Structural and functional implications of the interaction between macrolide antibiotics and bile acids.

Macrolide antibiotics, such as azithromycin and erythromycin, are in widespread use for the treatment of bacterial infections. Macrolides are taken up and excreted mainly by bile. Additionally, they have been implicated in biliary system diseases and to modify the excretion of other drugs through bile. Despite mounting evidence for the interplay between macrolide antibiotics and bile acids, the molecular details of this interaction remain unknown. Herein, we show by NMR measurements that macrolides directly bind to bile acid micelles. The topology of this interaction has been determined by solvent paramagnetic relaxation enhancements (solvent PREs). The macrolides were found to be bound close to the surface of the micelle. Increasing hydrophobicity of both the macrolide and the bile acid strengthen this interaction. Both bile acid and macrolide molecules show similar solvent PREs across their whole structures, indicating that there are no preferred orientations of them in the bile micelle aggregates. The binding to bile aggregates does not impede macrolide antibiotics from targeting bacteria. In fact, the toxicity of azithromycin towards enterotoxic E. coli (ETEC) is even slightly increased in the presence of bile, as was shown by effective concentration (EC50 ) values.

Phenol-quinone tautomerism in (arylazo)naphthols and the analogous Schiff bases: benchmark calculations.

Tautomerization energies of a series of isomeric [(4-R-phenyl)azo]naphthols and the analogous Schiff bases (R = N(CH3)2, OCH3, H, CN, NO2) are calculated by LPNO-CEPA/1-CBS using the def2-TZVPP and def2-QZVPP basis sets for extrapolation. The performance of various density functionals (B3LYP, M06-2X, PW6B95, B2PLYP, mPW2PLYP, PWPB95) as well as MP2 and SCS-MP2 is evaluated against these results. M06-2X and SCS-MP2 yield results close to the LPNO-CEPA/1-CBS values. Solvent effects (CCl4, CHCl3, CH3CN, and CH3OH) are treated by a variety of bulk solvation models (SM8, IEFPCM, COSMO, PBF, and SMD) as well as explicit solvation (Monte Carlo free energy perturbation using the OPLSAA force field).

A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione.

The reaction of cyclobutane-1,2-dione with hydroxide was studied by a variety of ab initio (MP2, SCS-MP2, CCSD(T), CEPA/1) and density functional (M06-2X) methods. Three possible reaction paths of the initially formed tetrahedral adduct leading to either 1-hydroxycyclopropane-1-carboxylate (benzilic acid type rearrangement, path A), α-oxobutanoate (path B) or γ-oxobutanoate (path C) were considered. Although the latter two products show similar or even more negative Gibbs free energies of reaction than calculated for the benzilic acid type rearrangement, the Gibbs free energies of activation are substantially higher. According to the calculations, the only feasible reaction appears to be the formation of 1-hydroxycyclopropane-1-carboxylate, which is corroborated by previous experimental observations.

Unusual C=C bond isomerization of an α,ß-unsaturated γ-butyrolactone catalysed by flavoproteins from the old yellow enzyme family.

An unexpected, redox-neutral C=C bond isomerization of a γ-butyrolactone bearing an exo-methylene unit to the thermodynamically more favoured endo isomer (k(cat) =0.076 s(-1) ) catalysed by flavoproteins from the Old Yellow Enzyme family was discovered. Theoretical calculations and kinetic data support a mechanism through which the isomerization proceeds through FMN-mediated hydride addition onto exo-Cß, followed by hydride abstraction from endo-Cß', which is in line with the well-established C=C bond bioreduction of OYEs. This new isomerase activity enriches the catalytic versatility of ene-reductases.

A substrate-driven approach to determine reactivities of α,ß-unsaturated carboxylic esters towards asymmetric bioreduction.

The degree of C=C bond activation in the asymmetric bioreduction of α,ß-unsaturated carboxylic esters by ene-reductases was studied, and general recommendations to render these "borderline-substrates" more reactive towards enzymatic reduction are proposed. The concept of "supported substrate activation" was developed. In general, an additional α-halogenated substituent proved to be beneficial for enzymatic activity, whereas ß-alkyl or ß-aryl substituents were detrimental for the reactivity of nonhalogenated substrates, and α-cyano groups showed little effect. The alcohol moiety of the ester functionality was found to have a strong influence on the reaction rate. Overall, activities were determined by both steric and electronic effects.

A highly efficient ADH-coupled NADH-recycling system for the asymmetric bioreduction of carbon-carbon double bonds using enoate reductases.

The asymmetric bioreduction of activated alkenes catalyzed by flavin-dependent enoate reductases from the OYE-family represents a powerful method for the production of optically active compounds. For its preparative-scale application, efficient and economic NADH-recycling is crucial. A novel enzyme-coupled NADH-recycling system is proposed based on the concurrent oxidation of a sacrificial sec-alcohol catalyzed by an alcohol dehydrogenase (ADH-A). Due to the highly favorable position of the equilibrium of ene-reduction versus alcohol-oxidation, the cosubstrate is only required in slight excess.

Reductive biotransformation of nitroalkenes via nitroso-intermediates to oxazetes catalyzed by xenobiotic reductase A (XenA).

A novel reductive biotransformation pathway for ß,ß-disubstituted nitroalkenes catalyzed by flavoproteins from the Old Yellow Enzyme (OYE) family was elucidated. It was shown to proceed via enzymatic reduction of the nitro-moiety to furnish the corresponding nitroso-alkene, which underwent spontaneous (non-enzymatic) electrocyclization to form highly strained 1,2-oxazete derivatives. At elevated temperatures the latter lost HCN via a retro-[2 + 2]-cycloaddition to form the corresponding ketones. This pathway was particularly dominant using xenobiotic reductase A, while pentaerythritol tetranitrate-reductase predominantly catalyzed the biodegradation via the Nef-pathway.

Coordination of methanol clusters to benzene: a computational study.

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.

Biocatalytic carboxylation.

Dwindling petroleum feedstocks and increased CO(2)-concentrations in the atmosphere currently open the concept of using CO(2) as raw material for the synthesis of well-defined organic compounds. In parallel to recent advances in the chemical CO(2)-fixation, enzymatic (biocatalytic) carboxylation is currently being investigated at an increased pace. On the one hand, this critical review provides a concise overview on highly specific biosynthetic pathways for CO(2)-fixation and, on the other hand, a summary of biodegradation (detoxification) processes involving enzymes which possess relaxed substrate specificities, which allow their application for the regioselective carboxylation of organic substrates to furnish the corresponding carboxylic acids (145 references).

Derivatives of schisandrin with increased inhibitory potential on prostaglandin E(2) and leukotriene B(4) formation in vitro.

Four derivatives of schisandrin, a major dibenzo[a,c]cyclooctadiene lignan of Schisandra chinensis (Turcz.) Baillon were synthesized and structurally characterized by means of NMR and mass spectroscopy. Furthermore, axial chirality of the biphenyl system was determined by comparison of calculated with measured circular dichroism (CD) spectra. Three of the obtained derivatives showed a ring contraction during chemical modification. While the original lignans were inactive on the performed bioassays, the compounds which showed the cycloheptadiene skeleton revealed remarkable activities. For the inhibition of LTB(4) production the IC(50) values of aR-6,7-dihydro-6-(1'-hydroxyethyl)-3,9-dimethoxy-6-methyl-5H-dibenzo[a,c]cycloheptene-1,2,10,11-tetraol (6) and aR-6-(1'-iodoethyl)-1,2,3,9,10,11-hexamethoxy-6-methyl-5H-dibenzo[a,c]cycloheptene (8) were 4.2+/-0.3microM and 4.5+/-0.2microM, respectively. aR-6,7-Dihydro-6-(1'-hydroxyethyl)-6-methyl-5H-dibenzo[a,c]cycloheptene-1,2,3,9,10,11-hexaol (5) revealed dual inhibition on COX-2 (IC(50) 32.1+/-2.5microM) and on LTB(4) production (37.3+/-5.5% inhibition at 50microM).

Theoretical prediction of pKa values of seleninic, selenenic, sulfinic, and carboxylic acids by quantum-chemical methods.

Aqueous acid dissociation constants of substituted areneseleninic, areneselenenic, arenesulfinic, and benzoic acids are calculated by ab initio (MP2) and DFT (B3LYP) methods in combination with bulk solvation models (IEFPCM, CRSrad) from appropriate thermodynamic cycles. Mean absolute deviations (MAD) between experimental and calculated pK(a) values are quite large for basis sets without diffuse functions; however, trends are reasonably well described. Best agreement with experiment as described by MAD as well as correlation coefficient and slope of the correlation equation pK(a) = a*ΔG(calc)/RT ln(10) + b is obtained with the CPCM solvation model using the defaults optimized within COSMO-RS (CRSrad; MAD = 1.54, R(2) = 0.94, a = 0.83). Sulfenic (selenenic) acid tautomers are significantly more stable than the corresponding sulfoxide (selenoxide) forms.

Absolute configuration of eremophilane sesquiterpenes from Petasites hybridus: comparison of experimental and calculated circular dichroism spectra.

In-depth conformational analyses of 10 known eremophilane (= (1S,4aR,7R,8aR)-decahydro-1,8a-dimethyl-7-(1-methylethyl)napththalene) sesquiterpenes, 1-10, from Petasites hybridus were performed with molecular mechanics as well as density functional theory methods. Electronic transition energies and rotational strengths of these eight eremophilane lactones and two petasins were calculated by time-dependent density functional theory (B3PW91/TZVP). The absolute configurations of the constituents could be assigned by comparison of their simulated and experimental circular dichroism (CD) spectra in methanol as (4S,5R,8S,10R) (1, 2), (2R,4S,5R,8S,10R) (3, 4, 5), (2R,4S,5R,8R,9R,10R) (6), (2R,4S,5R,8R,10R) (7, 8), and (3R,4R,5R) (9, 10). Single-crystal X-ray diffraction data of 8beta-hydroxyeremophilanolide ((8S)-8-hydroxyeremophil-7(11)-en-12,8-olide) (1) served as starting point for the theoretical conformational calculations of the 8beta-epimers of the eremophilane lactones. Experimental CD spectra as well as (1)H NMR spectra of compound 1 in methanol were considerably dependent on sample concentration.

One-way biohydrogen transfer for oxidation of sec-alcohols.

Quasi-irreversible oxidation of sec-alcohols was achieved via biocatalytic hydrogen transfer reactions using alcohol dehydrogenases employing selected ketones as hydrogen acceptors, which can only be reduced but not oxidized. Thus, only 1 equiv of oxidant was required instead of a large excess. For the oxidation of both isomers of methylcarbinols a single nonstereoselective short-chain dehydrogenase/reductase from Sphingobium yanoikuyae was identified and overexpressed in E. coli.

Antimycobacterial and H1-antihistaminic activity of 2-substituted piperidine derivatives.

2-Substituted derivatives of the antihistaminic agents Bamipine, Diphenylpyraline and of their 1-phenyl analogues were tested for their antimycobacterial and H(1)-antagonistic activities. They are strong H1-receptor antagonists and also inhibit the growth of mycobacterials with a maximum MIC of 6.25 microg/mL against Mycobacterium tuberculosis H(37)Rv. H1-receptor antagonistic potency was slightly decreased by substitution in ring position 2 and distinctly diminished by N-aryl substitution. The antimycobacterial potency of Diphenylpyraline was in general increased by substitution in ring position 2, whereas only a few Bamipine derivatives showed markedly improved activity. A correlation between the two activities was not detected for those compounds.

Interaction of methyl beta-D-xylopyranoside with metal ions: density functional theory study of cationic and neutral bridging and pendant complexes.

Density functional theory calculations on complexes of 4C1, 1C4 and 2SO ring conformations of methyl beta-D-xylopyranoside 1 with divalent metal cations, M = Mg2+, Ca2+, Zn2+, and Cd2+, are presented. Bridging and pendant cationic, [M(H2O)41]2+ and [M(H2O)(5)1]2+, as well as neutral complexes, [M(OH)2(H2O)(2)1] and [M(OH)2(H2O)(3)1], and neutral complexes involving a doubly deprotonated sugar, [M(H2O)(4)1(2-)], are considered. In aqueous and chloroform solution the stability of cationic and pendant neutral complexes is greatly diminished compared with gas-phase results. In contrast, bridging neutral complexes [M(OH)2(H2O)(2)1] and those of type [M(H2O)(4)1(2-)], are stabilized with increasing solvent polarity. Solvation also profoundly influences the preferred binding position and ring conformation. Compared with complexes of bare metal cations, additional ligands, e.g., H2O or OH-, significantly reduce the stability of 1C4 ring complexes. Irrespective of the cation, the most stable structure of bridging complexes [M(H2O)(4)1]2+ results from coordination of the metal to O3 and O4 of methyl beta-D-xylopyranoside in its 4C1 ring conformation.

Theoretical study of the enol imine <--> enaminone tautomeric equilibrium in organic solvents.

The tautomeric enol imine <--> enaminone (phenol <--> quinone) equilibrium of the 1-hydroxy-2-naphthaldehyde Schiff base (2-phenyliminomethyl-naphthalen-1-ol) was investigated by density functional theory (B3LYP) and ab initio (MP2) methods in the IEF-PCM polarizable continuum dielectric solvent approximation and by a combined ab initio + FEP/MC study by considering an explicit solvent model. Special emphasis was put on the effect of solvation on this equilibrium by using an apolar (CCl4), polar aprotic (CH3CN), and polar protic (CH3OH) solvent. Compared with experimental tautomerization Gibbs free energies, the IEF-PCM/B3LYP calculations apparently overestimate the stability of the quinone form both when the 6-31G(d,p) and the 6-311++G(d,p) basis sets are applied. IEF-PCM/MP2 studies with the above basis sets predict the preference of the aromatic phenol tautomer, in contrast to the experiment in methanol and acetonitrile solvent. Calculation of the total relative free energy as DeltaG(tot) = DeltaE(int)(IEF-PCM/QCISD(T)/6-31G(d)) + DeltaG(solv, FEP/MC) + DeltaG(thermal) provided agreement with the experimental values up to 0.6 kcal/mol in the three solvents, and the predominant tautomer was always correctly predicted. In-solution relevant atomic charges, derived by a fit to the molecular electrostatic potential generated by the IEF-PCM/B3LYP/6-31G(d,p) wave function, show strong dependence on the fitting procedure (CHELPG or RESP) and are fairly insensitive to the chemical nature of the actual solvent. Use of the CHELPG charges in FEP/MC simulations revealed to be superior in comparison with the use of the RESP charge set.

Hydration and Hydrolysis of alpha-Oxo Carboxylic Acid Derivatives and Conjugate Addition to alpha,beta-Unsaturated Carbonyl Compounds: A Density Functional Study.

Hydration of the keto group as well as hydrolysis (ester and amide) of alpha-oxo carboxylic acid derivatives has been studied by density functional theory (B3LYP/6-31G and B3LYP/6-311G). Both uncatalyzed as well as water-assisted processes have been considered. Solvent effects were approximated by the self-consistent isodensity surface polarized continuum (SCIPCM) model. For hydrolysis reactions a concerted as well as a stepwise mechanism was calculated. In the latter one, addition of the nucleophile to a tetrahedral intermediate was found to be rate determining. In uncatalyzed processes both concerted and stepwise mechanisms are calculated to have comparable activation energies and free enthalpies. In catalyzed reactions the stepwise mechanism is predicted to be considerably more favorable. Hydration of the alpha-oxo group should be much more feasible than either ester or amide hydrolysis.

Substituent Effects on Site Selectivity (C=C vs C=N) in Heterocumulene-Heterodiene [4 + 2] Cycloadditions: Density Functional and Semiempirical AM1 Molecular Orbital Calculations.

The effect of substituents on the site selectivity (C=C vs C=N) in the [4 + 2] cycloaddition between heterocumulenes (ketene imines) 2a-g with heterodienes (acroleines 9a-n and 4-acylfuran-2,3-diones 1a-d) is treated by semiempirical AM1 molecular orbital and density functional calculations using Becke's three-parameter hybrid method (B3LYP/6-31G). For some reactions calculations were also done at the B3LYP/6-31+G level of theory. For reaction of the oxa 1,3-dienes with ketene imines unsubstituted at the terminal carbon invariably addition across the C=C heterocumulene double bond has a lower activation energy than addition across the C=N double bond. Substitution of methyl or especially phenyl groups at the ketene imine C-terminus leads to a reversal of the respective activation energies. Incorporation of the oxa 1,3-diene system into the heterocyclic dione 1 substantially enhances the reactivity ( approximately 10 kcal mol(-1) lower activation energies) as compared to similarly substituted acroleins. At the DFT level of theory all reactions are found to proceed via a concerted asynchronous mechanism.

Atropisomers of Cofacial Heteroaromatic Rings with Two Positive Charges. Derivatives of 1,8-Di(3'-pyridyl)naphthalene.

The two nitrogen atoms in 1,8-di(3'-pyridyl)naphthalene were quaternized by the addition of either benzyl or methyl groups to give dications; the latter was oxidatively converted to the di(6'-pyridone). N-Oxidation gave the mono- and di-N-oxides. All these compounds in DMSO-d(6) show anti-syn atropisomerism at ambient temperatures by (1)H NMR analysis; similar amounts of both diastereomers are present.

Pericyclic versus Pseudopericyclic 1,5-Electrocyclization of Iminodiazomethanes. An ab Initio and Density Functional Theory Study.

Density functional (B3LYP/6-311+G) and ab initio (MP2/6-311+G and MP4(SDTQ)/6-311+G//MP2/6-311+G) calculations on the ring closure reactions of (E)- and Z-iminodiazomethane ((E)-5, (Z)--5), vinyldiazomethane 7, and formyldiazomethane 9 to 1H-1,2,3-triazole 6, 3H-pyrazole 8, and 1,2,3-oxadiazole 10, respectively, are reported. (E)-5 cyclizes via a low barrier (ca. 10 kcal mol(-)(1)) pseudopericyclic nonrotatory transition state. Ring closure of (Z)-5 and 7 proceeds by a monorotatory movement of the imino or vinyl group with a substantially higher barrier (ca. 25 kcal mol(-)(1)). Despite being endothermic, for the reaction 9 --> 10 also a rather low activation energy (ca. 10 kcal mol(-)(1)) is computed. The NBO analysis is used to interpret the electronic structures of the respective transition states in terms of their pericyclic monorotatory (TS ((Z)-5 --> 6), (TS (7 --> 8)) or pseudopericyclic nonrotatory ((TS ((E)-5 --> 6), (TS (9 --> 10)) nature.