Eigenvalue analysis of peroxisome proliferator-activated receptor gamma agonists

Eigenvalue analysis (EVA) was conducted on a series of potent agonists of peroxisome proliferator-activated receptor gamma (PPARgamma). Predictive EVA quantitative structure-activity relationship (QSAR) models were established using the SYBYL package, which had conventional r2 and cross-validated coefficient (q2) values up to 0.920 and 0.587 for the AM1 method and 0.863 and 0.586 for the PM3 method, respectively. These models were validated by a test set containing 18 compounds. The capability to predict by these two models for PPARgamma agonists, with the best predictive r2pred value of 0.614 for AM1 and 0.822 for PM3 methods, set a successful example for applying a similar approach in building QSAR models for PPARalpha and -delta that could potentially offer a new opportunity in the design of novel PPAR modulators.     

Screening for 2-quinolinone-derived selective androgen receptor agonists in doping control analysis

Selective androgen receptor modulators (SARMs) represent a class of emerging drugs with high potential for misuse in sports, and therefore members of this group are banned as anabolic agents by the World Anti-Doping Agency. Preventive approaches to restrict their use include early implementation of target analytes into doping control screening assays and evaluation of the mass spectrometric behavior of these drugs to allow their unequivocal identification as well as the characterization of structurally related compounds and metabolic products. Four model SARMs with the 6-alkylamino-2-quinolinone structure, including the advanced drug candidate LGD-2226, were synthesized. Fragmentation pathways after positive electrospray ionization and collision-induced dissociation were studied using an LTQ Orbitrap mass analyzer, and diagnostic product ions and common dissociation pathways were employed to establish a screening procedure targeting intact quinolinone-based SARMs as well as putative metabolic products such as dealkylated analogues. Therefore, features of a triple quadrupole mass analyzer such as multiple reaction monitoring and precursor ion scanning were utilized. Sample preparation based on commonly employed liquid-liquid extraction and subsequent liquid chromatographic/tandem mass spectrometric measurement allowed for detection limits of 0.01-0.2 ng/mL, and intra- and interday precisions between 3.2 and 8.5% and between 6.3 and 16.6%, respectively. Recoveries varied from 81 to 98%, and tests for ion suppression or enhancement effects were negative for all analytes.     

The role of adenosine receptor agonists in regulation of hematopoiesis

The review summarizes data evaluating the role of adenosine receptor signaling in murine hematopoietic functions. The studies carried out utilized either non-selective activation of adenosine receptors induced by elevation of extracellular adenosine or by administration of synthetic adenosine analogs having various proportions of selectivity for a particular receptor. Numerous studies have described stimulatory effects of non-selective activation of adenosine receptors, manifested as enhancement of proliferation of cells at various levels of the hematopoietic hierarchy. Subsequent experimental approaches, considering the hematopoiesis-modulating action of adenosine receptor agonists with a high level of selectivity to individual adenosine receptor subtypes, have revealed differential effects of various adenosine analogs. Whereas selective activation of A? receptors has resulted in suppression of proliferation of hematopoietic progenitor and precursor cells, that of A? receptors has led to stimulated cell proliferation in these cell compartments. Thus, A? and A? receptors have been found to play a homeostatic role in suppressed and regenerating hematopoiesis. Selective activation of adenosine A? receptors has been found to act curatively under conditions of drug- and radiation-induced myelosuppression. The findings in these and further research areas will be summarized and mechanisms of hematopoiesis-modulating action of adenosine receptor agonists will be discussed.     

Comparative analysis of the methods for measurement of membrane surface potential of planar lipid bilayers

Different methods for the measurement of the membrane surface potential Φ_m, or changes therein (ΔΦ_m), are described and compared with respect to their sensitivity, generality of application and ease of use. Examples of the measurement of ΔΦ_m for the determination of the surface charge density of planar lipid bilayers are presented.     

Structural basis for engineering of retinoic acid receptor isotype-selective agonists and antagonists.

BACKGROUND: Many synthetic retinoids have been generated that exhibit a distinct pattern of agonist/antagonist activities with the three retinoic acid receptors (RARalpha, RARbeta and RARgamma). Because these retinoids are selective tools with which to dissect the pleiotropic functions of the natural pan-agonist, retinoic acid, and might constitute new therapeutic drugs, we have determined the structural basis of their receptor specificity and compared their activities in animal and yeast cells. RESULTS: There are only three divergent amino acid residues in the ligand binding pockets (LBPs) of RARalpha, RARbeta and RARgamma. We demonstrate here that the ability of monospecific (class I) retinoid agonists and antagonists to bind to and induce or inhibit transactivation by a given isotype is directly linked to the nature of these residues. The agonist/antagonist potential of class II retinoids, which bind to all three RARs but depending on the RAR isotype have the potential to act as agonists or antagonists, was also largely determined by the three divergent LBP residues. These mutational studies were complemented by modelling, on the basis of the three-dimensional structures of the RAR ligand-binding domains, and a comparison of the retinoid agonist/antagonist activities in animal and yeast cells. CONCLUSIONS: Our results reveal the rational basis of RAR isotype selectivity, explain the existence of class I and II retinoids, and provide a structural concept of ligand-mediated antagonism. Interestingly, the agonist/antagonist characteristics of retinoids are not conserved in yeast cells, suggesting that yeast co-regulators interact with RARs in a different way than the animal cell homologues do.     

A multiplexed screening method for agonists and antagonists of the estrogen receptor protein

The estrogen receptor (ER) is regarded as a significant drug target because of its important physical and pathological function. In this article, we describe a novel screening method to obtain agonists and antagonists of ER. ER was immobilized onto an aldehyde-modified glass slide. The affinity of Cy3-labeled estradiol for ER protein microarrays was then determined. Two libraries, one containing 29 synthetic compounds and the other with 384 natural products that served as a model, were screened to find new ligands for ER. The IC₅₀ values obtained for tamoxifen and raloxifene were consistent with those found in the literature (4.85 × 10⁻⁷ M versus 1.74~4.23 × 10⁻⁷ M and 7.58 × 10⁻⁸ M versus 0.89~5.84 × 10⁻⁸ M, respectively). Finally, 65 active ligands (5 synthetic compounds and 60 natural products) of ER were identified. This novel method gave identical results to a conventional fluorescence polarization assay, thus verifying the accuracy of this simultaneous multireceptor screening method based on protein microarrays. The presented method is sensitive, accurate, and reliable, and shows great potential for use in high-throughput drug-screening research.     

Identification of arginine analogues as antagonists and agonists for the melanocortin-4 receptor

In the present study, conducted to explore potent and small molecular melanocortin-4 (MC4) receptor ligands, we found that tripeptide 3a, containing a D-Phe-Arg-2-Nal (Nal; naphthylalanine) sequence, exhibited a moderate affinity for the MC4 receptor. Structural optimization led to the identification of a compound with a high affinity for the MC4 receptor, namely, tripeptide 3e, which showed a 70-fold higher affinity for the MC4 receptor than the lead compound 3a. Moreover, in an effort to further reduce the peptidic characters of tripeptide 3e, we found that dipeptide 3g exhibited a relatively high affinity for the MC4 receptor. Furthermore, in these analogues, the substituted position (1' vs. 2') of the naphthyl ring of Nal residue at position 7 was found to be important for the differentiation of agonist and antagonist activity. The synthesis and structure-activity relationships of the arginine analogues as MC4 receptor ligands were described in this paper.     

Alpha7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach

A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.     

Interfaces for data processing in surface analysis

As computer controlled instruments for surface analysis are in common use for many years, the problem of exchangeability of analytical data has attracted interest in the surface analysis community. More and more examples for the development of standarized data formats as the VAMAS format [1] and the Standard for Chromatography Data Communication from the AIA [2] have been published. There are a few attempts to establish standardized “data dictionaries” e.g. the parameter lists describing AES and XPS spectra pusblished in Surface Science Spectra [3, 4]. If several different analysis methods (such as AES, SAM, XPS, SIMS, STM, AFM, EPMA, …) are applied to the same sample, a quite independent and open approach is needed to be able to combine data of various instruments in a common data evaluation procedure. It could be the basic concept of real mutli-method analysis. The public domain software package MAXMIND has been developed, as only a standardized data exchange and storage format based on data dictionaries can guarantee a high level of independence of proprietary measurement systems. Received: 16 January 1997 / Revised: 9 May 1997 / Accepted: 14 May 1997     

Interfaces for data processing in surface analysis

As computer controlled instruments for surface analysis are in common use for many years, the problem of exchangeability of analytical data has attracted interest in the surface analysis community. More and more examples for the development of standarized data formats as the VAMAS format [1] and the Standard for Chromatography Data Communication from the AIA [2] have been published. There are a few attempts to establish standardized “data dictionaries” e.g. the parameter lists describing AES and XPS spectra pusblished in Surface Science Spectra [3, 4]. If several different analysis methods (such as AES, SAM, XPS, SIMS, STM, AFM, EPMA, …) are applied to the same sample, a quite independent and open approach is needed to be able to combine data of various instruments in a common data evaluation procedure. It could be the basic concept of real mutli-method analysis. The public domain software package MAXMIND has been developed, as only a standardized data exchange and storage format based on data dictionaries can guarantee a high level of independence of proprietary measurement systems. Received: 16 January 1997 / Revised: 9 May 1997 / Accepted: 14 May 1997     

Preparation of samples for surface analysis

Analysis of single atomic layers at surfaces and interfaces is now possible routinely, using such techniques as Auger electron spectroscopy, X-ray photoelectron spectroscopy and secondary ion mass-spectroscopy. The handling of specimen surfaces before analysis is therefore critical to ensure a valid measurement of composition.     

Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents

We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.     

Activities and identification of aryl hydrocarbon receptor agonists in sediments from the Danube river

This study is a consequence of a distinct fish decline in the Danube river since the beginning of the 1990s. In contrast to the decline of fish population, former studies have repeatedly documented that the water quality along the Danube river is improving. However, the conclusion of a pilot study in 2002 was that a high hazard potential is associated with local sediments. The present study documents that sediment samples from the Danube river showed comparatively high aryl hydrocarbon receptor mediated activity in biotests, using the cell lines GPC.2D.Luc, H4IIE (DR-CALUX) and RTL-W1. The combination of chemical analysis, fractionation techniques and different in vitro tests revealed that priority pollutants could not explain the main induction, even though the concentrations of priority polycyclic aromatic hydrocarbons (PAHs) were very high (maximum in the tributary Schwarzach, sum of 16 EPA PAHs 26 mug/g). In conclusion, this investigation shows that nonpriority pollutants mainly mediate the high induction rates. Nevertheless, owing to the effects of PAHs towards fish and the connection between dioxin-like activity and carcinogenicity, the link between contamination and the fish population decline cannot be ruled out.