Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program

Summary In the preceding paper we reported on a docking study with the SYSDOC program for predicting the binding sites of huperzine A in acetylcholinesterase (AChE) [Pang, Y.-P. and Kozikowski, A.P., J. Comput.-Aided Mol. Design, 8 (1994) 669]. Here we present a prediction of the binding sites of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (E2020) in AChE by the same method. E2020 is one of the most potent and selective reversible inhibitors of AChE, and this molecule has puzzled researchers, partly due to its flexible structure, in understanding how it binds to AChE. Based on the results of docking 1320 different conformers of E2020 into 69 different conformers of AChE and on the pharmacological data reported for E2020 and its analogs, we predict that both the R- and the S-isomer of E2020 span the whole binding cavity of AChE, with the ammonium group interacting mainly with Trp⁸⁴, Phe³³⁰ and Asp⁷², the phenyl group interacting mainly with Trp⁸⁴ and Phe³³⁰, and the indanone moiety interacting mainly with Tyr⁷⁰ and Trp²⁷⁹. The topography of the calculated E2020 binding sites provides insights into understanding the high potency of E2020 in the inhibition of AChE and provides hints as to possible structural modifications for identifying improved AChE inhibitors as potential therapeutics for the palliative treatment of Alzheimer's disease.     

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.     

Isomorphic electron orbitals for vibronic flexibility in a cyclopropenyl radical molecular device

Summary The vibronic character of this molecular device has been studied using isomorphic electron orbitals. The leading role of the softest vibrational mode for the electron transport process is stressed by the quantum mechanical treatment of the rearrangement operator. The theory was used to investigate the possible function of the soliton valve, which has been suggested as a switching tip. The electronic flexibility of the cyclopropenyl radical with respect to molecular vibrations, which is important for the function of the molecular device, is well characterized by the hardness and softness of the electron structure in terms of the orbital energy-occupation number correlation diagram.     

A force field study of diacetylene molecule by kinetic constant method

The potential constants of diacetylene molecule has been evaluated using kinetic constants. The other molecular constants such as the generalised vibrational mean amplitudes, shrinkage constants, Coriolis coupling constants and centrifugal distortion constants are also calculated using the vibrational frequencies and the results discussed.     

Gel permeation chromatographic characterization of sodium hyaluronate and its fractions prepared by ultrasonic degradation

Summary High-molecular-weight sodium hyaluronate isolated from rooster combs was degraded by ultrasonication. The molecular weight of hyaluronate and its polydispersity was determined by gel-permeation chromatography. During 75-min treatment the molecular weight value decreased from 1.39×10⁶ Da to 2.25×10⁵ Da while the polydispersity of the molecular weight increased from 1.29 to 2.36. The reciprocal value of the square of the hyaluronate's molecular weight was linearly proportional to the time of ultrasonication.     

Size exclusion chromatographic characterization of sodium hyaluronate fractions prepared by high energetic sonication

Summary A high molecular weight sodium hyaluronate isolated from rooster combs was degraded by ultrasonication. High-performance size exclusion chromatography allowed rapid and accurate determination of molecular weight parameters (M_z, M_w, M_n) and distributions. The time dependence of hyaluronan ultrasonication to the molecular characteristics of the polymer was investigated. A non-random nature of the degradation process was demonstrated and the reciprocal M_n value was found to be linearly proportional to the time of ultrasonication.     

Optical sensor materials for the detection of amines in organic solvents

A new optical polymer-based sensor was developed, which is able to recognize amines in organic solvents with high sensitivity. Thin polymer membranes were prepared and investigated, which contain a chromogenic functional dye (reactand) that shows a significant colour change during a reversible chemical reaction with the analyte. For that purpose the azo dye 4-trifluoroacetyl-4′-[N-(methacryloxyethyl)-N-(ethyl)amino]-azobenzene (CR-465) was synthesized, which contains a trifluoroacetyl moiety (receptor for interaction with amines) and in addition, a polymerizable methacrylate group. The methacrylate group links the dye covalently to the polymer matrix and the receptor recognizes the analyte via covalent binding. For immobilisation of the dye cross-linked methacrylate polymers with different composition were used. The highly cross-linked polymer network was stable against most organic solvents and exhibited enhanced stability against mechanical strain compared to plasticized PVC. The sensitivity of the reaction between the analyte and the dye was tailored by the choice of the solvent in which the analysis of the sensor layer was performed, with equilibrium constants for 1-butylamine ranging from 80 to 2000 M⁻¹ in chloroform and DMSO, respectively. In toluene as the solvent, sensor layers typically exhibited equilibrium constants of 100 M⁻¹ for 1-butylamine, 1300 M⁻¹ for 1,4-diaminobutane and 20,000 M⁻¹ for tris-(2-aminoethyl)amine. We have also investigated the cross-linked sensor layers with respect to molecular imprinting and did not find any enhancement in selectivity through imprinting in the presence of different analyte molecules.     

Atomic structure of InAs quantum dots on GaAs

In recent years, the self-assembled growth of semiconductor nanostructures, that show quantum size effects, has been of considerable interest. Laser devices operating with self-assembled InAs quantum dots (QDs) embedded in GaAs have been demonstrated. Here, we report on the InAs/GaAs system and raise the question of how the shape of the QDs changes with the orientation of the GaAs substrate. The growth of the InAs QDs is understood in terms of the Stranski–Krastanow growth mode. For modeling the growth process, the shape and atomic structure of the QDs have to be known. This is a difficult task for such embedded entities.

In our approach, InAs is grown by molecular beam epitaxy on GaAs until self-assembled QDs are formed. At this point the growth is interrupted and atomically resolved scanning tunneling microscopy (STM) images are acquired. We used preparation parameters known from the numerous publications on InAs/GaAs. In order to learn more about the self-assemblage process we studied QD formation on different GaAs(0 0 1), (1 1 3)A, and ( )B substrates. From the atomically resolved STM images we could determine the shape of the QDs. The quantum “dots” are generally rather flat entities better characterized as “lenses”. In order to achieve this flatness, the QDs are terminated by high-index bounding facets on low-index substrates and vice versa. Our results will be summarized in comparison with the existing literature.     

Molecular imprinting in ultrathin titania gel films via surface sol-gel process

Recent progresses of molecular imprinting in metal oxide matrices were summarized. Application of the surface sol-gel process to mixtures of organic carboxylic acids and titanium alkoxide provides ultrathin layers of titania gel (10-20 nm thick), in which molecule-sized cavities are kept intact upon removal of the organic templates. The imprinted cavity reflects the structural and functional features of the template molecule, and the enantioselective imprinting of dipeptide isomers is observed. Robustness and flexibility of the ultrathin titania layer is demonstrated by the formation of interconnected titania hollow structures. Possible practical applications and unsolved problems of this technique are discussed.     

Chiral separation of 1,1'-bi-2-naphthol and its analogue on molecular imprinting monolithic columns by HPLC

Two molecular imprinting polymer (MIP) monolithic columns with (S)-(-)-1,1'-bi-2-naphthol and (R)-(+)-5,5',6,6',7,7',8,8'-octahydro-1,1'-bi-2-naphthol as the templating molecules, respectively, have been prepared by in situ polymerization using 4-vinylpyridine and ethylene dimethacrylate as functional monomer and cross-linker, respectively. The columns with good flow-through properties were obtained by changing the molar ratio of the functional monomer and the template molecule. The effects of mobile-phase composition on separation of enantiomers were systematically investigated. The results indicate that hydrophobic interaction in aqueous solution and hydrogen-bonding interaction in ACN between the enantiomers and polymers could play important roles in the retention and resolution. The effects of chromatographic conditions, such as flow rate, column temperature, sample loading, on the enantioseparation were also studied. Further, these two MIP columns show a cross-reactivity.