Novel sesquiterpenoids from the fermentation of Xylaria persicaria are selective ligands for the NPY Y5 receptor

Neuropeptide Y (NPY) is a polypeptide found in the peripheral and central nervous system and is involved in the regulation of feeding. Antagonists of NPY receptor activation could therefore have potential for development as antiobesity drugs. Fermentation of an isolate of Xylaria persicaria yielded two novel eremophilane sesquiterpenoids xylarenals A (1) and B (2). These compounds are selective for the NPY Y5 receptor but have only modest affinity. The isolation, structure elucidation, and biological activities of these compounds are described.     

Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings

This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute s AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems.     

A convenient 3-step synthesis of 3-acetamido-6-arylpyridazines directed to novel Y5 receptor antagonist

A 3-step synthesis of 3-acetamido-6-arylpyridazines as potential NPY5 antagonists.     

Chimeric protein probes for C5a receptors through fusion of the anaphylatoxin C5a core region with a small-molecule antagonist

Blockade of the interaction of anaphylatoxin C5a with its receptor C5aR1 has been actively studied as a potential treatment for many inflammatory diseases; but current C5a antagonists exhibit inadequate potency and poor species cross-reactivity, and novel biochemical tools are needed to investigate whether the core region of C5a contains important interaction epitopes that can explain these limitations. Herein, we report the development of chimeric protein C5a probes containing both the complete core region of rat or human C5a, and the small-molecule antagonist PMX53-1. These probes were chemically synthesized through hydrazide-based native chemical ligation of a linear peptide hydrazide with the requisite cyclopeptidic antagonist, both of which were made by solid-phase synthesis. Quasi-racemic X-ray crystallography established that attachment of PMX53-1 did not affect the structure of the core region of C5a. Subsequent C5aR1 activity assays demonstrated the probes can provide valuable insights into the development of C5a antagonists; for example, they exhibited significantly better binding affinity and much improved species cross-reactivity than PMX53-1, supporting the notion that the effect of some epitopes outside the C-terminus of C5a should be taken into consideration when designing better C5a antagonists. Surprisingly, the core region of C5a was found to partially agonize C5aR1, suggesting the presence of more than one agonistic interaction in the binding of C5a to C5aR1. This study exemplifies the value of chemical protein synthesis in developing novel receptor probes for drug discovery research.     

On the applicability of CNDO indices for the prediction of chemical reactivity

A series of CNDO/2 molecular orbital properties were evaluated to determine their utility in parameterizing chemical reactivities. Some of these indices were used previously for only electron methods and were extended here to include the framework. Theoretical rationales were given for this extension to the semi-empirical all valence electron methods. Four systems, the aromatic hydrocarbons, the benzene derivatives, the substituted benzoic acids, and the substituted phenyl amines, were studied to test how well these indices can parameterize chemical reactivities. This study focused on reactions involving both and electrons where the reactive site is not necessarily on the aromatic framework. For the nonplanar and heteropolar systems, these indices performed as well as the Hückel method did for the classical aromatics. These CNDO indices should perform effectively in multivariable regressions to parameterize the reactivities for more complicated problems such as those encountered in quantitative structure activity relationships of drugs.     

Precision heat capacity measurements for the characterization of two-phase polymers

Structure sensitive thermal analysis results on linear macromolecules can be obtained when correcting measurements with heat capacity instead of baseline data. The ATHAS (Advanced Thermal Analysis) effort in heat capacities of crystals, glasses and liquids is described, and applied to the interpretation of microphase separated samples. Semicrystalline homopolymers, block-copolymers, and blends are to be discussed.

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Zusammenfassung Ergebnisse der struktursensitiven thermischen Analyse von linearen Makromolekülen können erhalten werden, wenn die Messungen mit der Wärmekapazität anstatt mit Grundlinien- Daten korrigiert werden. Semikristalline Hochpolymere, Blockpolymere und Mischpolymere werden diskutiert.

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The ATHAS research has been supported by the U.S. National Science Foundation, Polymers Program. Present Grant Number DMR 83-17097.     

Experimental measurements and prediction of liquid densities for n-alkane mixtures

We present experimental liquid densities for n-pentane, n-hexane and n-heptane and their binary mixtures from (273.15 to 363.15) K over the entire composition range (for the mixtures) at atmospheric pressure. A vibrating tube densimeter produces the experimental densities. Also, we present a generalized correlation to predict the liquid densities of n-alkanes and their mixtures. We have combined the principle of congruence with the Tait equation to obtain an equation that uses as variables: temperature, pressure and the equivalent carbon number of the mixture. Also, we present a generalized correlation for the atmospheric liquid densities of n-alkanes. The average absolute percentage deviation of this equation from the literature experimental density values is 0.26%. The Tait equation has an average percentage deviation of 0.15% from experimental density measurements.     

A novel route for the synthesis of androgen receptor antagonist enzalutamide

A novel route of enzalutamide was developed in five steps. Starting from 4-amino-2-(trifluoromethyl)benzonitrile (7) and Boc-2-aminoisobutyric acid (16), condensation, deprotection, Ullmann coupling, cyclization and amination provided enzalutamide in 41.0% total yield. This route avoids the using of toxic chemical, unstable intermediate and high-risk reaction. It is a potential efficient and economical procedure for industrialization.     

Refinement and use of the approximate similarity in QSAR models for benzodiazepine receptor ligands

Several considerations for refining the approximate similarity measurements have been introduced in this paper: the use of topological invariants for the calculation of similarity indexes and the development of new similarity correction processes. The quality of the new similarity measurements obtained with the proposed methods has permitted the development of fast, cheap, and simple quantitative structure-activity relationship models for the prediction of biological activities of nonbenzodiazepine gamma-aminobutyric acid(A)/benzodiazepine receptor ligands (58 compounds). Internal and external validations were carried out for the approximate similarity matrices computed using different approaches. Satisfactory results which compare reasonably well with a 3D approach were obtained: Q2= 0.65 and standard error in cross validation SECV= 0.83 for the training stage; r = 0.79 and error in external prediction = 0.82 for the test step. In addition, the method proposed was compared with other topological approaches based on constitutional similarity and on fingerprints. Satisfactory results were obtained.     

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances

Summary This paper reports a comparison of several methods for measuring the degree of similarity between pairs of 3-D chemical structures that are represented by inter-atomic distance matrices. The methods that have been tested use the distance information in very different ways and have very different computational requirements. Experiments with 10 small datasets, for which both structural and biological activity data are available, suggest that the most cost-effective technique is based on a mapping procedure that tries to match pairs of atoms, one from each of the molecules that are being compared, that have neighbouring atoms at approximately the same distances.     

Structural characterization and prediction of Kovats retention indices (RI) for alkylbenzene compounds

A new molecular structural characterization (MSC) method called the molecular vertex eigenvalue correlative index (MVECI) is constructed and used to describe the structures of 122 alkylbenzene compounds. Through multiple linear regression (MLR) and stepwise multiple regression (SMR), a quantitative structure-retention relationship (QSRR) model with correlation coefficient (R) of 0.995 is obtained. Through partial least-square regression (PLS), another QSRR model with correlation coefficient (R) of 0.991 is obtained. The estimation stability and prediction ability of the two models are strictly analyzed by both internal and external validations. For the internal validation, the cross-validation (CV) correlation coefficients (R _CV) of the two models are 0.993 and 0.988. For the external validation, the correlation coefficients (R _test) of the two models are 0.996 and 0.995, respectively. The results show that the stability and predictability of the models are good, and the molecular vertex eigenvalue correlative index can successfully describe the structures of alkylbenzene compounds.     

Probing the interaction of a glycoprotein IIb/IIIa receptor antagonist with bound platelets using electrochemical impedance

A label-free assay is described to monitor the interaction of abciximab, a glycoprotein IIb/IIIa receptor antagonist (ReoPro), with platelets bound to a fibrinogen-functionalised electrode surface. Firstly, fibrinogen is deposited in a defined pattern onto a gold electrode using microcontact printing, and then platelets from whole blood are captured on the patterned surface. Patterning influences the spreading of platelets, which is strikingly different to that observed on homogeneously coated surfaces. The drug–platelet interaction has been investigated using AC impedance on uniform and patterned fibrinogen-modified surfaces. The results demonstrate that patterned fibrinogen surfaces can provide deep insights into the interaction of abciximab with different platelet sub-populations. The key advantages of this approach are that it is rapid, label free and does not require pre-processing of patient blood samples.     

Determination of the heterogeneous association constants of metal ions to omega-mercaptoalkanoic acids by using double-layer capacity measurements.

The binding of metal ions to ligands in homogeneous solutions and that to the same ligands anchored to metallic surfaces through self-assembled monolayers (SAMs) are expected to differ primarily due to the difference in the degree of freedom of the ligands and the surface potential. We studied the heterogeneous binding of CdII ions to omega-mercaptoalkanoic-acid SAMs on Au. This was accomplished by adding metal ions at a constant pH and following the changes in the double-layer capacity. A mathematical treatment, which is based on calculating the electrochemical-potential differences at the double layer-solution interface, has been developed. Our approach follows that proposed by White et al. and Kakiuchi, who used the acid-base equilibrium at the monolayer-electrolyte interface as a means of calculating the pK of ionizable SAMs. Experimentally, SAMs of omega-mercaptoalkanoic acids, HS(CH2)nCO2H, with different chain lengths (i.e., n=2, 5, and 10) in 0.1 M sodium perchlorate were assembled on Au surfaces and studied. The capacity was measured first in the absence of CdII at different pH values, and then at a constant pH while increasing the concentration of CdII in the solution. We found that the interfacial capacity decreased as the concentration (of either protons or CdII) increased. The results matched the model fairly well, which allowed the extraction of the thermodynamic equilibrium constant that is established at the monolayer-electrolyte interface. The suggested mathematical treatment of this model system is simple and yet very useful for estimating the heterogeneous association constants of metal ions by SAMs.