The class reconstruction number of maximal planar graphs

The reconstruction numberrn(G) of a graphG was introduced by Harary and Plantholt as the smallest number of vertex-deleted subgraphsG _i =G – v _i in the deck ofG which do not all appear in the deck of any other graph. For any graph theoretic propertyP, Harary defined theP-reconstruction number of a graph G P as the smallest number of theG _i in the deck ofG, which do not all appear in the deck of any other graph inP We now study the maximal planar graph reconstruction numberrn(G), proving that its value is either 1 or 2 and characterizing those with value 1.     

The aza-xylylene Diels-Alder approach for the synthesis of naturally occurring 2-alkyl tetrahydroquinolines

The recently discovered intramolecular aza-xylylene Diels-Alder reaction, based on a 1,4-dehydrohalogenation reaction, was extended in terms of substrates and leaving groups allowing the assembly of tetrahydroquinolines in two synthetic steps. Intramolecular cleavage of a thiocarbamate using triphenylphosphine and tetrachloromethane (Appel conditions) to give chloromethyl phenylisocyanate has been presented for the first time. The synthetic feasibility of this process was demonstrated in the first total syntheses of the alkaloids rac-Angustureine and 1-methyl-2-propyltetrahydroquinoline.     

Recent advances in microwave-assisted combinatorial synthesis and library generation

Progress and developments made in microwave-assisted combinatorial synthesis and library production since 2002 are reviewed. The use of microwave technology in both solution and solid phase synthesis is discussed with special reference to agrochemical applications where appropriate.     

Synthesis of a biotinated amphiphile

The synthesis of a biotinated amphiphile assembled from d-(+)-biotin, ethylene diamine as spacer, galactaric acid and 1-dodecylamine was achieved in six steps. The key step was the synthesis of a bisacetonide protected galactaric ester, the structure of which was determined by X-ray analysis. Aminolysis, spacer attachment, coupling with biotin and deprotection led to the amphiphilic galactaramide.     

Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

REDUCED PHOTOINACTIVATION OF 10-DODECYL ACRIDINE ORANGE-SENSITIZED YEAST CELLS AT HIGH FLUENCE RATES MEASUREMENTS AND COMPUTER SIMULATIONS

Abstract-During the development of a photodamage cell sorter several photosensitizers were tested for their ability to photoinactivate more than 90% of the sensitized cells after a brief irradiation with a fluence of 10 kJ/m². In pilot experiments, yeast cells sensitized with 10-dodecyl acridine orange (DAO) were effectively photoinactivated after receiving a fluence of 10 kJ/m² delivered in 8 s. However, when the same fluence was delivered in 3 μ s during passage through a focused laser beam in the cell sorter, all cells survived.
Computer simulations of the relevant photophysical and chemical reactions inside the irradiated cell were used to investigate the cause of this phenomenon. The results indicated that the absence of photoinactivation by DAO, after flash irradiations, was caused by the combined effects of (1) limited oxygen diffusion into the cell and (2) a reduced number of collisions between photosensitizer triplet and oxygen molecules during the irradiation due to saturation of the intracellular photosensitizer triplet concentration. The contributions of triplet-triplet annihilation and triplet quenching by ground state photosensitizer molecules were found to be minimal and not significant. These findings indicate that Type II photosensitizers are incapable of rapid selective photoinactivation in cell sorters.     

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP)

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.     

COSMO-RS: A novel view to physiological solvation and partition questions

Both, dielectric continuum solvation models as well as surface or group based methods using polarity and lipophilicity parameters have been proven to be useful tools for the analysis of solvation and partition questions. For the first time, COSMO-RS provides an integrated theory, which combines the aspects of continuum solvation and surface interactions, and which ends up with chemical potentials of molecules in almost arbitrary solvents and mixtures. Due to its sound theoretical basis, COSMO-RS does not only provide a new quantitative access to solvation and partition properties in well defined solvents, but it also opens a novel view and gives a better understanding of the general problem of solvation. Finally, this allows for a generalisation of COSMO-RS to sophisticatedphysiological partition problems involving as complex phases as blood, brain, or cell membranes. The use of COSMO-RS for drug discovery and design is demonstrated by applications to blood-brain partition coefficients, and water solubility.