Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Excess enthalpies of aqueous solutions of polyols at 25°

The excess enthalpies of aqueous solutions of nine polyols were determined at 25°C and reported in the virial form. The most interesting and new feature of this family of solutes is that the sign of the enthalpic pair interaction coefficients h_xx is positive for the first members of the series and negative for the higher homologues. Other points are the large differences found among the values of h_xx for stereoisomers, whereas pairs of enantiomers show the same values within experimental errors. An application of the group additivity method is also discussed.     

Molecular structure of di-aryl-aldimines by multinuclear magnetic resonance and X-ray diffraction

The complete ¹H, ¹³C and ¹⁵N NMR analyses for a series of 25 diaryl-aldimines containing phenyl, pyridyl, pyrazolone and furanyl moieties are described herein. Detailed evaluation of substituent chemical shift and coupling constant effects showed that interaction between the lone pair of the pyrazolone carbonyl group or the nitrogen of 2-substitued pyridines with the aldimine hydrogen increases the value and shifts the resonance signal for this hydrogen to high frequency, in the ¹H NMR spectra. The X-ray crystal structure analysis of pyrazolone substituted aldimines evidenced the planarity of the aryl groups which are conjugated with the CN double bond. In the case of the N-(2-pyridinemethylene)-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one, two rotamers were observed in the same unit cell.     

Calculations of concentration dependences of chemical shifts for acrylamide in water—DMSO mixed solvent

The lattice model of associated solutions was used to calculate the concentration dependences of the chemical shifts of¹³C magnetic nuclei in the acrylamide molecule in water—DMSO solvent. Each pair of bonds between the acrylamide group containing a magnetic nucleus and the neighboring solvent molecule was assumed to additively contribute to the change in the chemical shift of the nucleus in question. The new approach affords the same accuracy in describing the experimental data at any ratios of the solution components. It was shown that the chemical shifts and the excess heat of mixing of the water—DMSO binary solution can be simultaneously described using the same set of energy parameters of the model. The model makes it possible to employ experimental data on chemical shifts for studying intermolecular interactions in solutions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1983–1987, October, 1998.     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.     

Determination of thermodynamic properties of macroporous glycidyl methacrylate‐based copolymers by inverse gas chromatography

Macroporous crosslinked poly(glycidyl methacrylate‐co‐ethylene glycol dimethacrylate) (PGME) was synthesized by suspension copolymerization and modified by ring‐opening reaction of the pendant epoxy groups with ethylene diamine (EDA). Inverse gas chromatography (IGC) at infinite dilution was applied to determine the thermodynamic interactions of PGME and modified copolymer, PGME‐en. The specific surface areas of the initial and modified copolymer samples were determined by the BET method, from low‐temperature nitrogen adsorption isotherms. The specific retention volumes, V, of 10 organic compounds of different chemical nature and polarity (nonpolar, donor, or acceptor) were determined in the temperature range 333–413 K. The weight fraction activity coefficients of test sorbates, , and Flory–Huggins interaction parameters, , were calculated and discussed in terms of interactions of sorbates with PGME and PGME‐en. Also, the partial molar free energy, , partial molar heat of mixing, , sorption molar free energy, ΔG, sorption enthalpy ΔH, and sorption entropy, ΔS, were calculated. Glass transitions in PGME and PGME‐en, determined from IGC data, were observed in the temperature range 373–393 K and 363–373 K, respectively. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2524–2533, 2005     

Photocurrent generation in multilayer self-assembly films fabricated from water-soluble poly(phenylene vinylene)

A novel, water-soluble, cationic PPV derivative poly[(2,5-bis(3-bromotrimethylammoniopropoxy)-phenylene-1,4-divinylene)-alt-1,4-(2,5-bis(2-(2-hydroxyethoxy)ethoxy))phenylene vinylene] (BH-PPV) has been synthesized by a Heck coupling reaction. Multilayered assemblies of the BH-PPV and the sodium salt of hexa(sulfobutyl)fullerenes (C(60)-HS) were fabricated successfully by an alternate deposition technique. The multilayer structures were studied by UV/Vis spectroscopy, small angle X-ray diffraction, and atomic force microscopy. The photoinduced charge transfer property of the self-assembled multilayer film was also measured by a three-electrode cell technique. A steady and rapid cathodic 5.5 microA cm(-2) photocurrent response was measured as the irradiation of the multilayer film was switched on and off. Importantly, the response of on/off cycling is prompt and reproducible. A possible mechanism for the electron-transfer process is proposed.     

Application of the semilocalized approach to chemical reactivity of butadiene

The semilocalized approach to chemical reactivity (J. Mol. Struct. (Theochem) 588 (2002) 99; Int. J. Quant. Chem. 94 (2003) 302) is applied to study the addition reaction of an electrophile or nucleophile to the butadiene molecule. In accordance with the classical concept of the reaction center and its neighborhood (substituent), only one of the two H₂C=CH-fragments of butadiene is supposed to be under a direct attack of the reagent, whereas the remaining H₂C=CH-group is assumed to play the role of the substituent and thereby to participate in the process indirectly by exerting certain electron-donating or accepting effect upon the former group and/or the reagent. The main aim of the study consists in revealing the role of the H₂C=CH-substituent in the formation of the known higher reactivity of the terminal carbon atom of the attacked C=C-bond (as compared to the internal atom) irrespective of the nature of the reagent. To this end, we seek to obtain an explicit algebraic representation of the interdependence between the direction and the extent of the total influence of the H₂C=CH-substituent, on the one hand, and the nature of the reagent, on the other hand. The expressions for electron density and bond order redistributions among separate fragments of contacting molecules derived previously in the form of power series are shown to yield the above-anticipated representation. On this basis, it is demonstrated that the electron-donating effect of the initially occupied (bonding) orbital of the substituent and the electron-accepting effect of its initially vacant (antibonding) orbital upon the remaining fragments of the whole reacting system may be considered independently whatever the nature of the reagent. However, a strong interdependence is established between the actual relative extents of these two components of the total effect of the H₂C=CH-group and the electron-donating (accepting) properties of the reagent. Moreover, this group of atoms is shown to manifest itself as an electron-donating (accepting) substituent under influence of an electrophilic (nucleophilic) attack. Using this principal result of the paper, the actual reactivity of butadiene with respect to electrophile (nucleophile) is interpreted by invoking a model system of a substituted ethene containing a simple (one-orbital) electron-donating (accepting) substituent, and a terminal addition easily follows for both types of the reagent.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

Calculating the knowledge-based similarity of functional groups using crystallographic data

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs.