QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping.

An affinity fingerprint is the vector consisting of compound's affinity or potency against the reference panel of protein targets. Here, we present the QAFFP fingerprint, 440 elements long in silico QSAR-based affinity fingerprint, components of which are predicted by Random Forest regression models trained on bioactivity data from the ChEMBL database. Both real-valued (rv-QAFFP) and binary (b-QAFFP) versions of the QAFFP fingerprint were implemented and their performance in similarity searching, biological activity classification and scaffold hopping was assessed and compared to that of the 1024 bits long Morgan2 fingerprint (the RDKit implementation of the ECFP4 fingerprint). In both similarity searching and biological activity classification, the QAFFP fingerprint yields retrieval rates, measured by AUC (~ 0.65 and ~ 0.70 for similarity searching depending on data sets, and ~ 0.85 for classification) and EF5 (~ 4.67 and ~ 5.82 for similarity searching depending on data sets, and ~ 2.10 for classification), comparable to that of the Morgan2 fingerprint (similarity searching AUC of ~ 0.57 and ~ 0.66, and EF5 of ~ 4.09 and ~ 6.41, depending on data sets, classification AUC of ~ 0.87, and EF5 of ~ 2.16). However, the QAFFP fingerprint outperforms the Morgan2 fingerprint in scaffold hopping as it is able to retrieve 1146 out of existing 1749 scaffolds, while the Morgan2 fingerprint reveals only 864 scaffolds.

Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach.

TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.

Exploring of protein - protein interactions at the solid - aqueous interface by means of contact angle measurements.

In this article we present the results of the studies on interactions between the VC1 domain of the Receptor for Advanced Glycation End Products (RAGE) and its ligand, the S100B protein, performed by contact angle measurements. Histidine-tagged (His6) VC1-RAGE domain was covalently bonded to Cu(II) or Ni(II) complexes with dipyrromethene (DPM) self-assembled on gold surface. The method based on the theory of van Oss was used for the purpose of determining the Lifshitz-van der Waals (γ(LW)) component as well as the electron acceptor-electron donor (the Lewis acid-base, γ(+)-γ(-)) parameters of the VC1-RAGE-S100B complex. Moreover, the surface free energies of the interactions between the VC1 domain attached to the surface and the ligand present in the aqueous phase were determined. The specificity of the VC1- RAGE interactions with the ligand studied was also proved.

Synthesis and Validation of a Hydroxypyrone-Based, Potent, and Specific Matrix Metalloproteinase-12 Inhibitor with Anti-Inflammatory Activity In Vitro and In Vivo.

A hydroxypyrone-based matrix metalloproteinase (MMP) inhibitor was synthesized and assayed for its inhibitory capacity towards a panel of ten different MMPs. The compound exhibited selective inhibition towards MMP-12. The effects of inhibition of MMP-12 on endotoxemia and inflammation-induced blood-cerebrospinal fluid barrier (BCSFB) disruption were assessed both in vitro and in vivo. Similar to MMP-12 deficient mice, inhibitor-treated mice displayed significantly lower lipopolysaccharide- (LPS-) induced lethality compared to vehicle treated controls. Following LPS injection Mmp-12 mRNA expression was massively upregulated in choroid plexus tissue and a concomitant increase in BCSFB permeability was observed, which was restricted in inhibitor-treated mice. Moreover, an LPS-induced decrease in tight junction permeability of primary choroid plexus epithelial cells was attenuated by inhibitor application in vitro. Taken together, this hydroxypyrone-based inhibitor is selective towards MMP-12 and displays anti-inflammatory activity in vitro and in vivo.

2-Aminothiophene-3-carboxylic acid ester derivatives as novel highly selective cytostatic agents.

Cytostatic agents often do not discriminate in their cytostatic potential between different tumor cell types in vitro. In this study, several 2-aminothiophene-3-carboxylic acid ester derivatives were discovered that show an unusual cytostatic selectivity for several T-cell (but not B-cell) lymphoma, prostate cancer, kidney carcinoma and hepatoma cell lines. Their 50 % cytostatic concentrations were generally in the higher nanomolar range and were approximately 20- to 50-fold lower for these tumor cell types than for any other tumor cell line or non-tumorigenic cells. The tumor-selective compounds caused a more preferential suppression of protein synthesis than DNA or RNA synthesis and the prototype compound 3 resulted in an accumulation of prostate cancer cells in the G1 phase of their cell cycle. Compound 3 was also shown to induce apoptosis in prostate cancer cells. The 2-aminothiophene-3-carboxylic acid ester derivatives represent novel candidate cytostatic agents to be further explored for their tumor-selective potential.

Antihyperglycemic activity of extracts from Boldoa purpurascens leaves in alloxan-induced diabetic rats.

In order to investigate the potential use of Boldoa purpurascens against diabetes, the antihyperglycemic effect of an ethanol extract obtained from its leaves was evaluated at doses of 50, 100 and 200 mg/kg in rats after induction of hyperglycemia by alloxan. Insulin 5 IU/kg was used as positive control and NaCl 0.9% as negative control. A similar experiment was performed with the aqueous extract used at doses of 50 and 100 mg/kg using metformin at a dose of 50mg/kg as positive control. Statistical analysis was carried using the Kruskal-Wallis test with an interval of trust of 99%. The ethanolic and aqueous extract of B. purpurascens showed a significant decrease of blood glucose levels 72 h after administration. Phytochemical analysis of the ethanol extract showed the presence of D-pinitol, a compound known for its hypoglycemic properties. In conclusion, ethanolic as well as aqueous extracts of B. purpurascens leaves show antihyperglycemic activity, possibly due to the presence of D-pinitol and flavonoids.

Analysis of the exponential character of single molecule rotational correlation functions for large and small fluorescence collection angles.

Coarse-grained molecular dynamics simulations and single molecule fluorescence microscopy experiments have been performed in order to investigate the influence of the numerical aperture (NA) of the microscope objective on the exponential character of the rotational correlation functions of probes embedded in complex matrices. The results obtained by using either a dry lens (NA=0.95) or an oil objective (NA=1.4) show that, in the moderately (simulations) and deeply (experiment) supercooled melts, the rotational (linear dichroism) correlation functions of the single molecules (SMs) exhibit a nonexponential character. Furthermore, by fitting Kohlrausch-Williams-Watt functions to the correlation curves, the stretching parameters turn out to be very similar for both types of objectives. Our results demonstrate that the nonexponentiality is intrinsic to the complex rotational dynamics of the SM in the supercooled solid and point to the validity of the use of a high NA dry lens to perform such experiments.

Pharmacology of inositol trisphosphate receptors.

In almost all cells, cytosolic Ca(2+) is a crucial intracellular messenger, regulating many cellular processes. In non-excitable as well as in some excitable cells, Ca(2+) release from the intracellular stores into the cytoplasm is primarily initiated by the second messenger inositol 1,4,5-trisphosphate (IP(3)), which interacts with the IP(3) receptor (IP(3)R), a tetrameric intracellular Ca(2+)-release channel. This review focuses on the pharmacological modulation of the various functionally important sub-domains of the IP(3)R, including the IP(3)-binding domain, calmodulin-binding sites, adenine nucleotide-binding sites and the sites for interaction for FK506-binding proteins and other regulators. We will particularly focus on the pharmacological tools that interfere with these domains and discuss their relative specificity for the IP(3)R, thereby indicating their potential usefulness for unraveling the complex functional regulation of the IP(3)R.

Photolabile dendrimers using o-nitrobenzyl ether linkages

[reaction: see text] Benzyl aryl ether dendrimers containing photosensitive, veratryl-based o-nitrobenzyl AB linkages (bold bonds) were prepared to the third generation and shown to undergo site-specific degradation when irradiated with ultraviolet light.

N-Confused Calix

Next to the "normal" calix[4]pyrrole 1, the N-confused calix[4]pyrrole 2 is formed in substantial amounts (up to 22 % yield) as side product in the acid-catalyzed condensation reaction of ketones and pyrrole. In some cases, doubly N-confused calix[4]pyrroles are also formed.