HSF fraction spontaneously self-assembled into nanofibers, 10 to 100 μm long and 50 to 250 nm in diameter, within 2 to 8 h in aqueous conditions. Interestingly, these HSF nanofibers consisted of dozens of nanofibrils arranged in a parallel organization with assembled diameters of ∼30 nm, similar to the sophisticated hierarchical structure observed in native silk fibers. Dynamic morphology and conformation studies were carried out to determine the mechanisms underlying the HSF self-assembly process at both the nanoscale and mesoscale. The HSF self-assembled into nanofibers in a bottom-to-up manner, from "sticky" colloid particles to cylindrical globules, to form nanofibrous networks. Because of the enhanced HSF self-assembling kinetics and the hierarchical structure of HSF nanofibers, this hydrophilicity-driven approach provides further insight into silk fibroin (SF) self-assembly in vivo and also offers new tools for the recapitulation of high-performance materials for engineering applications.

A 1,2‐trans‐Selective Glycosyl Donor Bearing Cyclic Protection at the C‐2 and C‐3 Hydroxy Groups

A new 1,2‐trans‐selective glycosylation reaction is described. Glucosyl donors protected cyclically at the C‐2 and C‐3 hydroxy groups as six‐ (butane diacetal), seven‐ (tetraisopropyldisiloxanylidene), or eight‐ (2,3‐o‐xylylene) membered fused rings were synthesized in a straightforward manner. The glycosylation reactions of the glucosyl donors with various acceptors mainly generated β‐glycosides under conventional reaction conditions. The results show that the o‐xylylene group is a suitable 1,2‐trans‐directing group from the points of view of stereoselectivity and chemical stability. A conformational study of the oxocarbenium ion of an o‐xylylene‐protected glucose derivative by NMR spectroscopy and computational simulation was carried out. The results imply that the oxocarbenium ion mainly adopts a 4H3 conformation owing to the rigid trans‐fused ring at C‐2 and C‐3, while a noncyclically protected derivative might fluctuate between conformations. These results suggest that an eclipsing interaction between the pseudoequatorial xyloxy group at C‐2 and the incoming nucleophile hampers 1,2‐cis attack.

Hemin is able to disaggregate lysozyme amyloid fibrils into monomers

Lysozyme amyloidosis (ALys) is a disease of the gastrointestinal tract, liver and kidneys, which is caused by the accumulation of insoluble fibrils of lysozyme in the tissues of above organs. The ALys can be cured by disintegration and clearance of the fibrils from the affected tissues and organs. It is thought that protein fibrils are extremely stable. Consequently, small molecule-induced dissociation of fibrils under physiological conditions is really challenging. Here, we report kinetic and thermodynamic analyses of hemin-induced dissociation of hen egg white lysozyme amyloid fibrils. We examined the effect of hemin on the kinetics of dissociation of lysozyme fibrils. We observed that the hemin binding dissociates fibrils in a concentration dependent manner within a reasonable time. Studies of structural, morphological properties and gel filtration chromatography indicate that fibrils dissociate mainly into monomeric species. The conformational, hydrodynamic, unfolding and stability studies of the resolubilized proteins show that dissociated monomers possess characteristics of partially folded intermediate state of the protein. We also find that hemin-induced fibril dissociation mainly depends on the kinetic and thermodynamic stability of the fibrils. These results suggest that non-toxic derivatives of hemin and other porphyrins could pave a way for therapeutic intervention in amyloidosis and related pathologies.

Two-state model for nematic liquid crystals made of bent-core molecules.

Nematic (N) liquid crystals made of bent-core molecules exhibit unusual physical properties such as an intermediate phase between the N and isotropic (I) phases, a very weak NI transition as inferred from magnetic birefringence measurements in a low field, which is apparently incompatible with a large shift in the NI transition temperature (T_{ni}) measured under a high field. Using our conformational studies on the aromatic cores, we propose that only conformers which are more straightened than those in the ground state (GS) form clusters with a few layers, which persist even in the isotropic phase, as inferred from x-ray and rheological experiments. We present a Landau-de Gennes theory of the medium, including an orientational coupling between the clusters and the GS molecules, which accounts for all the unusual properties. The intermediate phase to isotropic transition is predicted to exhibit critical behavior at a very low magnetic field of <1kG.

Thermochemical and conformational study of optical active phenylbenzazole derivatives

The energetic study of 2-phenylbenzoxazole (PBO), 2-phenylbenzothiazole (PBT), 2-(2-hydroxyphenyl)benzoxazole (HBO) and 2-(2-hydroxyphenyl)benzothiazole (HBT) has been developed either using experimental techniques or computational calculations. The enthalpies of combustion and of sublimation of these compounds were determined and the gas-phase standard molar enthalpies of formation were derived. The experimental techniques used were static or rotating bomb combustion calorimetry, high temperature Calvet microcalorimetry and/or the Knudsen-effusion method. Additionally, we have obtained the gas-phase standard molar enthalpies of formation of these compounds, as well of 2-(2-hydroxyphenyl)benzimidazole (HBI), through high level ab initio calculations, at the G3(MP2)//B3LYP level. The computational study of the molecular structures of all these compounds has been carried out and four possible conformers were observed for the molecules of each compound, where the keto tautomers have always higher energy than the enol forms. Furthermore, the energetic effects associated to the presence of the hydroxyl group on the core of the 2-phenylbenzazole rings, in particular the hydrogen bond network, were also evaluated.

Antimicrobial activity of leucine-substituted decoralin analogs with lower hemolytic activity.

Linear cationic α-helical antimicrobial peptides are promising chemotherapeutics. Most of them act by different mechanisms, making it difficult to microorganisms acquiring resistance. Decoralin is an example of antimicrobial peptide; it was described by Konno et al. and presented activity against microorganisms, but with pronounced hemolytic activity. We synthesized leucine-substituted decoralin analogs designed based on important physicochemical properties, which depend on the maintenance of the amphiphilic α-helical tendency of the native molecule. Peptides were synthesized, purified, and characterized, and the conformational studies were performed. The results indicated that the analogs presented both higher therapeutic indexes, but with antagonistic behavior. While [Leu]10 -Dec-NH2 analog showed similar activity against different microorganisms (c.a. 0.4-0.8μmolL-1 ), helical structuration, and some hemolytic activity, [Leu]8 -Dec-NH2 analog did not tend to helical structure and presented antimicrobial activities two orders higher than the other two peptides analyzed. On the other hand, this analog showed to be the less hemolytic (MHC value=50.0μmolL-1 ). This approach provided insight for understanding the effects of the leucine substitution in the amphiphilic balance. They led to changes on the conformational tendency, which showed to be important for the mechanism of action and affecting antimicrobial and hemolytic activities. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Synthesis, conformational study and antiviral activity of l-like neplanocin derivatives

The l-like enantiomer of 9-(trans-2′, trans-3′-dihydroxycyclopent-4′-enyl)-3-deazaadenine (DHCDA) (1), its 3-deaza-3-bromo derivative (3), and the conformational restricted methanocarba (MC) nucleoside analogues (2 and 4) were synthesized. X-ray crystal structures showed the L isomer MC analogue 4 adopts a similar North-like locked conformation as conventional D-MC nucleosides, while the DHCDA analogue 3 preferred south-like conformer. Compounds 1 and 4 showed potent antiviral activity against norovirus, while compound 2 and 3 were less potent or inactive. The conformational behavior of “sugar” puckering (north/south) and nucleobase orientation (syn /anti) may contribute to the antiviral activity differences. For compound 3, antiviral activity was also found against Ebola virus.

Structural Insights into Selective Ligand-Receptor Interactions Leading to Receptor Inactivation Utilizing Selective Melanocortin 3 Receptor Antagonists.

Systematic N-methylated derivatives of the melanocortin receptor ligand, SHU9119, lead to multiple binding and functional selectivity toward melanocortin receptors. However, the relationship between N-methylation-induced conformational changes in the peptide backbone and side chains and melanocortin receptor selectivity is still unknown. We conducted comprehensive conformational studies in solution of two selective antagonists of the third isoform of the melanocortin receptor (hMC3R), namely, Ac-Nle-c[Asp-NMe-His6-d-Nal(2')7-NMe-Arg8-Trp9-Lys]-NH2 (15) and Ac-Nle-c[Asp-His6-d-Nal(2')7-NMe-Arg8-NMe-Trp9-NMe-Lys]-NH2 (17). It is known that the pharmacophore (His6-DNal7-Arg8-Trp9) of the SHU-9119 peptides occupies a β II-turn-like region with the turn centered about DNal7-Arg8. The analogues with hMC3R selectivity showed distinct differences in the spatial arrangement of the Trp9 side chains. In addition to our NMR studies, we also carried out molecular-level interaction studies of these two peptides at the homology model of hMC3R. Earlier chimeric human melanocortin 3 receptor studies revealed insights regarding the binding and functional sites of hMC3R selectivity. Upon docking of peptides 15 and 17 to the binding pocket of hMC3R, it was revealed that Arg8 and Trp9 side chains are involved in a majority of the interactions with the receptor. While Arg8 forms polar contacts with D154 and D158 of hMC3R, Trp9 utilizes π-π stacking interactions with F295 and F298, located on the transmembrane domain of hMC3R. It is hypothesized that as the frequency of Trp9-hMC3R interactions decrease, antagonistic activity increases. The absence of any interactions of the N-methyl groups with hMC3R suggests that their primary function is to modulate backbone conformations of the ligands.

Experimental and Theoretical Study for the Assessment of the Conformational Analysis of Pyrazolone Derivatives: Employing Quantitative Analysis for Intermolecular Interactions

AbstractSynthesis of four new flexible pyrazolone derivatives have been carried out for conformational studies. The conformational studies have been done with X‐ray crystallography in solid state and theoretical calculation in gaseous state. The solid state study has revealed that substituted pyrazole moiety linked with pthalimido moiety via oxaethylene linker i. e. compounds 5 and 6 have shown folded conformation while increasing one methylene more in compound 7 has shown open conformation. However, theoretical calculation revealed that all compound stable in folded conformation. The quantitative analyses for intermolecular interaction of all compounds have been carried out by Hirshfeld surface analysis and Pixel calculations.

Decoration of Chondroitin Polysaccharide with Threonine: Synthesis, Conformational Study, and Ice-Recrystallization Inhibition Activity.

Several threonine (Thr)- and alanine (Ala)-rich antifreeze glycoproteins (AFGPs) and polysaccharides act in nature as ice recrystallization inhibitors. Among them, the Thr-decorated capsular polysaccharide (CPS) from the cold-adapted Colwellia psychrerythraea 34H bacterium was recently investigated for its cryoprotectant activity. A semisynthetic mimic thereof was here prepared from microbial sourced chondroitin through a four-step strategy, involving a partial protection of the chondroitin polysaccharide as a key step for gaining an unprecedented quantitative amidation of its glucuronic acid units. In-depth NMR and computational analysis suggested a fairly linear conformation for the semisynthetic polysaccharide, for which the antifreeze activity by a quantitative ice recrystallization inhibition assay was measured. We compared the structure-activity relationships for the Thr-derivatized chondroitin and the natural Thr-decorated CPS from C. psychrerythraea.

The optical properties of the silver clusters and their applications in the conformational studies of human telomeric DNA

In this study, we investigated the optical properties of the silver nanoclusters (AgNCs) labeled on the 22 bases human telomeric DNA sequences (d[AG3(T2AG3)3], Hum 22AG). The steady state spectra indicate that the formation of the G-quadruplex structure will quench the fluorescence of the AgNCs. In contrast to the AgNCs labeled on the Hum 22AG, the absorption and emission spectra of the AgNCs labeled on the duplex structure are shifted due to the change of local environment and the cluster-base interactions. Moreover, the AgNCs also represent slower spectral relaxation dynamics in the duplex structure, and the result is associated with the stronger hydrogen bond networking and the higher structural rigidity of the duplex. By comparing fluorescence anisotropy dynamics of the Hum 22AG probed by different fluorescence probes, we found that labelling the AgNCs on the DNA would suppress the wobbling motion of the chromophore. The fluorescence anisotropy study also showed an increase in the structural rigidity of the duplex structure.

Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko (1988) provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially proximate have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko (1985) to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7A, and dihedral angles approximately 90° are most common”.

X-ray crystal structure and conformational flexibility study of a N-substituted 2,6-diphenylpiperidine derivative

Piperidine is one of the basic skeletons in many of pharmacological active compounds derived from natural or synthetic medicaments. Substitution of various groups in the piperidine ring regulates conformational flexibility due to the nature of the substituent on the nitrogen atom. One of the N-substituted piperidine derivatives, PMDPM, phenyl(3-methyl-2,6-diphenylpiperidin-1-yl)methanone, was crystallized and analysed by X-ray crystallography. The crystallographic data are: C23H25NO, M = 355.46, triclinic, space group P1, a = 8.2543(7), b = 10.5543(8), c = 12.6184(6) A, α = 77.901(7), β = 71.270(2)°, γ = 70.390(5)°; V = 974.3(1) A3, Z = 2, d cal = 1.212 Mg/m3, λ(MoK α) = 0.71073 A. The core piperidine ring of PMDPM shows a positional disorder and adopts dual conformations as chair and twisted boat. The phenyl rings are oriented axially to the piperidine ring with the dihedral angle of 22.0(1)° between them. The packing is stabilized by C–H⋯O intra molecular interactions including few C–H⋯π and π⋯π weak interactions.

Human DMBT1-Derived Cell-Penetrating Peptides for Intracellular siRNA Delivery.

Small interfering RNA (siRNA) is a promising molecule for gene therapy, but its therapeutic administration remains problematic. Among the recently proposed vectors, cell-penetrating peptides show great promise in in vivo trials for siRNA delivery. Human protein DMBT1 (deleted in malignant brain tumor 1) is a pattern recognition molecule that interacts with polyanions and recognizes and aggregates bacteria. Taking advantage of these properties, we investigated whether specific synthetic DMBT1-derived peptides could be used to formulate nanoparticles for siRNA administration. Using an electrophoretic mobility shift assay and UV spectra, we identified two DMBT1 peptides that could encapsulate the siRNA with a self- and co-assembly mechanism. The complexes were stable for at least 2 hr in the presence of either fetal bovine serum (FBS) or RNase A, with peptide-dependent time span protection. ζ-potential, circular dichroism, dynamic light scattering, and transmission electron microscopy revealed negatively charged nanoparticles with an average diameter of 10–800 nm, depending on the reaction conditions, and a spherical or rice-shaped morphology, depending on the peptide and β-helix conformation. We successfully transfected human MCF7 cells with fluorescein isothiocyanate (FITC)-DMBT1-peptide-Cy3-siRNA complexes. Finally, DMBT1 peptides encapsulating an siRNA targeting a fluorescent reporter gene showed efficient gene silencing in MCF7-recombinant cells. These results lay the foundation for a new research line to exploit DMBT1-peptide nanocomplexes for therapeutic siRNA delivery.