Improved pose and affinity predictions using different protocols tailored on the basis of data availability

The D3R 2015 grand drug design challenge provided a set of blinded challenges for evaluating the applicability of our protocols for pose and affinity prediction. In the present study, we report the application of two different strategies for the two D3R protein targets HSP90 and MAP4K4. HSP90 is a well-studied target system with numerous co-crystal structures and SAR data. Furthermore the D3R HSP90 test compounds showed high structural similarity to existing HSP90 inhibitors in BindingDB. Thus, we adopted an integrated docking and scoring approach involving a combination of both pharmacophoric and heavy atom similarity alignments, local minimization and quantitative structure activity relationships modeling, resulting in the reasonable prediction of pose [with the root mean square deviation (RMSD) values of 1.75 Å for mean pose 1, 1.417 Å for the mean best pose and 1.85 Å for the mean all poses] and affinity (ROC AUC = 0.702 at 7.5 pIC50 cut-off and R = 0.45 for 180 compounds). The second protein, MAP4K4, represents a novel system with limited SAR and co-crystal structure data and little structural similarity of the D3R MAP4K4 test compounds to known MAP4K4 ligands. For this system, we implemented an exhaustive pose and affinity prediction protocol involving docking and scoring using the PLANTS software which considers side chain flexibility together with protein–ligand fingerprints analysis assisting in pose prioritization. This protocol through fares poorly in pose prediction (with the RMSD values of 4.346 Å for mean pose 1, 4.69 Å for mean best pose and 4.75 Å for mean all poses) and produced reasonable affinity prediction (AUC = 0.728 at 7.5 pIC50 cut-off and R = 0.67 for 18 compounds, ranked 1st among 80 submissions).     

NMR spectra of some reduced symmetry peripheral fused-ring-substituted phthalocyanines: density functional calculations

Chemical shifts of some reduced symmetry peripheral fused-ring-substituted phthalocyanines, namely Zn3B1N, Zncis2B2N, Zntrans2B2N, Zn1B3N and Zn3B0N, have been calculated at density functional B3LYP level using the gauge-independent atomic orbital (GIAO) method. The geometries were optimized using the 6-31G(d) basis set and the following NMR calculations were performed using 6-31G(d) and 6-311G(d,p) basis sets, respectively. The calculated NMR shielding tensors and chemical shifts are compared with previous experimental results. The chemical shifts are assigned according to the calculated data and satisfying results are obtained. The NMR shielding tensor simulation of Zn3B0N has been raised as a significant theoretical topic.     

Effects of magnesium salts and amines on the stereoselectivity in the imine aldol reaction

In the imine aldol reactions of 1 with aromatic aldehydes using magnesium salts in the presence of amines, the threo/erythro ratios of products increased in the order Mg(ClO4)2>MgI2>MgBr2>MgCl2>Mg(OTf)2 and N,N,N',N'-tetramethylethylenediamine (TMEDA)>Et3N. This increase in the threo/erythro ratios of products was estimated to be caused by a retro-imine aldol reaction under thermodynamic control.     

Pressure-induced reentrant micellization of amphiphilic block copolymers in dilute aqueous solutions

The pressure-induced structural changes of a block copolymer, poly(2-ethoxyethoxyethyl vinyl ether)-block-poly(2-hydroxyethyl vinyl ether) (pEOEOVE-b-pHOVE) in aqueous solutions, were studied by means of small-angle neutron scattering (SANS) and dynamic light scattering (DLS) from atmospheric pressure up to 400 MPa. pEOEOVE-b-pHOVE formed a spherical micellar structure above 40 degrees C due to poor solubility of pEOEOVE. Micellization phase diagram was determined by DLS, and a covex-upward pressure-temperature (P-T) phase diagram was obtained having a peak around (P,T)=(150 MPa,48 degrees C). The SANS curves at 50 degrees C were analyzed as a function of P. The micellar core size decreased by pressurizing at low P's (P相似文献   

In situ surface-enhanced infrared absorption spectroscopy for the analysis of the adsorption and desorption process of Au nanoparticles on the SiO2/Si surface

The adsorption and desorption of Au nanoparticles (AuNP) in colloidal D2O suspension on the (3-aminopropyl)triethoxysilane treated SiO2/Si surface was investigated by in situ attenuated total reflection surface enhanced infrared absorption (ATR-SEIRA) spectroscopy with a liquid flow cell. With increasing surface density of AuNP, the absorption of the vibrational modes of D2O and of the citrate molecules covering the AuNP increases due to SEIRA. Repulsive electrostatic Coulomb forces between the AuNP lead to the saturation of the AuNP surface density at submonolayer coverage. We show that the adsorption kinetics can be investigated by monitoring in situ the molecular vibrational modes of D2O and the citrate molecules. Furthermore, we clarify that the adsorption process can be described very well by a diffusion-limited first-order Langmuir kinetics model. When exposing a saturated AuNP submonolayer to 2-aminoethanethiol (AET)/D2O solution, the AuNP are removed from the surface and the IR absorption of the D2O vibrational modes become weaker again. Taking into account the time dependencies of the OD and the CH peaks, we propose a microscopic model where the AET molecules quickly adsorb on the AuNP by replacing most of the precovering citrate molecules exposed to the AET solution. As this takes place, the AuNP agglomerate-as we could detect with scanning electron microscopy-and are finally removed from the surface.     

Liquid-liquid equilibria of polyrotaxane and poly(vinyl alcohol)

Liquid–liquid equillibria (LLE) of the tertiary system of hydroxypropylated polyrotaxane (HPPR)–poly(vinyl alcohol) (PVA)–solvent have been investigated by focusing on the internal structures of HPPR–PVA blend gels. The phase diagrams of the HPPR–PVA aqueous systems displayed two liquid phases at a high concentration and molecular weight of PVA. This result was consistent with the prediction of the Flory–Huggins lattice model. On the contrary, the HPPR–PVA–DMSO system exhibited only a single phase. The HPPR–PVA blend gels crosslinked in dimethylsulfoxide (DMSO) were highly transparent over a wide concentration range, while the gels prepared in water were opaque at high polymer concentrations. Spherical domains were observed in the opaque gels by laser scanning confocal microscopy, and the sizes of the domains were significantly dependent on the amount of cross-linking reagent utilized. These results indicated that the transparency of the HPPR–PVA blend gels was strongly affected by the competition between the liquid–liquid two-phase separation and the crosslinking HPPR and PVA polymers during the preparation of the blend gels.     

Geochemical association of137Cs and239,240Pu in the oligotrophic and mesotrophic lake sediments

Geochemical association of¹³⁷Cs and^239,240Pu in the surface sediments from two oligotrophic and mesotrophic lakes in Japan was studied by sequential chemical extractions. The fractions separated were exchangeable and bound to carbonate, bound to oxides, bound to organic mattersulfides, and residual. The¹³⁷Cs and^239,240Pu were mainly associated with the organic matter-sulfides and residual fractions but exhibited the different vertical profiles at both lakes. The differences in association patterns between the lakes may be controlled by transport of these nuclides by organic settling particles to the bottom sediments and decomposition of the organics in the sediments.     

Classical Skew Orthogonal Polynomials and Random Matrices

Skew orthogonal polynomials arise in the calculation of the n-point distribution function for the eigenvalues of ensembles of random matrices with orthogonal or symplectic symmetry. In particular, the distribution functions are completely determined by a certain sum involving the skew orthogonal polynomials. In the case that the eigenvalue probability density function involves a classical weight function, explicit formulas for the skew orthogonal polynomials are given in terms of related orthogonal polynomials, and the structure is used to give a closed-form expression for the sum. This theory treates all classical cases on an equal footing, giving formulas applicable at once to the Hermite, Laguerre, and Jacobi cases.