Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase

Many proteins undergo small side chain or even backbone movements on binding of different ligands into the same protein structure. This is known as induced fit and is potentially problematic for virtual screening of databases against protein targets. In this report we investigate the limits of the rigid protein approximation used by the docking program, GOLD, through cross-docking using protein structures of influenza neuraminidase. Neuraminidase is known to exhibit small but significant induced fit effects on ligand binding. Some neuraminidase crystal structures caused concern due to the bound ligand conformation and GOLD performed poorly on these complexes. A `clean' set, which contained unique, unambiguous complexes, was defined. For this set, the lowest energy structure was correctly docked (i.e. RMSD < 1.5 Å away from the crystal reference structure) in 84% of proteins, and the most promiscuous protein (1mwe) was able to dock all 15 ligands accurately including those that normally required an induced fit movement. This is considerably better than the 70% success rate seen with GOLD against general validation sets. Inclusion of specific water molecules involved in water-mediated hydrogen bonds did not significantly improve the docking performance for ligands that formed water-mediated contacts but it did prevent docking of ligands that displaced these waters. Our data supports the use of a single protein structure for virtual screening with GOLD in some applications involving induced fit effects, although care must be taken to identify the protein structure that performs best against a wide variety of ligands. The performance of GOLD was significantly better than the GOLD implementation of ChemScore and the reasons for this are discussed. Overall, GOLD has shown itself to be an extremely good, robust docking program for this system.     

IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers

We describe a novel approach for the automated localization of biotransformations, which we term IsoScore. Accurate mass measurement spectra of a parent drug and its metabolites are acquired. All virtual regioisomers of a given biotransformation are generated in silico by iterating over all plausible sites of oxidation around the parent drug. Each is then fragmented virtually using an exhaustive approach supplemented with chemical intelligence. Each fragment is scored based on the likelihood that it can be formed from the precursor structure. The fragment library of each virtual isomer is then compared with the experimentally observed ions. The likelihood that a regioisomer explains the observed fragmentation data is contained in its cumulated score. We include additional weightings, which take into account the level of similarity between the mass spectra of the metabolite and the parent compound. This concept was tested on a variety of metabolites from different chemical platforms formed via single biotransformations. For a very large proportion of the metabolites, IsoScore correctly located the biotransformation to the expected position. All ions above a defined threshold in the spectrum are used to contribute to the score with no predisposition to ignore minor ions or to weight conclusions based on readily interpretable fragments. The approach is found to be most successful when differential scoring is observed between related ions in the parent and the metabolite. Further improvements in the scoring function will result in increased differentiation between likely and unlikely structures, even when the parent and the metabolite spectra show little similarity. Copyright © 2008 John Wiley & Sons, Ltd.     

Inclusive and exclusive measurements in the projectile breakup of 7Li

The inclusive and exclusive measurements were carried out for ⁷Li projectile breakup on ²⁷Al target at 48 MeV. In the inclusive data we have observed a broad peak around the beam velocity for alphas and tritons. The exclusive data for alpha-triton coincidences show good agreement with the post-form DWBA theory of breakup reactions.     

Effect of alpha-tocopherol on pulmonary antioxidant defence system and lipid peroxidation in cigarette smoke inhaling mice

Background  

Free radicals generated in biological systems by cigarette smoke (CS) inhalation can cause oxidative stress in tissues, resulting in lipid peroxidation (LPO). In view of the antioxidant properties of α-tocopherol (AT), in the present study, effects of AT on antioxidant defence system and LPO were investigated in mice inhaling CS for different time intervals.     

Critical petermann K factor for intensity noise squeezing

We investigate the impact of the Petermann-excess-noise factor K>/=1 on the possibility of intensity noise squeezing of laser light below the standard quantum limit. Using an N-mode model, we show that squeezing is limited to a floor level of 2(K-1) times the shot noise limit. Thus, even a modest Petermann factor significantly impedes squeezing, which becomes impossible when K>/=1.5. This appears as a serious limitation for obtaining sub-shot-noise light from practical semiconductor lasers. We present experimental evidence for our theory.