Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Low-temperature heat capacities and standard molar enthalpy of formation of aspirin

Molar heat capacities (C-p,C-m) of aspirin were precisely measured with a small sample precision automated adiabatic calorimeter over the temperature range from 78 to 383 K. No phase transition was observed in this temperature region. The polynomial function of Cp, vs. T was established in the light of the low-temperature heat capacity measurements and least square fitting method. The corresponding function is as follows: for 78 Kless than or equal toTless than or equal to383 K, C-p,C-m/J mol(-1) K-1=19.086X(4)+15.951X(3)-5.2548X(2)+90.192X+176.65, [X=(T-230.50/152.5)]. The thermodynamic functions on the base of the reference temperature of 298.15 K, {DeltaH(T)-DeltaH(298.15)} and {S-T-S-298.15}, were derived.

Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis

Steroid derivatives show a complex interaction with P-glycoprotein (Pgp). To determine the essential structural requirements of a series of structurally related and functionally diverse steroids for Pgp-mediated transport or inhibition, a three-dimensional quantitative structure activity relationship study was performed by comparative similarity index analysis modeling. Twelve models have been explored to well correlate the physiochemical features with their biological functions with Pgp on basis of substrate and inhibitor datasets, in which the best predictive model for substrate gave cross-validated q(2) = 0.720, non-cross-validated r(2) = 0.998, standard error of estimate SEE = 0.012, F = 257.955, and the best predictive model for inhibitor gave q(2) = 0.536, r(2) = 0.950, SEE = 1.761 and F = 45.800. The predictive ability of all models was validated by a set of compounds that were not included in the training set. The physiochemical similarities and differences of steroids as Pgp substrate and inhibitor, respectively, were analyzed to be helpful in developing new steroid-like compounds. (C) 2004 Elsevier B.V. All rights reserved.

Low-temperature heat capacity and standard molar enthalpy of formation of 9-fluorenemethanol (C14H12O)

Low-temperature heat capacities of the 9-fluorenemethanol (C14H12O) have been precisely measured with a small sample automatic adiabatic calorimeter over the temperature range between T = 78 K and T = 390 K. The solid-liquid phase transition of the compound has been observed to be T-fus = (376.567 +/- 0.012) K from the heat-capacity measurements. The molar enthalpy and entropy of the melting of the substance were determined to be Delta(fus)H(m) = (26.273 +/- 0.013) kJ (.) mol(-1) and Delta(fus)S(m) = (69.770 +/- 0.035) J (.) K-1 (.) mol(-1). The experimental values of molar heat capacities in solid and liquid regions have been fitted to two polynomial equations by the least squares method. The constant-volume energy and standard molar enthalpy of combustion of the compound have been determined, Delta(c)U(C14H12O, s) = -(7125.56 +/- 4.62) kJ (.) mol(-1) and Delta(c)H(m)degrees(C14H12O, s) = -(7131.76 +/- 4.62) kJ (.) mol(-1), by means of a homemade precision oxygen-bomb combustion calorimeter at T = (298.15 +/- 0.001) K. The standard molar enthalpy of formation of the compound has been derived, Delta(f)H(m)degrees (C14H12O, s) = -(92.36 +/- 0.97) kJ (.) mol(-1), from the standard molar enthalpy of combustion of the compound in combination with other auxiliary thermodynamic quantities through a Hess thermochemical cycle. (C) 2004 Elsevier Ltd. All rights reserved.

Quantitative structure-property relationships (QSPRs) on direct photolysis of PCDDs

By the use of partial least squares (PLS) method and 27 quantum chemical descriptors computed by PM3 Hamiltonian, a statistically significant QSPR were obtained for direct photolysis quantum yields (Y) of selected Polychlorinated dibenzo-p-dioxins (PCDDs). The QSPR can be used for prediction. The direct photolysis quantum yields of the PCDDs are dependent on the number of chlorine atoms bonded with the parent structures, the character of the carbon-oxygen bonds, and molecular polarity. Increasing bulkness and polarity of PCDDs lead to decrease of log Y values. Increasing the frontier molecular orbital energies (E-lumo and E-homo) and heat of formation (HOF) values leads to increase of log Y values. (C) 2001 Elsevier Science Ltd. All rights reserved.

Quasi-3D Cytoskeletal Dynamics of Osteocytes under Fluid Flow

Osteocytes respond to dynamic fluid shear loading by activating various biochemical pathways, mediating a dynamic process of bone formation and resorption. Whole-cell deformation and regional deformation of the cytoskeleton may be able to directly regulate this process. Attempts to image cellular deformation by conventional microscopy techniques have been hindered by low temporal or spatial resolution. In this study, we developed a quasi-three-dimensional microscopy technique that enabled us to simultaneously visualize an osteocyte's traditional bottom-view profile and a side-view profile at high temporal resolution. Quantitative analysis of the plasma membrane and either the intracellular actin or microtubule (MT) cytoskeletal networks provided characterization of their deformations over time. Although no volumetric dilatation of the whole cell was observed under flow, both the actin and MT networks experienced primarily tensile strains in all measured strain components. Regional heterogeneity in the strain field of normal strains was observed in the actin networks, especially in the leading edge to flow, but not in the MT networks. In contrast, side-view shear strains exhibited similar subcellular distribution patterns in both networks. Disruption of MT networks caused actin normal strains to decrease, whereas actin disruption had little effect on the MT network strains, highlighting the networks' mechanical interactions in osteocytes.

A QSAR study of the antiallergic activities of substituted benzamides and their structures

Multiple regression analysis (MRA) and comparative molecular field analysis (CoMFA) have been used in studies of the correlation between the antiallergic activities of substituted benzamides and their structures. The results achieved using Coh IFA based on 3D factors are much better than those obtained using MRA based on mainly 2D structural information. The CoMFA results reveal that the steric effects are more important than the electrostatic effects for the activities of substituted benzamides. (C) 1999 Elsevier Science B.V. All rights reserved.

Method for measuring two-qubit entanglement of formation by local operations and classical communication

We present a parametrically efficient method for measuring the entanglement of formation E-f in an arbitrarily given unknown two-qubit state rho(AB) by local operations and classical communication. The two observers, Alice and Bob, first perform some local operations on their composite systems separately, by which the desired global quantum states can be prepared. Then they estimate seven functions via two modified local quantum networks supplemented a classical communication. After obtaining these functions, Alice and Bob can determine the concurrence C and the entanglement of formation E-f.

tilt menu: using the 3d orientation information of pen devices to extend the selection capability of pen-based user interfaces

We present a new technique called‘Tilt Menu’ for better extending selection capabilities of pen-based interfaces.The Tilt Menu is implemented by using 3D orientation information of pen devices while performing selection tasks.The Tilt Menu has the potential to aid traditional onehanded techniques as it simultaneously generates the secondary input (e.g., a command or parameter selection) while drawing/interacting with a pen tip without having to use the second hand or another device. We conduct two experiments to explore the performance of the Tilt Menu. In the first experiment, we analyze the effect of parameters of the Tilt Menu, such as the menu size and orientation of the item, on its usability. Results of the first experiment suggest some design guidelines for the Tilt Menu. In the second experiment, the Tilt Menu is compared to two types of techniques while performing connect-the-dot tasks using freeform drawing mechanism. Results of the second experiment show that the Tilt Menu perform better in comparison to the Tool Palette, and is as good as the Toolglass.

the tilt cursor: enhancing stimulus-response compatibility by providing 3d orientation cue of pen

In order to improve stimulus-response compatibility of touchpad in pen-based user interface, we present the tilt cursor, i.e. a cursor dynamically reshapes itself to providing the 3D orientation cue of pen. We also present two experiments that evaluate the tilt cursor’s performance in circular menu selection and specific marking menu selection tasks. Results show that in a specific marking menu selection task, the tilt cursor significantly outperforms the shape-fixed arrow cursor and the live cursor [4]. In addition, results show that by using the tilt cursor, the response latencies for adjusting drawing directions are smaller than that by using the other two kinds of cursors.