A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A,a selective kappa opioid receptor agonist

Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based “agonist-bound” hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental pK _i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Comparative protein modeling of 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme from Plasmodium falciparum: a potential target for antimalarial drug discovery

Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Pf-DXR) is a potential target for antimalarial chemotherapy. The three-dimensional model (3D) of this enzyme was determined by means of comparative modeling through multiple alignment followed by intensive optimization, minimization, and validation. The resulting model demonstrates a reasonable topology as gauged from the Ramachandran plot and acceptable three-dimensional structure compatibility as assessed by the Profiles-3D score. The modeled monomeric subunit consists of three domains: (1) N-terminal NADPH binding domain, (2) connective or linker domain (with most of the active site residues located in this domain), and (3) a C-terminal domain. This structure proved to be consistent with known DXR crystal structures from other species. The predicted active site compared favorably with those of the templates and appears to have an active site with a highly conserved architecture. Additionally, the model explains several site-directed mutagenesis data. Besides using several protein structure-checking programs to validate the model, a set of known inhibitors of DXR were also docked into the active site of the modeled Pf-DXR. The docked scores correlated reasonably well with experimental pIC50 values with a regression coefficient (R2) equal to 0.84. Results of the current study should prove useful in the early design and development of inhibitors by either de novo drug design or virtual screening of large small-molecule databases leading to development of new antimalarial agents.     

The role of the t-SNARE SNAP-25 in action potential-dependent calcium signaling and expression in GABAergic and glutamatergic neurons

Background  

The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, comprised of SNAP-25, syntaxin 1A, and VAMP-2, has been shown to be responsible for action potential (AP)-dependent, calcium-triggered release of several neurotransmitters. However, this basic fusogenic protein complex may be further specialized to suit the requirements for different neurotransmitter systems, as exemplified by neurons and neuroendocrine cells. In this study, we investigate the effects of SNAP-25 ablation on spontaneous neuronal activity and the expression of functionally distinct isoforms of this t-SNARE in GABAergic and glutamatergic neurons of the adult brain.     

Chiral separation of lobeline analogs using high performance capillary electrophoresis and derivatized cyclodextrins as chiral additives

High performance capillary electrophoresis (HPCE) methods are described that will separate the enantiomers of various lobeline analogs synthesized in these laboratories. "Cyclodextrin array analysis" was used for preliminary screening and electrophoresis conditions were optimized for each investigated analog. The lobeline analogs under consideration were investigated as potential nicotinic agonists for the treatment of neurodegenerative disorders, such as Alzheimer's disease. Native alpha (alpha)-, beta (beta)-, and gamma (gamma)-cyclodextrins, methyl-beta-cyclodextrin (M-beta-CD), heptakis-(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD), and heptakis-(2,3,6-tri-O-methyl)-beta-cyclodextrin (TM-beta-CD), hydroxypropyl-alpha-cyclodextrin (HP-alpha-CD), hydroxypropyl-beta-cyclodextrin (HP-beta-CD) and hydroxypropl-gamma-cyclodextrin (HP-gamma-CD) were used as run buffer additives and their effect on the enantiomeric resolution of the lobeline analogs was investigated. The effect of pH, buffer concentration, voltage, temperature and organic modifier concentration on the enantiomeric resolution of the lobeline analogs was investigated. The most suitable conditions for each compound were chosen and, with detection at a wavelength of 200 nm, optimized.     

Apparent molar heat capacities and volumes of aqueous electrolytes: CaCl2, Cd(NO3)2, CoCl2, Cu(ClO4)2, Mg(ClO4)2, and NiCl2

We have used a flow calorimeter and a flow densimeter for measurements leading to apparent molar heat capacities and apparent molar volumes of six 21 electrolytes in aqueous solution at 25°C. Results of these measurements have been used to derive apparent molar heat capacities and volumes at infinite dilution for all six electrolytes: CaCl₂, Cd(NO₃)₂, CoCl₂, Cu(ClO₄)₂, Mg(ClO₄)₂, and NiCl₂.     

Ultra-sensitive Mass Spectrometric and Other Advanced Methods Applied to Biological Samples; Second interlaboratory comparison study for the analysis of 239Pu in synthetic urine at the µBq (~100 aCi) level by mass spectrometry

Summary As a follow up to the initial 1998 intercomparison study, a second study was initiated in 2001 as part of the ongoing evaluation of the capabilities of various ultra-sensitive methods to analyze ²³⁹Pu in urine samples. The initial study¹ was sponsored by the Department of Energy, Office of International Health Programs to evaluate and validate new technologies that may supersede the existing fission tract analysis (FTA) method for the analysis of ²³⁹Pu in urine at the µBq/l level. The ultra-sensitive techniques evaluated in the second study included accelerator mass spectrometry (AMS) by LLNL, thermal ionization mass spectrometry (TIMS) by LANL and FTA by the University of Utah. Only the results for the mass spectrometric methods will be presented. For the second study, the testing levels were approximately 4, 9, 29 and 56 µBq of ²³⁹Pu per liter of synthetic urine. Each test sample also contained ²⁴⁰Pu at a ²⁴⁰Pu/²³⁹Pu atom ratio of ~0.15 and natural uranium at a concentration of 50 µBq/ml. From the results of the two studies, it can be inferred that the best performance at the µBq level is more laboratory specific than method specific. The second study demonstrated that LANL-TIMS and LLNL-AMS had essentially the same quantification level for both isotopes. Study results for bias and precision and acceptable performance compared to ANSI N13.30 and ANSI N42.22 have been compiled.     

Surface Interactions of Radicals During Plasma Processing of Polymers

Surface interactions of radical species were investigated using the imaging of radicals interacting with surfaces (IRIS) technique during plasma surface modification of polymers. Three plasma systems were investigated by spatially probing the laser induced fluorescence of individual radical species and determining their surface scattering coefficients, S. The behavior of CF₂ moieties on polymer surfaces was studied using the fluorocarbon plasmas C₂F₆ and hexafluoropropylene oxide (HFPO). Three types of surface interactions were observed, surface generation of CF₂ (S > 1), surface loss of CF₂ (S < 1), and unit scattering (S = 1). Surface loss of CF₂ was seen in HFPO plasmas, while CF₂ was generated in C₂F₆ systems. The differences between these systems is believed to be the result of different overall surface interactions, specifically film deposition in the HFPO system and etching in the C₂F₆ system. Using NH₃ plasmas, the surface interactions of NH₂ radicals with polymers was also investigated. Here, NH₂ is generated at the surface of polyethylene and polytetrafluoroethylene substrates, but is consumed on polyimide substrates. Ion effects were also investigated by placing a grounded mesh in the path of the molecular beam to remove charged species.