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Biomedical subjects

L Orfi

Publications and source records attributed to L Orfi.

At least 19 recordsLinked to original sources
PubMed2006

Prediction oriented QSAR modelling of EGFR inhibition.

Epidermal Growth Factor Receptor (EGFR) is a high priority target in anticancer drug research. Thousands of very effective EGFR inhibitors have been developed in the last decade. The known inhibitors are originated from a very diverse chemical space but--without exception--all of them act at the Adenosine TriPhosphate (ATP) binding site of the enzyme. We have collected all of the diverse inhibitor structures and the relevant biological data obtained from comparable assays and built prediction oriented Quantitative Structure-Activity Relationship (QSAR) which models the ATP binding pocket's interactive surface from the ligand side. We describe a QSAR method with automatic Variable Subset Selection (VSS) by Genetic Algorithm (GA) and goodness-of-prediction driven QSAR model building, resulting an externally validated EGFR inhibitory model built from pIC50 values of a diverse structural set of 623 EGFR inhibitors. Repeated Trainings/Evaluations (RTE) were used to obtain model fitness values and the effectiveness of VSS is amplified by using predictive ability scores of descriptors. Numerous models were generated by different methods and viable models were collected. Then, intensive RTE were applied to identify ultimate models for external validations. Finally, suitable models were validated by statistical tests. Since we use calculated molecular descriptors in the modeling, these models are suitable for virtual screening for obtaining novel potential EGFR inhibitors.

Enzyme Inhibitors↗
PubMed2004

Comparison of measured and calculated lipophilicity of substituted aurones and related compounds.

A molecule library containing 55 aurone- and thioaurone-type structures has been designed and synthesised. Reversed phase high performance liquid chromatographic (RP-HPLC) method has been developed to separate these compounds and to characterise their lipophilicity by experimental method (k'). The experimental lipophilicity data have been compared with the computer calculated lipophilicity parameters (CLOGPs) of the same molecules. In general, good correlations between the measured and calculated lipophilicities have been found with the exception of structure isomers and compounds capable for hydrogen bonding. The chromatographic method was suitable to separate the structure (ortho and para) isomers of aurone and thioaurones and was sensitive enough to differentiate their lipophilicities. Our findings suggest the usefulness of the chromatographic method in fast characterisation of the lipophilicity of structurally closely related molecules.

Benzofurans↗
PubMed2003

Pro-apoptotic and anti-apoptotic molecules affecting pathways of signal transduction.

Selective inhibition of the "false" proliferative signals via targeting tyrosine kinases resulting in the induction of apoptosis by depletion of the "survival factors" is one of the most studied and widely accepted concepts of modern chemotherapy. We have synthesized a series of potent tyrosine kinase inhibitors and tested these compounds for apoptosis induction. Some of the tyrosine kinase inhibitors caused either apoptotic or cytoplasmic vacuolar cell death in various tumor cell cultures. The somatostatin analogue oligopeptide TT-232, which indirectly inhibits tyrosine kinases, exerted a dose-dependent apoptosis-inducing effect. The tumor growth-inhibitory effect of TT-232 and some tyrosine kinase inhibitors has also been proven by in vivo experiments, using human tumor xenografts. On the other hand, a dose-dependent pro- or anti-apoptotic activity of (-)-deprenyl has been shown in melanoma cell cultures, the lower doses inhibiting and the higher doses inducing apoptosis. Various metabolites of (-)-deprenyl are responsible for these actions. The effect of (-)-deprenyl is connected with depolarization of mitochondrial membranes. The kinase inhibitors act on the growth factor receptor signaling pathways (survival factor pathways) and initiate the caspase cascade. The key enzyme for the action of both pro-apoptotic and anti-apoptotic compounds is caspase 3.

Animals↗
PubMed2002

Reliability of logP predictions based on calculated molecular descriptors: a critical review.

Correct QSAR analysis requires reliable measured or calculated logP values, being logP the most frequently utilized and most important physico-chemical parameter in such studies. Since the publication of theoretical fundamentals of logP prediction, many commercial software solutions are available. These programs are all based on experimental data of huge databases therefore the predicted logP values are mostly acceptable - especially for known structures and their derivatives. In this study we critically reviewed the published methods and compared the predictive power of commercial softwares (CLOGP, KOWWIN, SciLogP/ULTRA) to each other and to our recently developed automatic QS(P)AR program. We have selected a very diverse set of 625 known drugs (98%) and drug-like molecules with experimentally validated logP values. We have collected 78 reported "outliers" as well, which could not be predicted by the "traditional" methods. We used these data in the model building and validation. Finally, we used an external validation set of compounds missing from public databases. We emphasized the importance of data quality, descriptor calculation and selection, and presented a general, reliable descriptor selection and validation technique for such kind of studies. Our method is based on the strictest mathematical and statistical rules, fully automatic and after the initial settings there is no option for user intervention. Three approaches were applied: multiple linear regression, partial least squares analysis and artificial neural network. LogP predictions with a multiple linear regression model showed acceptable accuracy for new compounds therefore it can be used for "in-silico-screening" and/or planning virtual/combinatorial libraries.

Combinatorial Chemistry Techniques↗
PubMed1999

Application of neural networks in structure-activity relationships.

Methodology and application of artificial neural networks in structure-activity relationships are reviewed focusing on the most frequently used three-layer feedforward back-propagation procedure. Two applications of neural networks are presented and a comparison of the performance with those of CoMFA and a classical QSAR analysis is also discussed.

Drug Design↗
PubMed1999

A novel normalized retention factor in micellar electrokinetic chromatography.

Characteristic properties of the expression k'' = (t(m)-t(o))/(t(mc)-t(o)) and its applicability in micellar electrokinetic capillary chromatography (MEKC) were compared to the previous expression, k' = (t(m)-t(o))/t(o)(1-t(m)/t(mc)), introduced by Terabe. It was proved with theoretical calculations (curve shape analysis) that the properties of function k'' are in full accordance with the properties of the MEKC system and k'' could be applied advantageously to characterize hydrophobicity of the analytes. This conclusion is now supported by experimental data obtained with homolog series of alkylbenzenes and alkylphenones as well as with hydrophobic protected peptides. Migration times, k', k'' values, and software-calculated hydrophobicity data are summarized and analyzed in the present study. Since k'' is a normalized parameter, good relationships between the migration time, the software-calculated hydrophobicity, and the k'' values were obtained. Differences in hydrophobicity of the analytes could be estimated in a more realistic way with the aid of function k'' than by using function k'. Hydrophobicity data estimated on the basis of the k'' values proved to be in good accordance with the expectations based on the migration times and on the chemical structures of the compounds investigated.

Benzene↗
PubMed1999

[Preparation and characterization of potential antineoplastic agents].

A parallel combinatorial library of over sixteen hundred compounds has been designed and synthesized for the development of new potential peptidomimetic protein tyrosine kinase (PTK) inhibitor leads that is aimed for intervening with the substrate binding site of the pp60c-src enzyme. The new structures were based on known PTK inhibitors having at least two variously substituted aromatic moieties attached by spacer groups of different length and flexibility. Eleven bis-aryl type inhibitory compounds were found in the range of 18-100 micromolar IC50 concentrations from combinations of twelve different substituents. Molecular modeling of the active compounds showed a characteristic distance of 13-14 A between the farthest sp2 carbon atoms of the two aromatic rings. Conformational analysis of several peptide substrates recently found for pp60c-src PTK [5,6,7] showed that the energy minimized conformers had the same distance between two aromatic moieties. Several compounds in the library not only showed remarkable PTK inhibitory activity but also a significant apoptosis inducing effect on HT-29 human colon tumor cells.

Antineoplastic Agents↗
PubMed1999

[Biological activity and structure of antitumor compounds from Plantago media L].

Tyrosine kinase inhibition and tumor growth inhibition activity of verbascoside and homoplantaginin are described. Both molecules proved to be equally significant inhibitors of isolated EGF-R tyrosine kinases, nevertheless their in vitro antiproliferative activity was variable in cellular assays. Their different inhibitory efficacies could be interpreted on the basis of conformational analysis and lipophilicity evaluation.

Antineoplastic Agents, Phytogenic↗
PubMed1997

Physicochemical characterization of psychosine by 1H nuclear magnetic resonance and electron microscopy.

Krabbe's disease is an autosomal recessive disease that affects the lysosomal enzyme galactosylceramidase. The storage of one of its substrates, psychosine (beta-galactosyl-sphingosine), is thought to be responsible for the induction of pathological changes. Psychosine has a free amine group which is necessary for the mediation of its toxic effects. In the present study, the physicochemical properties of psychosine were investigated. Nuclear magnetic resonance (NMR) detected pH titration was used to determine that the amine group had a pKa of 7.18 +/- 0.05. Pulsed-field gradient NMR spectroscopy was used to determine that the diffusion coefficient of 2.8 mM psychosine in D2O at pD 4.46 or 7.04 is 1.16 +/- 0.02 x 10(-10) m2/s or 0.77 +/- 0.02 x 10(-10) m2/s, respectively. Negative staining electron microscopy (EM) studies of acidic and neutral solutions of psychosine also were performed. At pH 4.5, spherical structures were formed, which were relatively stable between 3, 120, and 216 h following preparation; the diameter ranged from approximately 14 nm at the earliest time point to approximately 18 nm at the last time point. The critical micelle concentration (CMC) was 1.26 mM at pH 4.0. At pH 7.1, the structures changed from spherical structures with a diameter of 15-23 nm, at the earliest time point, to a heterogeneous population of structures ranging from spherical structures, with a diameter of only a few nm, to irregularly shaped oblong structures that had one or more dimensions exceeding 100 nm. The NMR and EM data indicate that the deprotonation of the amine group causes psychosine to form aggregates that are unstable, which prevents a determination of the CMC at a neutral pH. These data indicate that molecular interactions of psychosine at the acidic pH of the lysosome, where it is normally digested, are more orderly than those at the pH of the cytoplasm or extracellular space where psychosine goes during disease.

Diffusion↗
PubMed1996

Flk-1 as a target for tumor growth inhibition.

A number of growth factor receptor tyrosine kinases have been implicated in angiogenesis, including epidermal growth factor receptor, fibroblast growth factor receptor, platelet-derived growth factor receptor, Flk-1/KDR, Flt-1, Tie-1, and Tek/Tie-2. Flk-1/KDR, a receptor for vascular endothelial growth factor (VEGF), is expressed exclusively in endothelial cells. Using dominant-negative methods, Flk-1 was shown to play a role in angiogenesis and the growth of a variety of tumor types. Because of this, a drug discovery effort was established to identify Flk-1 kinase inhibitors. For initial screening, an ELISA in, a 96-well format was used to measure VEGF-induced Flk-1 tyrosine phosphorylation in whole cells. Compounds that inhibited ligand-induced receptor autophosphorylation were confirmed by antiphosphotyrosine immunoblotting. Inhibition of VEGF-stimulated DNA synthesis in human endothelial cells was also assessed. Inhibitors were further evaluated for their effects on vessel formation using the chorioallantoic membrane assay. Using these methods, antiangiogenesis compounds that inhibit Flk-1 tyrosine kinase activity, endothelial cell mitogenesis, and blood vessel formation in the chorioallantoic membrane assay have been found.

3T3 Cells↗
PubMed1996

Heterocondensed quinazolones: synthesis and protein-tyrosine kinase inhibitory activity of 3,4-dihydro-1H,6H-[1,4] oxazino-[3,4-b]quinazolin-6-one derivatives.

1-Benzylidene (2-14) and 1-phenylhydrazono derivatives (15-29) of 3,4-dihydro-1H,6H-[1,4]oxazino[3,4-b]quinazolin-6-one (1) were obtained from the condensation reactions of 1 with a series of aromatic aldehydes and by direct diazonium coupling with aryl-diazonium chlorides. The substances were tested for their ability to inhibit the tyrosine kinase activity of SW-620 (human colon carcinoma) cells. Compounds 8, 10, 12 and 13 showed remarkable inhibitory activity.

Antineoplastic Agents↗
PubMed1995

Two antithrombotic quinazolone derivatives.

The structures of two antithrombotic quinazolone derivatives, 1,2,3,5-tetrahydro-2-benzylimidazo[5,1-b]-quinazolin-5-one, (I), and 3-benzyl-2-[1-(2,5-xylidino)-ethyl]quinazolin-4(3H)-one, (II), display significant differences in the bond lengths in one region of the quinazolone moiety.

Crystallography, X-Ray↗
PubMed1995

Tyrphostin induces non-apoptotic programmed cell death in colon tumor cells.

The programmed cell death inducing effect of the EGF receptor tyrosine kinase inhibitor alpha-cyano-3,4-dihydroxycinnamthioamide (AG213) was investigated in vitro on HT-29 human colon tumor. AG213 at concentrations between 45 to 450 microM blocks the proliferation of HT-29 cells. Morphological findings suggest that the selective tyrosine kinase inhibitor AG213 induces Clarke III type (non-lysosomal vesiculate cytoplasmic) programmed cell death; unlike ATP analog non-selective tyrosine kinase inhibitors like Genistein which were found to induce apoptosis. Cycloheximide and Actinomycin-D reduced the effect of AG213 pointing to the fact that protein and RNA synthesis are also needed for this form of cell death. Acid phosphatase activity was found in the Golgi and in the newly formed intracytoplasmic vacuoles 3 hours after AG213 treatment which disappeared by 6 hours. The induction of Clarke III cell death by tyrosine kinase inhibitors may open a new modality to selective killing of tumor cells.

Acid Phosphatase↗
PubMed1995

[Synthesis of potential CCK antagonist quinazolone derivatives. II].

An alternative route has been developed for the synthesis of [1,4]diazepino[3,4-b]quinazolones (2), a new ring system of heterocondensed quinazolones. 2,3-Bifunctional quinazolones (4) were synthesized by halogenation of 2-alkyl-quinazolone-3-propionic acids, yield from the reaction of 2-alkyl-benzoxazone (3) with beta-alanine. The reaction of haloalkyl compounds (5,6) with N-nucleophiles produces [1,4]oxazepino-[3,4-b]quinazolones (8), a new heterocyclic ring system, and 3-[2'-hydroxi-ethyl-, or 3-[2'-chloro-ethyl-4' oxo(3'H)-quinazoline-3'-yl]propionamides (7, 9) in consecutive reaction. The cyclisation of 2-aminoalkyl-3-propionates (13) resulted in the title compounds (14). Physical data and properties of the newly synthesized compounds such as IR, UV and NMR spectra were obtained for all compounds reported.

Cholecystokinin↗
PubMed1995

[Synthesis of potential CCK antagonist quinazolone derivatives].

An original route has been found for the synthesis of [1,4]diazepino-quinazolones, a new ring system of heterocondensed quinazolones. These anthranilicacid-alanin-beta-alanin cyclopeptide derivatives constitute a structural moiety of asperlicin, the first natural cholecystokinin antagonist alkaloid. These compounds are therefore potential CCK antagonists. The new compounds were prepared via condensation of 2-amino-alkyl-quinazolones, obtained from 2-alkyl-quinazolones by side-chain substitution, with 1,3-bifunctional-reagents. We studied the cyclisation process under basic, acidic and phase-transfer catalyzed conditions. The structures of the synthesized compounds were characterized by IR, UV and NMR spectroscopy.

Cholecystokinin↗
PubMed1991

[HPLC-investigations of imidazoquinazolone derivatives. Part 2].

In a previous paper (2) authors, reported good correlation between the HPLC (log k') and TLC (RM) retention data and the 1-octanol/water partition coefficient (log l') of imidazoquinazolone derivatives synthetized in their laboratory. In the present work the behaviour of the compounds in HPLC systems containing ion-pairing agents (camphorsulfonic acid, Na-dodecyl sulfate) has been studied. While, in reversed phase systems no change of retention indicating the formation of ion-pairs or molecule complexes was observed, camphor-sulfonic acid caused significant increase of retention in the chromatographic systems with bare silica as stationary phase. This phenomenon is interpreted by the formation of camphorsulfonic acid double layer on the silica surface and as a consequence of mixed retention mechanism. The results of a detailed study on the latter subject will be published in a next paper. Double peak formation was observed in reversed phase system in case of C1-C3 disubstituted derivatives. This was interpreted with the formation of isomeric mixtures. Theoretical considerations as well as the identical spectra of the two peaks make plausible the appearance and separation of conformational isomers.

Chromatography, High Pressure Liquid↗