Sesquiterpenes from Warburgia ugandensis and their antimycobacterial activity

The dichloromethane extract of the stem bark of Warburgia ugandensis afforded three new coloratane sesquiterpenes, namely: 6alpha,9alpha-dihydroxy-4(13),7-coloratadien-11,12-dial (1), 4(13),7-coloratadien-12,11-olide (2), and 7beta-hydroxy-4(13),8-coloratadien-11,12-olide (3), together with nine known sesquiterpenes, i.e., cinnamolide-3beta-acetate (4), muzigadial (5), muzigadiolide (6), 11alpha-hydroxymuzigadiolide (7), cinnamolide (8), 7alpha-hydroxy-8-drimen-11,12-olide (9), ugandensolide (10), mukaadial (11), ugandensidial (12), and linoleic acid (13). Their structures were assigned on the basis of 1D and 2D-NMR spectroscopic and GC-MS analysis. The compounds were examined for their antimycobacterial activity against Mycobacterium aurum, M. fortuitum, M. phlei and M. smegmatis; and the active constituents showed MIC values ranged from 4 to 128 microg/ml compared to the antibiotic drugs ethambutol (MIC ranged from 0.5 to 8 microg/ml) and isoniazid (MIC ranged from 1 to 4 microg/ml).     

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.     

Steered molecular dynamics simulation of the binding of the β2 and β3 regions in domain-swapped human cystatin C dimer

The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur between the two molecules may be important for the further aggregation of the protein. In this work, we performed steered molecular dynamics (SMD) simulations to investigate the dissociation of the β2 and β3 strands in the hCC dimer. The energy changes observed during the SMD simulations showed that electrostatic interactions were the dominant interactions involved in stabilizing the two parts of the dimer during the early stages of SMD simulation, whereas van der Waals (VDW) interactions and electrostatic interactions were equally matched during the latter stages. Furthermore, our data indicated that the two parts of the dimer are stabilized by intermolecular hydrogen bonds among the residues Arg51 (β2), Gln48 (β2), Asp65 (β3), and Glu67 (β3), salt bridges among the residues Arg53 (β2), Arg51 (β2), and Asp65 (β3), and VDW interactions among the residues Gln48 (β2), Arg51 (β2), Glu67 (β3), Asp65 (β3), Phe63 (β3), and Asn61 (β3). The residues Gln48 (β2), Arg51 (β2), Asp65 (β3) and Glu67 (β3) appear to be crucial, as they play important roles in both electrostatic and VDW interactions. Thus, the present study determined the key residues involved in the stabilization of the domain-swapped dimer structure, and also provided molecular-level insights into the dissociation process of the hCC dimer.     

The origin of the generalized anomeric effect: possibility of CH/n and CH/π hydrogen bonds

Ab initio MO calculations were carried out at the MP4/6-311++G(3df,3pd)//MP2/6-311++G(3df,3pd) level to investigate the conformational Gibbs energy of a series of methyl ethers CH₃O-CH₂-X (X = OH, OCH₃, F, Cl, Br, CN, CCH, C₆H₅, CHO). It was found that the Gibbs energy of the gauche conformers is lower in every case than that of the corresponding anti conformers. In the more stable gauche conformers, the interatomic distance between X and the hydrogen atom was shorter than the sum of the van der Waals radii. The natural bonding orbital (NBO) charges of group X were more negative in the gauche conformers than in the anti conformers. We suggest that the CH/n and CH/π hydrogen bonds play an important role in stabilizing the gauche conformation of these compounds.     

Molecular modeling of poly(ethylene oxide) model cofactors; 1,3,6-tri-O-galloyl-β-<Emphasis Type="SmallCaps">d</Emphasis>-glucose and corilagin

The most stable structures of two poly(ethylene oxide) (PEO) model cofactors, beta-1-O-galloyl-3,6-( R)-hexahydroxydiphenoyl- d-glucose (corilagin) and 1,3,6-tri-O-galloyl-beta- d-glucose (TGG), are calculated using molecular modeling and PM3 semiempirical molecular orbital theories. The theoretical PM3 structures agree with interpreted structures from experimental NMR; the glucopyranose ring of corilagin has a boat and TGG a chair conformation, for which the heats of formation, torsion angles, distances, van der Waals surface, and the infrared spectra are calculated.     

Effect of branching in 4-alkylpyrazoles on liver alcohol dehydrogenase inhibition: A shape analysis study

Shape analysis methodology is applied to the study of 4-alkylpyrazoles which are known inhibitors of liver alcohol dehydrogenase. Elongation of the alkyl chain increases the inhibitory power, whereas branching of the chain diminishes the activity. These two counterpoised effects are studied simultaneously in a selected set of 4-alkylpyrazoles. A systematic conformational analysis followed by topological characterization of the van der Waals surfaces of all the local minima restricts the conformational space to potential bioactive structures. The analysis of the interrelation between the molecular electrostatic potential and van der Waals surfaces provides certain shape codes characteristic of each 4-alkylpyrazole. In both topological analyses van der Waals surfaces and molecular electrostatic potential van der Waals surface interrelations) graphical representations and analytical methods were used. A good correlation between the shape codes and the inhibitory activity is found for the linear derivatives. For branched pyrazoles, a tendency in their inhibitory power is predicted. Isopentylpyrazole is suggested to have the same inhibitory profile as 4-butylpyrazole, the linear derivative with one less carbon atom.     

Antimicrobial activity in cultures of endophytic fungi isolated from Garcinia species

The aim of the present study was to screen for antimicrobial activity in endophytic fungi isolated from surface sterilized leaves and branches of five Garcinia plants, G. atroviridis, G. dulcis, G. mangostana, G. nigrolineata and G. scortechinii, found in southern Thailand. Fermentation broths from 377 isolated fungi were tested for antimicrobial activity by the agar diffusion method. Minimum inhibitory concentrations (MICs) were obtained for crude ethyl acetate extracts. Seventy isolates (18.6%) displayed antimicrobial activity against at least one pathogenic microorganism, such as Staphylococcus aureus, a clinical isolate of methicillin-resistant S. aureus, Candida albicans and Cryptococcus neoformans. The results revealed that 6-10%, 1-2% and 18% of the crude ethyl acetate extracts inhibited both strains of S. aureus (MIC 32-512 microg mL(-1)), Ca. albicans and Cr. neoformans (MIC 64-200 microg mL(-1)), and Microsporum gypseum (MIC 2-64 microg mL(-1)), respectively. Isolates D15 and M76 displayed the strongest antibacterial activity against both strains of S. aureus. Isolates M76 and N24 displayed strong antifungal activity against M. gypseum. Fungal molecular identification based on internal transcribed spacer rRNA gene sequence analysis demonstrated that isolates D15 (DQ480353), M76 (DQ480360) and N24 (DQ480361) represented Phomopsis sp., Botryosphaeria sp. and an unidentified fungal endophyte, respectively. These results indicate that some endophytic fungi from Garcinia plants are a potential source of antimicrobial agents.     

Synthesis of 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-substituted-benzenes: "thymine replacement" analogs of thymidine for evaluation as anticancer and antiviral agents

A group of unnatural 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluorobenzenes having a variety of C-5 two-carbon substituents [-C...C-X, X = I, Br; -C...CH; (E)-CH=CH-X, X = I, Br; -CH=CH2; -CH2CH3; -CH(N3) CH2Br], designed as nucleoside mimics, were synthesized for evaluation as anticancer and antiviral agents. The 5-substituted (E)-CH=CH-I and -CH2CH3 compounds exhibited negligible cytotoxicity in a MTT assay (CC50 = 10(-3) to 10(-4)M range), relative to thymidine (CC50 = 10(-3) to 10(-5)M range), against a variety of cancer cell lines. In contrast, the C-5 substituted -C...C-I and -CH(N3)CH2Br compounds were more cytotoxic (CC50 = 10(-5) to 10(-6)M range). The -C...C-I and -CH2CH3 compounds exhibited similar cytotoxicity against non-transfected (KBALB, 143B) and HSV-1 TK+ gene transfected (KBALB-STK, 143B-LTK) cancer cell lines expressing the herpes simplex virus type 1 (HSV-1) thymidine kinase gene (TK+). This observation indicates that expression of the viral TK enzyme did not provide a gene therapeutic effect. The parent group of 5-substituted compounds, that were evaluated using a wide variety of antiviral assay systems [HSV-1, HSV-2, varicella-zoster virus (VZV), vaccinia virus, vesicular stomatitis, cytomegalovirus (CMV), and human immunodeficiency (HIV-1, HIV-2) viruses], showed that this class of unnatural C-aryl nucleoside mimics are inactive and/or weakly active antiviral agents.     

Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12

The mechanism of C-H bond activation of ethane was catalyzed by palladium halide cations (PdX+ (X = F, Cl, Br, H, and CH3)), which was investigated using density functional theory (DFT) at B3LYP level. The reaction mechanism was taken into account in triplet and singlet spin state potential energy surfaces. For PdF+, PdCl+, and PdBr+, the high spin states were the ground states, whereas the ground states were the low spin states in PdH+ and PdCH3+. The reaction of PdF+, PdCl+, and PdBr+ with ethane occurred via a typical “two-state reactivity” mechanism. In contrast, for PdH+ and PdCH3+, the overall reaction performed on the ground state PESs in a spin-conserving manner. The crossing points between two potential energy surfaces were observed and effectively decreased the activation barrier in PdX+/C2H6 (X = F, Cl, and Br). The minimum energy crossing points (MECP) were obtained used the algorithm in Harvey method. The natural valence electron configuration calculations were analyzed by natural bond orbital. The distribution and contribution of the front molecular orbital of the initial complexes could be further understand by the density of states. The feature of the bonding evolution in the main pathways was studied using topological analysis including localized orbital locator and atoms in molecules.     

Quantitative structure-activity relationship studies for antioxidant hydroxybenzalacetones by quantum chemical- and 3-D-QSAR(CoMFA) analyses

Antioxidant activities for a series of hydroxybenzalacetones, OH-BZ, evaluated by their inhibitory potencies against lipid peroxidation induced by gamma-ray irradiation or t-BuOOH, were analyzed quantitatively using quantum-chemical parameters calculated by semi-empirical molecular orbital (MO) calculations. The energy of the highest occupied molecular orbital (E(HOMO)) and frontier electron densities (HOMO) on the phenolic oxygen atom (F(H,O)), together with the steric parameter (E(s)) for the substituent ortho to the phenolic oxygen, showed excellent correlations. We also performed 3D-QSAR studies by using the comparative molecular field analysis (CoMFA) model. The results were compared with the corresponding classical QSAR correlations.     

Peptide folding driven by Van der Waals interactions

Contrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin-like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide-solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge-charge interactions, these simulation results will give us a new view of the folding mechanism.     

Resolution of sertraline with (R)-mandelic acid: chiral discrimination mechanism study

The chiral discrimination mechanism in the resolution of sertraline with mandelic acid was investigated by examining the weak intermolecular interactions (such as hydrogen bond, CH/π, and van der Waals interactions) and molecular packing difference in crystal structures of the resulting diastereomeric salts. A new one-dimensional chain-like hydrogen-bonding network and unique supramolecular packing mode are disclosed. The investigation demonstrated that stable hydrogen-bonding pattern, herringbone-like arrangement of aromatic rings, and planar boundary surface in the hydrophobic region are the three most important structural characteristics expected in less soluble diastereomeric salts. The existence and magnitude of hydrogen bond, CH/π interaction, and van der Waals interaction related to three characteristic structures, determine the stability of diastereomeric salt. The hydrogen bond is not necessarily the dominant factor while the synergy and optimization of all weak intermolecular interactions attribute to the chiral recognition.     

Molecular similarity analysis between insect juvenile hormone and N, N-diethyl-m-toluamide (DEET) analogs may aid design of novel insect repellents

Molecular similarity analysis of stereoelectronic properties between natural insect juvenile hormone (JH), -a synthetic insect juvenile hormone mimic (JH-mimic, undecen-2-yl carbamate), and N, N-diethyl-m-toluamide (DEET) and its analogs reveals similarities that may aid the design of more efficacious insect repellents and give a better insight into the mechanism of repellent action. The study involves quantum chemical calculations using the AM1 semi-empirical computational method enabling a conformational search for the lowest and most abundant energy conformers of JH, JH-mimic, and 15 DEET compounds, followed by complete geometry optimization of the conformers. Similarity analyses of stereoelectronic properties such as structural parameters, atomic charges, dipole moments, molecular electrostatic potentials, and highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were performed on JH, JH-mimic and the DEET compounds. The similarity of stereoelectronic attributes of the amide/ester moiety, the negative electrostatic potential regions beyond the van der Waals surface, and the large distribution of hydrophobic regions in the compounds appear to be the three important factors leading to a similar interaction with the JH receptor. The similarity of electrostatic profiles beyond the van der Waals surface is likely to play a crucial role in molecular recognition interaction with the JH receptor from a distance. This also suggests electrostatic bioisosterism of the amide group of the DEET compounds and JH-mimic and, thus, a model for molecular recognition at the JH receptor. The insect repellent property of the DEET analogs may thus be attributed to a conflict of complementarity for the JH receptor binding sites.     

The structures of solvated methylmercury(II) chlolade,bromide and iodide in pyridine solution; Implications for aqueous solution

The structures of solvated methylmercury(II) halides in pyridine solution were determined by a large angle X-ray scattering technique. Near-linear CH₃HgX (X = Cl, Br and I) species solvated by two weakly-coordinated pyridine molecules are indirectly interpreted. Additional mercury-pyridine interactions, through van der Waals forces, are found at the sum of the van der Waals radii. The HgX bond distances in the methylmercury(II) halides are found to be 2.325(8), 2.480(3) and 2.649(3) Å for chloride, bromide and iodide, respectively. The HgC bond distances are assumed to be ∼2.08 Å. This interaction is indicated in the radial distribution functions. The bond distance between mercury and the two solvating pyridine molecules is ∼2.8 Å, e.g., 2.84(2) Å in methylmercury(II) bromide. The additional mercury interactions with roughly two pyridine molecules at the sum of van der Waals radii are revealed at around 3.15 Å. Comparison between Raman stretching vibrations and the solvated structures of methylmercury(II) complexes found in various solvents indicates a lower limit in solvent donor property for the formation of solvate bonds to mercury for the methylmercury(II) halides.     

Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity

In addition to hydrogen bonds, van der Waals forces contribute to the affinity of protein-carbohydrate interactions. Nonpolar van der Waals contacts in the complexes of the L-arabinose-binding protein (ABP) with monosaccharides have been studied by means of site-directed mutagenesis, equilibrium and rapid kinetic binding techniques, and X-ray crystallography. ABP, a periplasmic transport receptor of Escherichia coli, binds L-arabinose, D-galactose, and D-fucose with preferential affinity in the order of Ara greater than Gal much greater than Fuc. Well-refined, high-resolution structures of ABP complexed with the three sugars revealed that the structural differences in the ABP-sugar complexes are localized around C5 of the sugars, where the equatorial H of Ara has been substituted for CH3 (Fuc) or CH2OH (Gal). The side chain of Met108 undergoes a sterically dictated, ligand-specific, conformational change to optimize nonpolar interactions between its methyl group and the sugar. We found that the Met108Leu ABP binds Gal tighter than wild-type ABP binds Ara and exhibits a preference for ligand in the order of Gal much greater than Fuc greater than Ara. The differences in affinity can be attributed to differences in the dissociation rates of the ABP-sugar complexes. We have refined at better than 1.7-A resolution the crystal structures of the Met108Leu ABP complexed with each of the sugars and offer a molecular explanation for the altered binding properties.     

Genetic control of methyl halide production in Arabidopsis

Methyl chloride (CH(3)Cl) and methyl bromide (CH(3)Br) are the primary carriers of natural chlorine and bromine, respectively, to the stratosphere, where they catalyze the destruction of ozone, whereas methyl iodide (CH(3)I) influences aerosol formation and ozone loss in the boundary layer. CH(3)Br is also an agricultural pesticide whose use is regulated by international agreement. Despite the economic and environmental importance of these methyl halides, their natural sources and biological production mechanisms are poorly understood. Besides CH(3)Br fumigation, important sources include oceans, biomass burning, tropical plants, salt marshes, and certain crops and fungi. Here, we demonstrate that the model plant Arabidopsis thaliana produces and emits methyl halides and that the enzyme primarily responsible for the production is encoded by the HARMLESS TO OZONE LAYER (HOL) gene. The encoded protein belongs to a group of methyltransferases capable of catalyzing the S-adenosyl-L-methionine (SAM)-dependent methylation of chloride (Cl(-)), bromide (Br(-)), and iodide (I(-)) to produce methyl halides. In mutant plants with the HOL gene disrupted, methyl halide production is largely eliminated. A phylogenetic analysis with the HOL gene suggests that the ability to produce methyl halides is widespread among vascular plants. This approach provides a genetic basis for understanding and predicting patterns of methyl halide production by plants.     

Interaction of uridine diphosphate glucose analogs with calf liver uridine diphosphate glucose dehydrogenase. Influence of substituents at C-5 of pyrimidine nucleus.

The interaction of alpha-D-glucopyranosyl pyrophosphates of 5-X-uridines (X = CH3, NH2, CH3O, I, Br, Cl, OH) with uridine diphosphate glucose (UDPGlc) dehydrogenase (EC 1.1.1.22) from calf liver has been studied. All the derivatives investigated were able to serve as substrates for the enzyme. The apparent Michaelis constants for UDPGlc-analogs were dependent both on electronic and steric factors. Increase of substituent negative inductive effect lead to decrease of pKa for ionization of the NH-group in the uracil nucleus and, consequently, to a diminishing of the proportion of the active analog species under the conditions of assay. After correction for the ionization effect, the Km values were found to depend on the van der Waals radius of the substituent. The value of 1.95 A seems to be critical, as the analogs with bulkier substituents at C-5 showed a decreased affinity to the enzyme. The maximal velocity values of the analogs were also dependent on nature of the substituent. Good linear correlation between log V and substituent hydrophobic phi-constant was observed for a number of the analogs, although V values for the nucleotides with X = H, OH or NH2 were higher than would be expected on the basis of the correlation. The significance of the results for understanding of the topography of UDPGlc dehydrogenase active site is discussed.