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  • 1
    ISSN: 1573-904X
    Keywords: QSPR, Quantitative Structure-Property Relationship ; correlation analysis ; regression models ; molecular modeling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Purpose. In the present paper, linear and nonlinear models forcomplexation of α- β- and γ-cyclodextrin with guest molecules are developed,with the aim of free energy prediction and interpretation of theassociation process. Methods. Linear and nonlinear regression is used to correlateexperimental free energies of complexation with calculated moleculardescriptors. Molecular modeling supports the interpretation of the results. Results. Highly predictive models are obtained, although the structuralvariability of the compounds used for their deduction is large, reachingfrom synthetic heterocycles to steroids and prostaglandins. Conclusions. The scaled regression coefficients give insight to thecomplexation mechanisms, which appear to be different for the threetypes of cyclodextrins.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Pharmaceutical research 15 (1998), S. 303-311 
    ISSN: 1573-904X
    Keywords: antiarrhythmics ; molecular dynamics ; partial least squares regression ; genetic function approximation ; quantitative structure-activity relationships
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Purpose. This study was done to explore the relationships of both macroscopic and molecular level physicochemical properties to in-vivo antiarrhythmic activity and interactions with phospholipid membranes for a set of cationic-amphiphilic analogs. Methods. The 4D-QSAR method, recently developed by Hopfinger and co-workers (1), was employed to establish 3D-QSAR/QSPR models. Molecular dynamics simulations provided the set of conformational ensembles which were analyzed using partial least squares regression in combination with the Genetic Function Approximation algorithm to construct QSAR and QSPR models. Results. Significant QSAR models for in-vivo antiarrhythmic activity were constructed in which logP (the partition coefficient), and specific grid cell occupancy (spatial) descriptors are the main activity correlates. LogP is the most significant QSAR descriptor. 4D-QSPR models were also developed for two analog-membrane interaction properties, the change in a membrane transition temperature and the ability of the analogs to displace adsorbed Ca2+-ions from phosphatidylserine mono-layers. Conclusions. Spatial features, represented by grid cell occupancy descriptors, supplement partition coefficient, which is the most important determinant of in-vivo antiarrhythmic activity, to provide a comprehensive model for drug action. The QSPR models are less significant in statistical measures, and limited to interpretation of possible molecular mechanisms of action.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 29 (1997), S. 79-93 
    ISSN: 1573-1111
    Keywords: Cyclodextrins ; host–guest systems ; molecular recognition ; molecular surfaces ; solvation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Complexation trajectories and the variation ofinduced circular dichroism are calculated for thedocking of phenol and 2,4,6-trimethyl-phenol withβ-cyclodextrin. The results are compared toexperimental chirality data to elucidate themechanism of nonspecific molecular recognitionprocesses in aqueous solution. Large geometricalchanges along nearly isoenergetic Dynamic Monte Carlotrajectories show the conformational flexibility ofsuch host–guest systems. This proves diffuseintermolecular interactions, van der Waals orelectrostatic in nature, as the main contributions to thebinding energy. The number and position of the methylsubstituents of the guest reduces the complexityof the conformational space as the guest‘s positionbecomes fixed by steric constraints. The solvation free energy is calculated from thesolvent accessible surface area weighted byrespective atomic solvation parameters. Consideringthe solvation term in the dynamic simulationsrestricts the conformational flexibility of themacromolecular system. The relative importance ofvarious contributions to the solvation energy isdiscussed and it is shown that those terms arisingfrom the interaction of hydrophobic groups with theaqueous environment are essential for thedetermination of the complex structure. Consideringthese terms in the dynamic simulation model, the signand strength of the calculated rotatory strength isin perfect agreement with induced circular dichroismobtained from experimentally determined averagedspectra. The results demonstrate the accuracy of thegeometrical properties of host–guest systems obtainedfrom these simulations.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 36 (2000), S. 409-423 
    ISSN: 1573-1111
    Keywords: host-guest systems ; linear regression ; molecular descriptors ; statistical models ; correlation analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract In the present work, linear regression models for theprediction of the free energies of complexationbetween guest molecules and β-cyclodextrin arededuced. For 70 compounds (mostly pharmaca), theexperimentally determined 1 : 1 stability constants aretransformed into the respective free energies, whichare then correlated with molecular descriptors. The statistically significant descriptors, which leadto models with remarkable predictive power, indicatethat besides volume, shape and lipophilicity, whichhave the largest contribution to the complexationenergy, complexation is also significantly influencedby the flexibility and the hydrogen bonding capacityof the guest molecule.
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  • 5
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Kinetic studies are presented for the growth and fermentation of the yeast Pichia stipitis with xylose as the carbon source. Ethanol is produced from xylose under anaerobic as well as under oxygen-limiting conditions but only at dissolved oxygen concentrations up to 3 μmol/L Maximum yields and production rates were obtained under oxygen-limiting conditions, where the xylose metabolism may be considered to be consisted of three different components (assimilation, respiration, fermentation). The contribution of each pathway is determined by the availability of oxygen and the energy yield of each pathway. In order to describe the course of oxygen-limited fermentations, a mathematical model has been developed with the assumption that growth is coupled to the energy production. The resulting model requires only four independent parameters (Yx/O2, YATPmax, mATP, and P/O). These parameters were estimated on the basis of eight separate batch fermentations.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1983 (1983), S. 1638-1639 
    ISSN: 0170-2041
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conversion of Phenolic α-Amino Acids into α-Keto acidsA one-pot conversion of tyrosine (1a) and 3,4-dihydroxyphenylalanine (DOPA) (1b) into 3-(4-hydroxyphenyl)pyruvic acid (2a) and 3-(3,4-dihydroxyphenyl)pyruvic acid (2b), respectively, via 2-trifluoromethyl-3-oxazolin-5-ones 5 is described.
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  • 7
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1983 (1983), S. 1623-1637 
    ISSN: 0170-2041
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Conversion of ω-guanidino- and ω-Ureido-α-amino Acids into α-Keto Acids and Heterocycles Derived TherefromTreatment of basic α-amino acids 1, with trifluoroacetic anhydride readily leads to 2-trifluoromethyl-3-oxazolin-5-ones, 2, which in turn may be hydrolyzed to yield α-keto acids 4 under mild conditions. Type 4 compounds carrying ω-guanidino or ω-ureido functions may undergo a ring closure reaction, the ease and outcome of which is strongly dependent on the chain length and the nature of the terminal functional group. The species occurring in aqueous solutions of 4 have been investigated by means of 1H and 13C NMR spectroscopy. The α-keto acid 4a derived from arginine can be isolated in crystalline form either as such or as its pyrrolidine derivative, 10a. Strongly acidic conditions lead to the formation of a tetrahydro-1,3-diazepine, 6c. An analogous compound, 6f, is obtained in the citrulline series. In contrast, the keto acids of homoarginine and homocitrulline (4c, g) are converted into bicyclic compounds of type 16 and 17. Under the same conditions the N∊-methyl derivative 4d is cyclized to give a hexahydro-1,3-diazocine, 14d. Depending on the reaction conditions, 2-amino-4-guanidinobutyric acid (1e) may be converted into the pyrimidine derivatives 18 or 19. The factors responsible for the unusual behaviour of α-keto acids 4 under cyclization conditions are discussed.
    Notes: Milde Hydrolyse der aus den basischen Aminosäuren 1 mit Trifluoressigsäureanhydrid leicht erhältlichen 2-Trifluormethyl-3-oxazolin-5-one 2 liefert die α-Ketosäuren 4. In ihnen vorhandene ω-Guanidino- oder ω-Ureidofunktionen können zur Bildung von Heterocyclen führen, wobei die Ringschlußtendenz stark von der Kettenlänge und der Art der dritten Funktion abhängt. Die in wäßrigen Lösungen von 4 vorliegenden Spezies wurden 1H- und 13C-NMR-spektroskopisch untersucht. Die vom Arginin abgeleitete α-Ketosäure 4a kann sowohl als solche als auch als Pyrrolidin-Derivat 10a, kristallisiert erhalten werden. Unter sauren Bedingungen liefern sowohl 4a als auch das aus Citrullin erhältliche 10f bevorzugt die Tetrahydrodiazepine 6a und 6f. Die Ketosäuren des Homoarginis und Homocitrullins (4c, g) ergeben dagegen Bicyclen des Typs 16 und 17. Wird wei bei 4d die Cyclisierung zum Sechsring durch Methylierung von N∊ verhindert, so entsteht das Hexahydro-1,3-diazocin 14d. Aus 2-Amino-4-guanidinobuttersäure (1e) sind je nach den Reaktionsbedingungen die Pyrimidin-Derivate 18 und 19, zugänglich. Faktoren, die das unterschiedliche Cyclisierungsverhalten der α-Ketosäuren 4 bedingen, werden diskutiert.
    Additional Material: 1 Tab.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1470-1481 
    ISSN: 0192-8651
    Keywords: protein folding ; simulated annealing ; Monte Carlo dynamics ; multiple minima problem ; global minimum conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new and efficient method for overcoming the multiple minima problem of polypeptides, the systematic stepsize variation (SSV) method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly chosen dihedral angles are updated starting with a small stepsize (i.e., magnitude of rotation). A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of ±0.0004 kcal/mol from the reference structure and, consequently, are perfectly superposable. For comparison, Metropolis Monte Carlo simulated annealing (MMC-SA) is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1470-1481, 1998
    Additional Material: 5 Ill.
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  • 9
    Publication Date: 2020-03-30
    Description: In the adult brain, vascular endothelial growth factor D (VEGFD) is required for structural integrity of dendrites and cognitive abilities. Alterations of dendritic architectures are hallmarks of many neurologic disorders, including stroke-induced damage caused by toxic extrasynaptic NMDA receptor (eNMDAR) signaling. Here we show that stimulation of eNMDARs causes a rapid shutoff of VEGFD expression, leading to a dramatic loss of dendritic structures. Using the mouse middle cerebral artery occlusion (MCAO) stroke model, we have established the therapeutic potential of recombinant mouse VEGFD delivered intraventricularly to preserve dendritic architecture, reduce stroke-induced brain damage, and facilitate functional recovery. An easy-to-use therapeutic intervention for stroke was developed that uses a new class of VEGFD-derived peptide mimetics and postinjury nose-to-brain delivery.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2019-12-30
    Description: Cancer immunotherapies are increasingly combined with targeted therapies to improve therapeutic outcomes. We show that combination of agonistic anti-CD40 with antiangiogenic antibodies targeting 2 proangiogenic factors, vascular endothelial growth factor A (VEGFA) and angiopoietin 2 (Ang2/ANGPT2), induces pleiotropic immune mechanisms that facilitate tumor rejection in several tumor models. On the one hand, VEGFA/Ang2 blockade induced regression of the tumor microvasculature while decreasing the proportion of nonperfused vessels and reducing leakiness of the remaining vessels. On the other hand, both anti-VEGFA/Ang2 and anti-CD40 independently promoted proinflammatory macrophage skewing and increased dendritic cell activation in the tumor microenvironment, which were further amplified upon combination of the 2 treatments. Finally, combined therapy provoked brisk infiltration and intratumoral redistribution of cytotoxic CD8+T cells in the tumors, which was mainly driven by Ang2 blockade. Overall, these nonredundant synergistic mechanisms endowed T cells with improved effector functions that were conducive to more efficient tumor control, underscoring the therapeutic potential of antiangiogenic immunotherapy in cancer.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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