Fully automated molecular mechanics based induced fit protein-ligand docking method

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by a protein side-chain refinement stage that models protein flexibility. The final step of the process is an energy minimization of the ligand pose in the presence of the rigid receptor. Thus the algorithm models flexibility of the protein at two stages, before and after ligand placement. We validated this method by performing docking and cross docking studies of eight protein systems for which crystal structures were available for at least two bound ligands. The resulting rmsd values of the 21 docked protein-ligand complexes showed values of 2 A or less for all but one of the systems examined. The method has two critical benefits for high throughput virtual screening studies. First, no user intervention is required in the docking once the initial binding site selection has been made in the protein. Second, the initial protein conformation generation needs to be performed only once for a given binding region. Also, the method may be customized in various ways depending on the particular scenario in which dockings are being performed. Each of the individual steps of the method is fully independent making it straightforward to explore different variants of the high level workflow to further improve accuracy and performance.     

Stratigraphic analysis of organic materials in wall painting samples using micro-FTIR attenuated total reflectance and a novel sample preparation technique

Wall paintings typically contain low concentrations of organic materials within a largely inorganic matrix and are characterised by their high porosity and long-term exposure to severe environmental conditions. The identification of organic materials within specific paint or plaster layers is challenging and the inherent characteristics of wall painting samples present further complications. Embedding materials (such as epoxy, polyester and acrylic-based resins) used to produce cross-sections often infiltrate porous and leanly bound samples, and compromise the interpretation of Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectra and the qualitative identification of natural organic materials. An alternative method for the preparation of cross-sections of wall painting samples was developed using cyclododecane (C(12)H(24)) as a temporary consolidant and barrier coating to encapsulate the sample, and to provide necessary support to produce a cross-section through microtoming. Impacts of traditional and novel sample preparation techniques on the identification of organic materials with micro-FTIR-ATR were examined for both replica and real wall painting samples.     

A miniaturized glucocorticoid receptor translocation assay using enzymatic fragment complementation evaluated with qHTS

Nuclear translocation is an important step in glucocorticoid receptor (GR) signaling and assays that measure this process allow the identification of nuclear receptor ligands independent of subsequent functional effects. To facilitate the identification of GR-translocation agonists, an enzyme fragment complementation (EFC) cell-based assay was scaled to a 1536-well plate format to evaluate 9,920 compounds using a quantitative high throughput screening (qHTS) strategy where compounds are assayed at multiple concentrations. In contrast to conventional assays of nuclear translocation the qHTS assay described here was enabled on a standard luminescence microplate reader precluding the requirement for imaging methods. The assay uses beta-galactosidase alpha complementation to indirectly detect GR-translocation in CHO-K1 cells. 1536-well assay miniaturization included the elimination of a media aspiration step, and the optimized assay displayed a Z' of 0.55. qHTS yielded EC(50) values for all 9,920 compounds and allowed us to retrospectively examine the dataset as a single concentration-based screen to estimate the number of false positives and negatives at typical activity thresholds. For example, at a 9 microM screening concentration, the assay showed an accuracy that is comparable to typical cell-based assays as judged by the occurrence of false positives that we determined to be 1.3% or 0.3%, for a 3sigma or 6sigma threshold, respectively. This corresponds to a confirmation rate of approximately 30% or approximately 50%, respectively. The assay was consistent with glucocorticoid pharmacology as scaffolds with close similarity to dexamethasone were identified as active, while, for example, steroids that act as ligands to other nuclear receptors such as the estrogen receptor were found to be inactive.     

A high throughput fluorescence polarization assay for inhibitors of the GoLoco motif/G-alpha interaction

The GoLoco motif is a short Galpha-binding polypeptide sequence. It is often found in proteins that regulate cell-surface receptor signaling, such as RGS12, as well as in proteins that regulate mitotic spindle orientation and force generation during cell division, such as GPSM2/LGN. Here, we describe a high throughput fluorescence polarization (FP) assay using fluorophore-labeled GoLoco motif peptides for identifying inhibitors of the GoLoco motif interaction with the G-protein alpha subunit Galpha (i1). The assay exhibits considerable stability over time and is tolerant to DMSO up to 5%. The Z'-factors for robustness of the GPSM2 and RGS12 GoLoco motif assays in a 96-well plate format were determined to be 0.81 and 0.84, respectively; the latter assay was run in a 384-well plate format and produced a Z'-factor of 0.80. To determine the screening factor window (Z-factor) of the RGS12 GoLoco motif screen using a small molecule library, the NCI Diversity Set was screened. The Z-factor was determined to be 0.66, suggesting that this FP assay would perform well when developed for 1,536-well format and scaled up to larger libraries. We then miniaturized to a 4 microL final volume a pair of FP assays utilizing fluorescein- (green) and rhodamine- (red) labeled RGS12 GoLoco motif peptides. In a fully-automated run, the Sigma-Aldrich LOPAC(1280) collection was screened three times with every library compound being tested over a range of concentrations following the quantitative high throughput screening (qHTS) paradigm; excellent assay performance was noted with average Z-factors of 0.84 and 0.66 for the green- and red-label assays, respectively.     

Aqueous behaviour of cationic surfactants containing a cleavable group

The aggregation behaviour of two novel cationic RAFT agents (transfer surfactants); N,N-dimethyl-N-(4-(((phenylcarbonothioyl)thio)methyl)benzyl)ethanammonium bromide (PCDBAB) and N-(4-((((dodecylthio)-carbonothioyl)thio)methyl)benzyl)-N,N-dimethylethanammonium bromide (DCTBAB) in diluted solutions have been investigated by surface tension, conductimetry and microcalorimetry measurements. The thermodynamic parameters i.e. the critical micelle concentration (cmc), the degree of micelle ionization (alpha), the head group surface area (a 0), Delta H mic, Delta G mic and T Delta S mic are reported at 303 K. The thermodynamic parameters have been compared to those of the conventional surfactant cetyltrimethylammonium bromide (CTAB) in order to specify structural relationships. The obtained results have been discussed considering the hydrophobic behaviour of the S-C=S- linkage and the specific interactions that arise from the introduction of the benzene ring into the hydrophobic part.     

Novel ion traps using planar resistive electrodes: Implications for miniaturized mass analyzers

In radiofrequency ion traps, electric fields are produced by applying time-varying potentials between machined metal electrodes. The electrode shape constitutes a boundary condition and defines the field shape. This paper presents a new approach to making ion traps in which the electrodes consist of two ceramic discs, the facing surfaces of which are lithographically imprinted with sets of concentric metal rings and overlaid with a resistive material. A radial potential function can be applied to the resistive material such that the potential between the plates is quadrupolar, and ions are trapped between the plates. The electric field is independent of geometry and can be optimized electronically. The trap can produce any trapping field geometry, including both a toroidal trapping geometry and the traditional Paul-trap field. Dimensionally smaller ion trajectories, as would be produced in a miniaturized ion trap, can be achieved by increasing the potential gradient on the resistive material and operating the trap at higher frequency, rather than by making any physical changes to the trap or the electrodes. Obstacles to miniaturization of ion traps, such as fabrication tolerances, surface smoothness, electrode alignment, limited access for ionization or ion injection, and small trapping volume are addressed using this design.     

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.     

Confinement-Driven Photophysics in Hydrazone-Based Hierarchical Materials

Confinement-imposed photophysics was probed for novel stimuli-responsive hydrazone-based compounds demonstrating a conceptual difference in their behavior within 2D versus 3D porous matrices for the first time. The challenges associated with photoswitch isomerization arising from host interactions with photochromic compounds in 2D scaffolds could be overcome in 3D materials. Solution-like photoisomerization rate constants were realized for sterically demanding hydrazone derivatives in the solid state through their coordinative immobilization in 3D scaffolds. According to steady-state and time-resolved photophysical measurements and theoretical modeling, this approach provides access to hydrazone-based materials with fast photoisomerization kinetics in the solid state. Fast isomerization of integrated hydrazone derivatives allows for probing and tailoring resonance energy transfer (ET) processes as a function of excitation wavelength, providing a novel pathway for ET modulation.     

Toward [18F]-labeled aryltrifluoroborate radiotracers: in vivo positron emission tomography imaging of stable aryltrifluoroborate clearance in mice

The use of a boronic ester as a captor of aqueous [(18)F]-fluoride has been previously suggested as a means of labeling biomolecules in one step for positron emission tomography (PET) imaging. For this approach to be seriously considered, the [(18)F]-labeled trifluoroborate should be humorally stable such that it neither leaches free [(18)F]-fluoride to the bone nor accumulates therein. Herein, we have synthesized a biotinylated boronic ester that is converted to the corresponding trifluoroborate salt in the presence of aqueous [(18)F]-fluoride. In keeping with its in vitro aqueous kinetic stability at pH 7.5, the trifluoroborate appears to clear in vivo quite rapidly to the bladder as the stable trifluoroborate salt with no detectable leaching of free [(18)F]-fluoride to the bone. When this labeled biotin is preincubated with avidin, the pharmacokinetic clearance of the resulting complex is visibly altered. This work validates initial claims that boronic esters are potentially useful as readily labeled precursors to [(18)F]-PET reagents.     

Electrochemical and structural properties of a polymer electrolyte system based on the effect of CeO<Subscript>2</Subscript> nanofiller with PVDF-co-HFP for energy storage devices

In the present work, a series of five different nanocomposite polymer electrolytes (NCPEs) have been reported with varying contents of ceria, CeO₂ nanofiller suitably incorporated within an optimized composition having 75:25 wt% ratio of poly(vinylidenefluoride-co-hexafluoropropylene) [(PVDF-co-HFP)] and zinc trifluoromethanesulfonate (ZnTf) in the form of films obtained by mean of solution casting technique with a general formula [75 wt% PVDF-co-HFP:25 wt% ZnTf]-x wt% CeO₂ where x = 1, 3, 5, 7, and 10, respectively. The chosen NCPE system is found to exhibit the maximum electrical conductivity of 3 × 10^?4 S cm^?1 for 5 wt% loading of CeO₂ nanofiller at ambient temperature. The observed conductivity enhancement has been attributed to the occurrence of an increase in the amorphous content as confirmed by X-ray diffraction (XRD) analysis. Detailed Fourier transform infrared (FTIR) spectral analysis has indicated the feasibility of complexation of the host polymer matrix with ZnTf salt and CeO₂ nanofiller. The incorporation of CeO₂ nanofiller has further increased the decomposition voltage of the polymer electrolyte from 2.4 to 2.7 V as revealed from the voltammetric studies performed on such NCPEs, thereby suggesting the suitability of these NCPE films with an enhanced electrical conductivity as new electrolytes in order to design and fabricate eco-friendly zinc rechargeable batteries and other electrochemical devices.