The effect of the cyclopropyl group on the conformation of chemotactic formyl tripeptides

Certain formyl peptides are powerful chemoattractants towards neutrophils. In this study, several formyl tripeptides were synthesized and used to investigate the effects of different amino acid residues in position 1 on their ability to stimulate neutrophil chemotaxis. Pig neutrophil chemotaxis towards the formyl tripeptide, HCO-Ac(3)C-Leu-Phe-OMe 1, where Ac(3)C represents 1-amino-1-cyclopropane carboxylic acid, was observed. Pig neutrophil chemotaxis towards a very similar formyl tripeptide, HCO-Aib-Leu-Phe-OMe 2, where Aib represents alpha-amino isobutyric acid, was not observed. Compared to the isopropyl group, it was shown that the cyclopropyl group induces a greater percentage of the E conformation about the formamide functionality in these peptides. For 1 and 2, the E isomer distributions in CDCl3 are 36 and 9%, respectively. Since a major difference between these two peptides is the Z/E isomeric distribution, one implication is that the peptide-receptor site interactions involving the E conformer are more effective than those of the Z conformer. No pig neutrophil chemotaxis towards the formyl tripeptides, HCO-Ala-Leu-Phe-OMe 3 and HCO-Gly-Leu-Phe-OMe 4 was observed. These formyl tripeptides exhibit a low percentage of the E isomer, similar to that of peptide 2.     

Ab initio conformational maps for disaccharides in gas phase and aqueous solution

Ab initio conformational maps for beta-lactose in both the gas phase and in aqueous solution have been constructed at the HF/6-31G(d,p) level of calculation. The results of the gas-phase ab initio calculations allow us to conclude that a rigid conformational map is able to predict the regions of the minima in the potential energy surface of beta-lactose, in full agreement with those found in the relaxed conformational map. The solvation effects do not give rise to any new local minimum in the potential energy surface of beta-lactose, but just change the relative Boltzmann populations of the conformers found in the gas-phase calculations. The values obtained for heteronuclear spin coupling constant (3J(H,C)), using the seven most stable conformers in solution are in good agreement with the available experimental values. This is a good indication that ab initio rigid conformational maps can be reliably used to sort the most stable conformers of beta-lactose.     

Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior

The structure of a previously calculated transition state (TS) was used to design the [tetrahydro-2-(methylthio)furan-2-yl]methyl phosphate dianion (1) as a new scaffold for transition-state analogs of reactions catalyzed by the inverting glycosyltransferases. This scaffold contains relevant features of the donor and acceptor and represents a new type of potential inhibitors for these enzymes. Available conformational space of 1 was explored using DFT quantum chemical methods by means of two-dimensional potential-energy maps calculated as a function of Phi, Psi, and omega dihedral angles at the B3LYP/6-31+G* level. The calculated potential energy surfaces revealed the existence of several low-energy domains. Structures from these regions were refined at the 6-311++G** level and led to 14 conformers. The stability of conformers is influenced by their environment, and in aqueous solution two conformers dominate the equilibrium. A superposition of calculated conformers with the predicted TS structure revealed that the preferred conformers in solution nicely mimic structural features of the TS. These results imply that 1 has structural properties required to mimic the TS and therefore can be used as a scaffold for further development of TS-analog inhibitors for retaining glycosyltransferases.     

Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: Utility in exploration of endangered plants

Background

Endangered plant species are an important resource for new chemistry. Lindera melissifolia is native to the Southeastern U.S. and scarcely populates the edges of lakes and ponds. Quantum mechanics (QM) used in combination with NMR/ECD is a powerful tool for the assignment of absolute configuration in lieu of X-ray crystallography.

Methods

The EtOAc extract of L. melissifolia was subject to chromatographic analysis by VLC and HPLC. Spin–spin coupling constant (SSCC) were calculated using DFT at the MPW1PW91/6-31G(d,p) level for all staggered rotamers. ECD calculations employed Amber* force fields followed by PM6 semi-empirical optimizations. Hetero- and homo-nuclear coupling constants were extracted from 1D ¹H, E.COSY and HETLOC experiments.

Results

Two meroterpenoids, melissifolianes A (1) and B (2) were purified and their 2-D structures elucidated using NMR and HRESIMS. The relative configuration of 1 was established using the combination of NOE-based distance restraints and the comparisons of experimental and calculated SSCCs. The comparison of calculated and experimental ECD assigned the absolute configuration of 1. The relative configuration of a racemic mixture, melissifoliane B (2) was established utilizing J-based analysis combined with QM and NMR techniques.Conclusion Our study of the Lindera melissifolia metabolome exemplifies how new chemistry remains undiscovered among the numerous endangered plant species and demonstrates how analysis by ECD and NMR combined with various QM calculations is a sensible approach to support the stereochemical assignment of molecules with conformationally restricted conformations.

General significance

QM–NMR/ECD combined approaches are of utility for unambiguous assignment of 3-D structures, especially with limited plant material and when a molecule is conformationally restricted. Conservation of an endangered plant species can be supported through identification of its new chemistry and utilization of that chemistry for commercial purposes.     

The effect of storage and active ingredient properties on the drug release profile of poly(ethylene oxide) matrix tablets

Different molecular weight forms of poly(ethylene oxide) can be used successfully in controlled release drug delivery due to their excellent matrix forming properties. Drug release of these materials follows nearly zero order kinetics, and is mainly governed by polymer swelling and erosion and diffusion of drug molecules. Because of its partly amorphous structure, poly(ethylene oxide) undergoes structural changes caused by elevated temperature and relative humidity of the storage medium resulting in an increased drug release. This physical process can be highly influenced by the structure of different drug molecules, such as polymer-binding ability and hydration tendency. These properties of two basic drugs embedded into poly(ethylene oxide) matrices were characterized by molecular modelling and an attempt was made to reveal their effect on the change of drug release stability, a prerequisite of the marketing authorization of dosage forms. The findings suggest that both the hydration properties of the active ingredient and the molecular weight of the polymer influence the effect of physical ageing of poly(ethylene oxide) on the drug release properties of the matrix.     

The effect of three-dimensional structure on the solid state isotope exchange of hydrogen in polypeptides with spillover hydrogen

The effect of the three-dimensional structure of polypeptides and proteins on their ability to undergo isotopic exchange under the action of spillover hydrogen (SH) in the high temperature solid state catalytic isotope exchange reaction (HSCIE) was theoretically and experimentally studied. The HSCIE reaction in the beta-galactosidase protein from Thermoanaerobacter ethanolicus (83kDa) was studied. The influence of the beta-galactosidase structure on isotopic exchange as peptide fragments with spillover tritium was studied. The most accessible peptide fragment, which does not contribute to alpha-helix and beta-strand formations (KEMQKE215-220), had the largest relative reactivity. The one located in the contact area between the subunits (YLRDSE417-422) showed the smallest relative reactivity. The relative reactivities of these peptides differ more than 150 times. Data collected during a study devoted to the HSCIE reaction of the beta-galactosidase protein indicate that the HSCIE reaction might be employed for acquiring information about their three-dimensional structure and protein-protein interactions. The results of ab initio calculations have shown that alpha-helix formation in polypeptides decreases the reactivity in HSCIE. Hydrogen exchange in the alpha-helical fragment Trp1-Leu8 of zervamycin IIB was also analyzed using theoretical methods. It was shown by ab initio quantum-chemical calculations that the high degree of substitution of C(alpha)H for tritium in Gln3 might be associated with the participation of electron donor O and N atoms in transition state stabilization in the HSCIE reaction.     

The influence of alveolar structures on the torsional strain field in a gorilla corporeal cross-section

Anthropologists have often used mandibular torsional properties to make inferences about primate dietary adaptations. Most of the methods employed are based on assumptions related to periodontal and alveolar properties. This study uses the finite element method to evaluate some of these assumptions with a cross-section through the third molar of a gorilla. Results indicate that the properties of alveolar bone play an important role in determining the strain field. In comparison, the exact stiffness values of the periodontal ligaments seem to have a much smaller impact. Replacing the dental roots and periodontal ligaments with alveolar bone, however, has a significant influence on the strain field. It underestimates the maximum shear strain by about 28% along its periosteal aspect when alveoli are modeled as cortical bone. It overestimates the strain by a smaller amount when alveoli are modeled as trabecular bone.This study supports the assumption that primate mandibles behave like a closed-section under torsion under the limiting condition that the alveolar bone stiffness is more than half of the value of cortical bone; alveolar bone can then be modeled as cortical bone with a minimal loss of accuracy. In addition, this study suggests that the minimum cortical thickness should be considered for torsional strength. Finally, modeling accuracy can be significantly increased if both dental and periodontal structures can be realistically incorporated into mandibular biomechanical models. However, this may not be always feasible in studies of fossil mandibles. This is due mainly to the difficulties involved in estimating alveolar bone densities and in distinguishing boundaries between cortical bone, alveolar bone, periodontal ligaments, and dental roots in fossil specimens.     

Peptides and Peptoids - A Systematic Structure Comparison

A systematic analysis of the conformational space of the basic structure unit of peptoids in comparison to the corresponding peptide unit was performed based on ab initio MO theory and complemented by molecular mechanics (MM) and molecular dynamics (MD) calculations both in the gas phase and in aqueous solution.The calculations show three minimum conformations denoted as C_7ß, a_D and a that do not correspond to conformers on the gas phase peptide potential energy hypersurface. The influence of aqueous solvation was estimated by means of continuum models. The MD simulations indicate the a_D form as the preferred conformation in solution both in cis and trans peptide bond orientations.     

A theoretical model of the catalytic mechanism of the Delta5-3-ketosteroid isomerase reaction

The present paper describes a theoretical approach to the catalytic reaction mechanism involved in the conversion of 5-androstene-3,17-dione to 4-androstene-3,17-dione. The model incorporates the side chains of the residues tyrosine (Tyr(14)), aspartate (Asp(38)) and aspartic acid (Asp(99)) of the enzyme Delta(5)-3-ketosteroid isomerase (KSI; EC 5.3.3.1). The reaction involves two steps: first, Asp(38) acts as a base, abstracting the 4beta-H atom (proton) from C-4 of the steroid to form a dienolate as the intermediate; next, the intermediate is reketonized by proton transfer to the 6beta-position. Each step goes through its own transition state. Functional groups of the Tyr(14) and Asp(99) side chains act as hydrogen bond donors to the O1 atom of the steroid, providing stability along the reaction coordinate. Calculations were assessed at high level Hartree-Fock theory, using the 6-31G(*) basis set and the most important physicochemical properties involved in each step of the reaction, such as total energy, hardness, and dipole moment. Likewise, to explain the mechanism of reaction, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), atomic orbital contributions to frontier orbitals formation, encoded electrostatic potentials, and atomic charges were used. Energy minima and transition state geometries were confirmed by vibrational frequency analysis. The mechanism described herein accounts for all of the properties, as well as the flow of atomic charges, explaining both catalytic mechanism and proficiency of KSI.     

Theoretical study of N<Subscript>4</Subscript>X (X = O,S, Se) systems

A series of N₄X (X = O, S, Se) compounds have been examined with ab initio and density functional theory (DFT) methods. To our knowledge, these compounds, except for the C_2v ring and the C_3v towerlike isomers of N₄O, are first reported here. The ring structures are the most energetically favored for N₄X (X = O and S) systems. For N₄Se, the cagelike structure is the most energetically favored. Several decomposition and isomerization pathways for the N₄X species have been investigated. The dissociation of C_2v ring N₄O and N₄S structures via ring breaking and the barrier height are only 1.1 and −0.2 kcal mol⁻¹ at the CCSD(T)/6-311+G*//MP2/6-311+G* level of theory. The dissociation of the cagelike N₄X species is at a cost of 12.1–16.2 kcal mol⁻¹. As for the towerlike and triangle bipyramidal isomers, their decomposition or isomerization barrier heights are all lower than 10.0 kcal mol⁻¹. Although the C_S cagelike N₄S isomer has a moderate isomerization barrier (18.3–29.1 kcal mol⁻¹), the low dissociation barrier (−1.0 kcal mol⁻¹) indicates that it will disappear when going to the higher CCSD(T) level. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The Interplay of Angle Strain and Aromaticity: Molecular and Electronic Structures of [0n]Paracyclophanes

The belt-like polyphenylenes, [0_n]paracyclophanes, (n = 5 and 6), have been investigated using semi-empirical, ab initio and DFT methods. The molecular structure, rotational barrier on twisting a single phenyl ring and the aromatic character within each ring as well as in the whole molecule have been evaluated. [0₅]Paracyclophane is predicted to have a quinonoid structure. In contrast, the equatorial pentaphenyl fragment found in C₇₀ as well as the hexagons of the less strained [0₆]paracyclophane have benzenoid character. Approximate band structures have been derived for larger cycles of [0_n] paracyclophanes.Electronic Supplementary Material available.     

The in vivo construction of 4-chloro-2-nitrophenol assimilatory bacteria

Pseudomonas sp. N31 was isolated from soil using 3-nitrophenol and succinate as sole source of nitrogen and carbon respectively. The strain expresses a nitrophenol oxygenase and can use either 2-nitrophenol or 4-chloro-2-nitrophenol as a source of nitrogen, eliminating nitrite, and accumulating catechol and 4-chlorocatechol, respectively. The catechols were not degraded further. Strains which are able to utilize 4-chloro-2-nitrophenol as a sole source of carbon and nitrogen were constructed by transfer of the haloaromatic degrading sequences from either Pseudomonas sp. B13 or Alcaligenes eutrophus JMP134 (pJP4) to strain N31. Transconjugant strains constructed using JMP134 as the donor strain grew on 3-chlorobenzoate but not on 2,4-dichlorophenoxyacetate. This was due to the non-induction of 2,4-dichlorophenoxyacetate monooxygenase and 2,4-dichlorophenol hydroxylase. Transfer of the plasmid from the 2,4-dichlorophenoxyacetate negative transconjugant strains to a cured strain of JMP134 resulted in strains which also had the same phenotype. This indicates that a mutation has occurred in pJP4 to prevent the expression of 2,4-dichlorophenoxyacetate monooxygenase and 2,4-dichlorophenol hydroxylase.     

Probing conformations of the glycerol backbones of triacyglycerols in the active site of lipase by 1,2-cyclopentane-carbamates: The meso effect for the enzyme inhibition

The aim of this study is to probe the glycerol backbone conformation of the substrate (or inhibitor) in the active site of Pseudomonas species lipase by the 1,2-cyclopentandiol analogues of the ethylene glycerol carbamate inhibitors. Cyclopentane-carbamates, cis-1,2-di-N-n- butylcarbamyl-cyclopentane (1) and trans-1,2-di-N-n-butylcarbamyl-cyclopentane (2), are the conformationally constrained analogues of 1,2-di-N-n-butylcarbamyl ethane (3). All carbamates are synthesized and characterized as the pseudo-substrate inhibitors of the enzyme. Cis-cyclopentane-di-carbamate (1) is a more potent inhibitor than both ethane-di-carbamate (3) and trans-cyclopentane-di-carbamate (2) probably because the glycerol backbone conformations of cis-cyclopentane-di-carbamate (1) are constrained by the cyclopentane ring and cis-cyclopentane-di-cabamate (1) is a meso compound but trans-cyclopentane-di-carbamate (2) is a racemate.     

Ab initio and DFT study on the electrophilic addition of bromine to endo-tricyclo[3.2.1.02,4]oct-6-ene

Full geometric optimization of endo-tricyclo[3.2.1.0^2,4]oct-6-ene (endo-TCO) by ab initio and DFT methods allowed us to investigate the structure of the molecule. The double bond is endo-pyramidalized and its two faces are no longer found to be equivalent. The exo face of the double bond has regions with far more electron density (q_i,HOMO) and more negative electrostatic potential. The endo-TCO-Br₂ system was investigated at the B3LYP/6-311+G** level and the endo-TCO···Br₂(exo) molecular complex was found to be relatively more stable than the endo-TCO···Br₂(endo) complex. The cationic intermediates of the reaction were studied by ab initio and DFT methods. The bridged exo-bromonium cation(I) is relatively more stable than the endo-bromonium cation(II). An absolute exo-facial selectivity should be observed in the addition reaction of Br₂ to endo-TCO, which is caused by steric and electronic factors. The nonclassical rearranged cation IV was found to be the most stable ion among the cationic intermediates and the ionic addition occurs via the formation of this cation. The mechanism of the addition reaction is also discussed.     

Bis(2-methyltetrazole)dichlorocopper(II) is a layered coordination polymer built from dinuclear chloro-bridged Cu units linked by bridging tetrazoles. The first structurally and magnetically characterized complex of 2-monosubstituted tetrazoles

The data on synthesis, crystal structure, magnetic susceptibility and thermal properties of coordination compound of copper(II) chloride with 2-methyltetrazole (2mtet) of Cu(2mtet)₂Cl₂ composition are reported. The Cu atom environment forms an elongated octahedron, with two 2-methyltetrazole ligands (N4 bound) and two Cl atoms in the equatorial positions. Symmetry related 2-methyltetrazole ligand and Cl atom are in the axial positions. One of the two 2-methyltetrazole molecules of the asymmetric unit exhibits bridging properties being linked to two Cu atoms through two N atoms (i.e., N4 and N1) of the tetrazole ring, while the other ligand molecule is coordinated in monodentate fashion via one tetrazole N4 atom. The Cu-octahedra form dinuclear building bricks by sharing edges with equatorial and axial Cl atoms. These dinuclear units are linked together via bridging 2-methyltetrazole ligands to form infinite layers parallel to the plane. Magnetic properties of Cu(2mtet)₂Cl₂ and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for 2mtet using B3LYP/6-31G^* level of theory are in agreement with the structural data obtained.     

The effect of 4-isothiocyanatobenzoic acid on the oxygen-linked chloride binding sites in human hemoglobin: Influence on the alkaline Bohr effect

Human oxyhemoglobin reacted with 4-isothiocyanatobenzoic acid shows a decreased oxygen affinity that does not change with increasing chloride concentration indicating that all of the oxygen-linked chloride binding sites are blocked in the modified protein. By contrast, reaction of oxyhemoglobin with 4-isothiocyanatobenzenesulfonamide produces a modified protein with increased oxygen affinity below pH 7.3 that shows the expected decrease in oxygen affinity with increasing chloride concentration. The latter result demonstrates the importance of the negatively charged moiety in producing both the decrease in oxygen affinity and the effect on the oxygen-linked chloride binding sites produced by 4-isothiocyanatobenzoic acid. Reduction in the alkaline Bohr effect by 50% in the protein modified by 4-isothiocyanatobenzoic acid indicates that contribution to the alkaline Bohr effect is evenly divided between chloride dependent and chloride independent groups.     

The anomeric effect revisited. A possible role of the CH/n hydrogen bond

Ab initio MO calculations were carried out at the MP2/6-311++G(d,p) level to investigate the conformational energy of 2-substituted oxanes and 1,3-dioxanes. It has been found that the Gibbs free energies of the axial conformers are smaller than those of the corresponding equatorial conformers in every case when the 2-substituent Z is electron withdrawing (OCH(3), F, Cl, Br). The difference in Gibbs energy between the equatorial and axial conformers DeltaG(eq-ax) increases from Z=OCH(3) to F, Cl, and then to Br. In the axial conformers, the interatomic distance between Z and the axial C-H, separated by four covalent bonds, has been found to be appreciably shorter than the van der Waals distance, suggesting the importance of the five-membered CH/n (CH/O or CH/halogen) hydrogen bond in stabilizing these conformations. Natural bonding orbital (NBO) charges of the relevant atoms have been shown to be different between the two conformers: more positive for H and more negative for C in the axial conformers than in the corresponding equatorial conformers. In view of the above findings, we suggest that the CH/n hydrogen bond plays an important role in stabilizing the axial conformation in 2-substituted oxanes and 1,3-dioxanes, and by implication, in the anomeric effect in carbohydrate chemistry.     

The inhibitory effect of naringenin on atopic dermatitis induced by DNFB in NC/Nga mice

Aims

Atopic dermatitis (AD) is a chronic and relapsing inflammatory dermatitis characterized by pruritic and eczematous skin lesions. Here, we investigated the therapeutic effect of the fruit flavonoid naringenin on DNFB induced atopic dermatitis mice model.

Main methods

AD-like skin lesion was induced by repetitive skin contact with DNFB in NC/Nga mice and the effects of the fruit flavonoid naringenin were evaluated on the basis of histopathological findings of skin, ear swelling and cytokine production of CD4⁺T cells.

Key findings

Intraperitoneal injection of naringenin for one week after DNFB challenge significantly lowered ear swelling and improved back skin lesions. In addition, naringenin significantly suppressed production of interferon-gamma (IFN-γ) by activated CD4⁺ T cells and serum IgE level. Furthermore, naringenin reduced DNFB-induced infiltration of eosinophils, mast cells, CD4⁺ T cells, and CD8⁺ T cells in skin lesions.

Significance

Naringenin may suppress the development of AD-like skin lesions in DNFB-treated NC/Nga mice by reducing IFN-γ production of activated CD4⁺ T cells, serum IgE levels and infiltration of immune cells to skin lesion.