IDSite: An accurate approach to predict P450-mediated drug metabolism

Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.     

Effect of reduction treatment on copper modified activated carbons on NO(x) adsorption at room temperature

Activated carbon was impregnated with copper salt and then exposed to reductive environment using hydrazine hydrate or heat treatment under nitrogen at 925 °C. On the obtained samples, adsorption of NO(2) was carried out at dynamic conditions at ambient temperature. The adsorbents before and after exposure to nitrogen dioxide were characterized by X-ray diffraction (XRD), thermal analysis, scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM-EDX), X-ray photoelectron spectroscopy (XPS), N(2)-sorption at -196 °C, and potentiometric titration. Copper loading improved the adsorption capacity of NO(2) as well as the retention of NO formed in the process of NO(2) reduction on the carbon surface. That improvement is linked to the presence of copper metal and its high dispersion on the surface. Even though both reduction methods lead to the reduction of copper, different reactions with the carbon surface take place. Heat treatment results in a significant percentage of metallic copper and a reduction of oxygen functional groups of the carbon matrix, whereas hydrazine, besides reduction of copper, leads to an incorporation of nitrogen. The results suggest that NO(2) mainly is converted to copper nitrates although the possibility to its reduction to N(2) is not ruled out. A high capacity on hydrazine treated samples is linked to the high dispersion of metallic copper on the surface of this carbon.     

Protonation of water clusters induced by hydroperoxyl radical surface adsorption

We have investigated the HO(2) adsorption and acid dissociation process on the surface of (H(2)O)(20) and (H(2)O)(21) clusters by using quantum-chemistry calculations. Our results show that the radical forms a stable hydrogen-bond complex on the cluster. The HO(2) acid dissociation is more favorable in the case of the (H(2)O)(21) cluster, for which the inner water molecule plays a crucial role. In fact, acid dissociation of HO(2) is found to occur in two steps. The first step involves H(2) O autoionization in the cluster, and the second one involves the proton transfer from the HO(2) radical to the hydroxide anion. The presence of the HO(2) radicals on the surface of the cluster facilitates water autoionization in the cluster.     

Effect of terminal N-substitution in 2-oxo-1,2-dihydroquinoline-3-carbaldehyde thiosemicarbazones on the mode of coordination, structure, interaction with protein, radical scavenging and cytotoxic activity of copper(II) complexes

Four 2-oxo-1,2-dihydroquinoline-3-carbaldehyde N-substituted thiosemicarbazone ligands (H(2)-OQtsc-R, where R = H, Me, Et or Ph) and their corresponding new copper(II) complexes [CuCl(2)(H(2)-OQtsc-H)]·2H(2)O (1), [CuCl(2)(H(2)-OQtsc-Me)]·2H(2)O (2), [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)]Cl (3) and [CuCl(H-OQtsc-Ph)]·CH(3)OH (4) have been synthesized in order to correlate the effect of terminal N-substitution on coordination behaviour, structure and biological activity. Single crystal X-ray diffraction studies revealed that the complexes 1, 2 and 3 have square pyramidal geometry around the central metal ion. In the complexes 1 and 2, the copper ion is coordinated by the ligand with ONS donor atoms, one chloride ion in apical position and the other chloride in the basal plane. Complex 3 consists of [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)](+) cation and a chloride as counter ion. The copper ion is coordinated by the ligand with ONS donor atoms and by one chloride ion in the basal plane. One methanol molecule is bonded through its neutral oxygen in the apical position. Complex 4 is square planar with the ligand coordinating through uni-negative tridentate ONS(-) and by one chloride ion in the basal plane. The binding of complexes with lysozyme protein was carried out by fluorescence spectroscopy. Investigations of antioxidation properties showed that all the copper(II) complexes have strong radical scavenging properties. The cytotoxicity of the complexes 3 and 4 against NIH 3T3 and HeLa cell lines showed that synergy between the metal and ligands results in a significant enhancement in the cell death with IC(50) of ~10-40 μM. A size dependence of substitution at terminal N in the thiosemicarbazones on the biological activities of the complexes has been observed.     

Linear and nonlinear optical properties of cationic bipyridyl iridium(III) complexes: tunable and photoswitchable?

A series of cationic Ir(III) substituted bipyridyl ()(N(∧)N (N(∧)N-bpy) complexes incorporating electron-donor and -acceptor substituents, [Ir(C(∧)N-ppy-R')(2)(N(∧)N-bpy-CH═CH-C(6)H(4)-R)][X] (X(-) = PF(6)(-) or C(12)H(25)SO(3)(-)), 2 (a, R = NEt(2) and R' = Me; b, R = O-Oct and R' = Me; c, R = NO(2) and R' = C(6)H(13); C(∧)N-ppy = cyclometalated 2-phenylpyridine, [Ir(C(∧)N-ppy-Me)(2)(N(∧)N-bpy-CH═CH-thienyl-Me)][PF(6)], 2d, and the dithienylethene (DTE)-containing complex 2e have been synthesized and characterized, and their absorption, luminescence, and quadratic nonlinear optical (NLO) properties are reported. Density functional theory (DFT) and time-dependent-DFT (TD-DFT) calculations on the complexes facilitate a detailed assignment of the excited states involved in the absorption and emission processes. All five complexes are luminescent in a rigid glass at 77 K, displaying vibronically structured spectra with long lifetimes (14-90 μs), attributed to triplet states localized on the styryl-appended bipyridines. The second-order NLO properties of 2a-d and related complexes 1a-d with 1,10-phenanthrolines have been investigated by both electric field induced second harmonic generation (EFISH) and harmonic light scattering (HLS) techniques. They are characterized by high negative EFISH μβ values which decrease when the ion pair strength between the cation and the counterion (PF(6)(-), C(12)H(25)SO(3)(-)) increases. The EFISH response is mainly controlled by metal-to-ligand charge-transfer/ligand-to-ligand charge-transfer (MLCT/L'LCT) processes. A combination of HLS and EFISH techniques is used to evaluate both the dipolar and octupolar contributions to the total quadratic hyperpolarizability, demonstrating that the major contribution is controlled by the octupolar part. The incorporation of a photochromic DTE unit into the N(∧)N-bpy ligand (complex 2e) allows the luminescence to be switched ON or OFF. The photocyclisation of the DTE unit can be triggered by using either UV (365 nm) or visible light (430 nm), leading to an efficient quenching of the ligand-based 77 K luminescence, which can be restored upon irradiation of the closed form at 715 nm. In contrast, no significant modification of the EFISH μβ value is observed upon photocyclization, suggesting that the quadratic NLO response is dominated by the MLCT/L'LCT processes, rather than by the intraligand excited states localized on the substituted bipyridine ligand.     

Top-Down Mass Spectrometry of Supercharged Native Protein-Ligand Complexes

Tandem mass spectrometry (MS/MS) of intact, noncovalently-bound protein-ligand complexes can yield structural information on the site of ligand binding. Fourier transform ion cyclotron resonance (FT-ICR) top-down MS of the 29 kDa carbonic anhydrase-zinc complex and adenylate kinase bound to adenosine triphosphate (ATP) with collisionally activated dissociation (CAD) and/or electron capture dissociation (ECD) generates product ions that retain the ligand and their identities are consistent with the solution phase structure. Increasing gas phase protein charging from electrospray ionization (ESI) by the addition of supercharging reagents, such as m-nitrobenzyl alcohol and sulfolane, to the protein analyte solution improves the capability of MS/MS to generate holo-product ions. Top-down proteomics for protein sequencing can be enhanced by increasing analyte charging.     

Inhibition of Acinetobacter baumannii biofilm formation on a methacrylate polymer containing a 2-aminoimidazole subunit

A polymeric composite containing a 2-aminoimidazole derivative was synthesized. It was found that this polymer was resistant to biofilm colonization by Acinetobacter baumannii, no leaching of the 2-aminoimidazole derivative was observed after 2 weeks of treatment with deionized water, and the resulting polymer was not hemolytic.     

Ensemble and Single Molecule Studies on the Use of Metallic Nanostructures to Enhance the Intrinsic Emission of Enzyme Cofactors

We present a strategy for enhancing the intrinsic emission of the enzyme cofactors flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and nicotinamide adenine dinucleotide (NADH). Ensemble studies show that silver island films (SIFs) are the optimal metal enhanced fluorescence (MEF) substrates for flavins and gave emission enhancements of over 10-fold for both FAD and FMN. A reduction in the lifetime of FAD and FMN on SIFs was also observed. Thermally evaporated aluminum films on quartz slides were found to be the optimal MEF substrate for NADH and gave a 5-fold increase in the emission intensity of NADH. We present finite-difference time-domain (FDTD) calculations that compute the enhancement in the radiated power emitting from an excited state dipole emitting in the wavelength range of NADH in close proximity to an aluminum nanoparticle, and a dipole emitting in the emission wavelength of flavins next to a silver nanoparticle. These calculations confirm that aluminum serves as the optimal MEF substrate for NADH and silver was the optimal MEF substrate for flavins. This is because the plasmon resonance properties of aluminum lie in the UV-blue regime and that of silver lie in the visible region. We also present the results of single molecule studies on FMN which show SIFs can both significantly enhance the intrinsic emission from single FMN molecules, significantly reduce their lifetimes and also significantly reduce FMN blinking. This is the first report of the observation of MEF from cofactors both at the ensemble and single molecule level. We hope this study will serve as a platform to encourage the future use of metallic nanostructures to study cofactors using their intrinsic fluorescence to directly monitor enzyme binding reactions without the need of extrinsic labeling of the molecules.     

Energy deposition during electron-induced dissociation

We report studies of the internal energy deposited during activation of mass-selected ions through electron-ion collisions. Characteristic fragmentations of the molecular ion of limonene and W(CO) ^n/+ (n = 1–6) indicate that electron-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer proceeds via multiple collisions and that the average internal energy deposited during the activation process can be selected to be similar to that associated with electron-impact ionization. Control of the degree of ion excitation through selection of the electron energy, flux, and interaction time with the ions of interest is demonstrated, and advantages of this promising activation technique are discussed.