Peter Wolschann

Combinatorial QSAR of Ambergris Fragrance Compounds

A combinatorial quantitative structure-activity relationships (Combi-QSAR) approach has been developed and applied to a data set of 98 ambergris fragrance compounds with complex stereochemistry. The Combi-QSAR approach explores all possible combinations of different independent descriptor collections and various individual correlation methods to obtain statistically significant models with high internal (for the training set) and external (for the test set) accuracy. Seven different descriptor collections were generated with commercially available MOE, CoMFA, CoMMA, Dragon, VolSurf, and MolconnZ programs; we also included chirality topological descriptors recently developed in our laboratory (Golbraikh, A.; Bonchev, D.; Tropsha, A. J. Chem. Inf. Comput. Sci. 2001, 41, 147-158). CoMMA descriptors were used in combination with MOE descriptors. MolconnZ descriptors were used in combination with chirality descriptors. Each descriptor collection was combined individually with four correlation methods, including k-nearest neighbors (kNN) classification, Support Vector Machines (SVM), decision trees, and binary QSAR, giving rise to 28 different types of QSAR models. Multiple diverse and representative training and test sets were generated by the divisions of the original data set in two. Each model with high values of leave-one-out cross-validated correct classification rate for the training set was subjected to extensive internal and external validation to avoid overfitting and achieve reliable predictive power. Two validation techniques were employed, i.e., the randomization of the target property (in this case, odor intensity) also known as the Y-randomization test and the assessment of external prediction accuracy using test sets. We demonstrate that not every combination of the data modeling technique and the descriptor collection yields a validated and predictive QSAR model. kNN classification in combination with CoMFA descriptors was found to be the best QSAR approach overall since predictive models with correct classification rates for both training and test sets of 0.7 and higher were obtained for all divisions of the ambergris data set into the training and test sets. Many predictive QSAR models were also found using a combination of kNN classification method with other collections of descriptors. The combinatorial QSAR affords automation, computational efficiency, and higher probability of identifying significant QSAR models for experimental data sets than the traditional approaches that rely on a single QSAR method.

METABOLISM OF THE ANTICANCER DRUG FLAVOPIRIDOL, A NEW INHIBITOR OF CYCLIN DEPENDENT KINASES, IN RAT LIVER

Flavopiridol (FLAP) is a promising novel chemotherapeutic agent currently undergoing clinical phase I trials. To examine hepatic metabolism and biliary disposition of FLAP we applied the isolated perfused rat liver system. Besides FLAP two metabolites were detected by high performance liquid chromatography in bile and perfusate. Twenty-five min after FLAP (30 microM) addition to the perfusion medium, biliary secretion of metabolite 1 and 2 reached a maximum of 1.04 +/- 0.52 and 11.34 +/- 4.72 nmol/g.liver.min, respectively. Biliary excretion of parent FLAP, however, continuously increased for 60 min up to 406 +/- 134 pmol/g liver.min. In the perfusate, metabolite 1 was below detection limit and release of metabolite 2 was low (2.8 +/- 0.7 pmol/g liver.min after 60 min). Enzymatic hydrolysis with beta-glucuronidase, mass spectroscopy and electron absorption spectroscopy revealed that both metabolites are monoglucuronides with the glucuronide in position 5 and 7 of the flavonoid core, respectively. The amount of FLAP, metabolite 1 and metabolite 2 excreted into bile during the 60 min of perfusion was 1.94 +/- 0.91, 5.15 +/- 1.95 and 57.29 +/- 23.60% of FLAP cleared from the perfusate during 60 min, respectively. In contrast to the structurally similar flavonoids genistein and daidzein, no inhibition of UDP-glucuronyltransferase with methylumbelliferone as a substrate was observed indicating that different UDP-glucuronyltransferase isoforms are involved in FLAP metabolism. In conclusion, we find that glucuronidation is the major mechanism of hepatic FLAP biotransformation. Metabolites are mainly excreted into bile but also released into systemic circulation. The pharmacological and toxicological effects of these metabolites remain to be elucidated.

Investigating the structural basis of arylamides to improve potency against M. tuberculosis strain through molecular dynamics simulations

Arylamides have been identified as direct InhA inhibitors which overcome the drug-resistance problem of isoniazid, the first-line drug for tuberculosis treatment. However, arylamide properties are not yet optimal against Mycobacterium tuberculosis. Arylamides show high potency in InhA enzyme assay, but they fail in antimycobacterial assay. To achieve the structural basis to improve antimycobacterial activity, the dynamic behavior of arylamide inhibitors and a substrate, trans-2-hexadecenoyl-(N-acetylcysteamine)-thioester, were carried out by molecular dynamics (MD) simulations. Arylamide inhibitors and a substrate are positioned at the same site which indicates the competitive inhibitor function of arylamides. Based on our findings, the amide carbonyl oxygen causes the selectivity of arylamide inhibitors for InhA inhibition. Moreover, this moiety is crucial for the affinity of the arylamide-InhA interactions with Tyr158 and NADH to form hydrogen bonds. It is possible to enhance the selectivity of arylamide inhibitors to reach the InhA target by introducing a hydrophilic substituent into the aryl ring A. In order to increase the membrane permeability of arylamide inhibitors, more lipophilic properties should be incorporated into the substituent B. Therefore, based on the obtained results, the correct balance between the selectivity and the membrane permeability of arylamide inhibitors should improve their inhibitory activity against M. tuberculosis strain.

MANNICH BASES AS MODEL COMPOUNDS FOR INTRAMOLECULAR HYDROGEN BONDING. I. SOLID STATE STRUCTURES AND MOLECULAR CALCULATIONS

SummaryA survey of the structures and the properties of the hydrogen bonds inortho-aminomethylphenols and -naphthols in the solid state is presented. The results are compared with molecular structure calculations. The solid state complexes can exist in the molecular or in zwitterionic form. In the last case, only intermolecular hydrogen bonds forming cyclic dimers or linear chains were detected.ZusammenfassungEine Übersicht über Strukturen und Eigenschaften von Wasserstoffbrücken inortho-Aminomethylphenolen und -naphtholen wird präsentiert. Die Ergebnisse werden mit Molekülrechnungen verglichen. Im Festkörper existieren diese Verbindungen in neutraler oder in zwitterionischer Form. Für den zweiten Fall können nur intermolekulare Wasserstoffbrücken nachgewiesen werden, und zwar in Dimeren oder in linearen Ketten.

Spectroscopic and structural consequences of intramolecular hydrogen bond formation in ortho-dimethylaminomethylphenol

Abstract Ab initio and density functional calculations are applied to analyse the structure of the Mannich base ortho -dimethylaminomethylphenol with emphasis on a detailed description of the properties of the intramolecular hydrogen bond. The calculated structures of the components, phenol and dimethylbenzylamine, are compared to the geometries of the hydrogen-bonded and open forms of the Mannich base. Additionally, the gas-phase infrared spectra of the Mannich base and of dimethylbenzylamine are presented. The experimental spectra are confronted with theoretical infrared spectra and interpreted with the aid of a detailed normal coordinate analysis. Trends in the modifications of computed harmonic force constants upon closure of the intramolecular hydrogen bond are monitored and discussed.

Excited-State Intermolecular Proton Transfer Reactions of 7-Azaindole(MeOH)n (n = 1 - 3) Clusters in the Gas phase: On-the-Fly Dynamics Simulation

Ultrafast excited-state intermolecular proton transfer (PT) reactions in 7-azaindole(methanol)(n) (n = 1-3) [7AI(MeOH)(n=1-3)] complexes were performed using dynamics simulations. These complexes were first optimized at the RI-ADC(2)/SVP-SV(P) level in the gas phase. The ground-state structures with the lowest energy were also investigated and presented. On-the-fly dynamics simulations for the first-excited state were employed to investigate reaction mechanisms and time evolution of PT processes. The PT characteristics of the reactions were confirmed by the nonexistence of crossings between S(ππ*) and S(πσ*) states. Excited-state dynamics results for all complexes exhibit excited-state multiple-proton transfer (ESmultiPT) reactions via methanol molecules along an intermolecular hydrogen-bonded network. In particular, the two methanol molecules of a 7AI(MeOH)(2) cluster assist the excited-state triple-proton transfer (ESTPT) reaction effectively with highest probability of PT.

Density functional calculations on meloxicam–β-cyclodextrin inclusion complexes

The geometries of the cyclodextrin (CD) inclusion complexes with various tautomeric forms of meloxicam in gas phase were determined by DFT calculation (B3LYP/6-31G (d,p)). The interaction energies were estimated including basis set superposition error (BSSE) correction. Two orientations of the meloxicam guest were considered: the benzene ring located near the narrow rim and at the wider rim of the beta-cyclodextrin, respectively. The calculations show that in all cases the molecules are located inside the CD cavity. The preferred complexation orientation is that one, in which the benzene ring of meloxicam is located near the wider rim with the secondary hydroxyl groups of the CD. The stabilization energies for the encapsulation of the meloxicam guest molecules show an overall affinity ranking for the meloxicam guest molecule in the following order: anionic (deprotonated) form>zwitterionic form approximately enolic form>cationic (protonated) form. A comparison of the enolic and zwitterionic neutral forms shows, that the zwitterionic structure is better stabilized upon complexation due to the geometry of two extra hydrogen bonds between host and guest.

Beiträge zur Chemie der Pyrrolpigmente, 38. Mitt.: Zur Assoziation von Gallenpigmenten

The long standing problem of solvent dependent absorption spectra of certain bile pigments such as bilirubindimethylester has been solved by measurement of molecular masses by means of vapour pressure osmometry. Using this method and the investigation of the concentration and temperature dependence of the absorption spectra on several model compounds an association equilibrium for pigments of the rubinoid structural type could be confirmed. Moreover the optical properties of the coexisting species and the corresponding equilibrium constants could be deduced by spectroscopic techniques. Verdinoid pigments lacking free carboxylic functions on the other hand tend to be monomeric in solution. A heteroassociated species involving equimolar amounts of a verdinoid and a rubinoid pigment could be verified existing on adsorbents like silicagel.

Solubility enhancement of low soluble biologically active compounds—temperature and cosolvent dependent inclusion complexation

The solubility enhancement of biologically active compounds was analysed in dependence on temperature, amount of cosolvents and on beta-cyclodextrin as complexing agent. The analysis was performed for the systemic fungicide triflumizole (TF), a poorly water soluble compound. All parameters lead to an improvement of the solubility, the largest effect was obtained for host-guest complexation with beta-cyclodextrin. Generally, the combination of cosolvents and beta-cyclodextrin does not increase the solubility of the compound, because cosolvents destabilize the inclusion complex. At higher cosolvent concentrations the solubility of TF is mainly determined by the solubility of the free non-complexed compound in the solvent mixtures. Raising temperature enhances the solubility in any cases. It could be shown that the temperature dependence of the solubility of TF is controlled by the solubility in the solvent mixtures and not by the inclusion reaction.

On the structure and torsional potential of trifluoromethoxybenzene: an ab initio and density functional study

Abstract The torsional potential of trifluoromethoxybenzene around the aryl–O bond was investigated with the aid of large-scale ab initio calculations performed at the Moller–Plesset second order (MP2) level, with several post-MP2 methods, and with a hybrid density functional method (B3LYP). Contrary to several recent reports, we do not find substantial qualitative differences between MP2 and B3LYP results, provided sufficiently large basis sets are used. The results are confronted with analogous MP2 and B3LYP data for methoxybenzene, for hypothetical anions as obtained by deprotonation at the para -position, and for ethylbenzene. The trends in the calculated torsional potentials, barrier heights and energy differences between conformers are discussed and correlated with selected structural parameters.