Ligand-based 3-D pharmacophore generation and molecular docking of mTOR kinase inhibitors

The 3-D structure of the human mTOR kinase domain was modeled based on the crystal structure of PI3Kγ using comparative modeling methods, and the ATP-binding site of mTOR was characterized. The mTOR kinase 3-D model structure is similar to the structure of the PI3Kγ kinase domain, and exhibits great similarity to PI3Kγ at the active site of the kinase. Pharmacophore generation, the docking of mTOR inhibitors, and molecular dynamics (MD) simulations of mTOR–inhibitor docked complexes were carried out in this work. The best pharmacophore model generated from 27 ATP-competitive mTOR inhibitors comprised two hydrogen-bond acceptors, one aromatic ring, and one hydrophobic feature. These 27 inhibitors were docked into the ATP-binding site comprising the DFG motif, and the interactions in each protein–inhibitor complex were characterized. Mapping the pharmacophore model onto the docked inhibitors explained the specificity of the features of the pharmacophore and how they were arranged inside the active site of mTOR kinase. MD studies revealed important structural features, such as the large hydrophobic pocket “HP” and hydrophilic pocket “A1,” and the solvent-exposed hydrophilic pocket “A2” at the active site of mTOR. Our results provide structural models of mTOR–inhibitor complexes and clues that should aid in the design of better mTOR kinase inhibitors.     

A Kunitz trypsin inhibitor of Entada scandens seeds: another member with single disulfide bridge

Sword bean (Entada scandens) is a tree climber that belongs to Mimosoideae, a subfamily of Leguminosae. A potent Kunitz type trypsin inhibitor (ESTI) was purified to homogeneity from Entada scandens seeds by sequential ammonium sulfate precipitation, affinity chromatography on trypsin-Sepharose and DEAE-Sephacel ion-exchange chromatography. ESTI is a single polypeptide chain of 19,766 Da. Both native PAGE as well as isoelectric focusing showed a single inhibitor species with a pI of 7.43. MALDI-TOF analysis also confirmed the monomeric nature. The amino-terminal sequence of ESTI reveals significant homology to the Kunitz-type protease inhibitors of legume plants. ESTI is unique in that it contains a single disulfide bridge, and unlike other inhibitors from Mimosoideae species is a single chain polypeptide. ESTI inhibited bovine trypsin with a stoichiometry of 1:1 and the apparent K(i) was 4.9 x 10(-9) M. In vitro assay showed that ESTI inhibited the midgut proteinase of the fifth instar larvae of Rice moth (Corcyra cephalonica) with an IC(50) of 26.4+/-0.01 nM. ESTI exhibits a mixed type competitive inhibition at lower concentration and pure competitive at higher inhibitor concentrations. Phylogenetic analyses depicted a clear divergence of single disulfide containing inhibitors from other tree legume Kunitz inhibitors. The homology of ESTI to Kunitz inhibitors together with the absence of Bowman-Birk type inhibitors in sword bean further supports the theory that there exists an evolutionary relationship between the families of inhibitors found in Leguminosae.     

An epidemiologically significant epitope of a 1998 human influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex

The crystal structure of the complex between neuraminidase (NA) of influenza virus A/Memphis/31/98 (H3N2) and Fab of monoclonal antibody Mem5 has been determined at 2.1A resolution and shows a novel pattern of interactions compared to other NA-Fab structures. The interface buries a large area of 2400 A2 and the surfaces have high complementarity. However, the interface is also highly hydrated. There are 33 water molecules in the interface>or=95% buried from bulk solvent, but only 13 of these are isolated from other water molecules. The rest are involved in an intricate network of water-mediated hydrogen bonds throughout the interface, stabilizing the complex. Glu199 on NA, the most critical side-chain to the interaction as previously determined by escape mutant analysis and site-directed mutation, is located in a non-aqueous island. Glu199 and three other residues that contribute the major part of the antigen buried surface of the complex have mutated in human influenza viruses isolated after 1998, confirming that Mem5 identifies an epidemiologically important antigenic site. We conclude that antibody selection of NA variants is a significant component of recent antigenic drift in human H3N2 influenza viruses, supporting the idea that influenza vaccines should contain NA in addition to hemagglutinin.     

Isolation, purification and characterization of beta-1,3-glucan binding protein from the plasma of marine mussel Perna viridis

A beta-1,3-glucan binding protein (betaGBP) specific for laminarin (a beta-1,3-glucan) was detected for the first time in a mollusc, Perna viridis. betaGBP was isolated and purified from the plasma using laminarin precipitation and affinity chromatography on laminarin-Sepharose 6B, respectively. It agglutinated bakers yeast, bacteria, and erythrocytes and enhanced prophenoloxidase (proPO) activity of the plasma in a dose-dependent manner. The purified betaGBP appeared as a single band in native-PAGE and the purity was conformed by HPLC. The protein has a molecular weight estimate of 510kDa as determined by SDS-PAGE and in isoelectric focusing the purified betaGBP was focused as a single band at pI 5.3. betaGBP was found to possess inherent serine protease activity but lacked beta-1,3-glucanase activity and all these results suggest that plasma betaGBP of P. viridis functions as a recognition molecule for beta-1,3-glucan on the surface of microbial cell walls. This recognition and binding lead to the activation of the prophenoloxidase cascade mediated by the inherent serine protease activity of betaGBP. Presence of agglutinating activity and serine protease activity shows that betaGBP is a bifunctional protein. The findings are discussed in light of the importance of this protein in the innate immune response of P. viridis, and they implicate evolutionary link with similar proteins found in other invertebrates.     

Anti-cataractogenic effect of curcumin and aminoguanidine against selenium-induced oxidative stress in the eye lens of Wistar rat pups: An in vitro study using isolated lens

The aim of this study was to investigate whether curcumin and aminoguanidine (AG) prevent selenium-induced cataractogenesis in vitro. On postpartum day 8, transparent isolated lens were incubated in 24 well plates containing Dulbecco's Modified Eagle Medium (DMEM). Isolated lens of group I were incubated with DMEM medium alone. Group II: lenses incubated in DMEM containing 100 μM sodium selenite; group III: lenses incubated in DMEM containing 100 μM sodium selenite and 100 μM curcumin; group IV: lenses incubated in DMEM containing 100 μM sodium selenite and 200 μM curcumin; group V: lenses incubated in DMEM containing 100 μM sodium selenite and 100 μM AG; group V: lenses incubated in DMEM containing 100 μM sodium selenite and 200 μM AG. On day 12, cataract development was graded using an inverted microscope and the lenses were analyzed for enzymic as well as non-enzymic antioxidants, lipid peroxidation (LPO), nitric oxide (NO), superoxide anion (O₂⁻) and hydroxyl radical generation (OH) and inducible nitric oxide synthase (iNOS) activity by Western blotting and RT-PCR. All control lenses in group I were clear (0). In groups II and III, all isolated lenses developed cataract with variation in levels (+++ or ++), whereas isolated lenses from groups IV, V and VI were clear (0). In agreement to this, a decrease in antioxidants and increased free radical generation and also iNOS expression were observed in selenium exposed lenses when compared to other groups. AG (100 μM) was found to be more effective in anti-cataractogenic effect than curcumin (200 μM). Curcumin and AG suppressed selenium-induced oxidative stress and cataract formation in isolated lens from Wistar rat pups, possibly by inhibiting depletion of enzymic as well as non-enzymic antioxidants, and preventing uncontrolled generation of free radicals and also by inhibiting iNOS expression. Our results implicate a major role for curcumin and AG in preventing cataractogenesis in selenite-exposed lenses, wherein AG was found to be more potent.     

25-hydroxycholesterol acts in the Golgi compartment to induce degradation of tyrosinase

Oxysterols play a significant role in cholesterol homeostasis. 25-Hydroxycholesterol (25HC) in particular has been demonstrated to regulate cholesterol homeostasis via oxysterol-binding protein and oxysterol-related proteins, the sterol regulatory element binding protein, and the rate-limiting enzyme of cholesterol biosynthesis, hydroxymethylglutaryl coenzyme A reductase. We have examined the effect of 25HC on pigmentation of cultured murine melanocytes and demonstrated a decrease in pigmentation with an IC(50) of 0.34 microM and a significant diminution in levels of melanogenic protein tyrosinase. Pulse-chase studies of 25HC-treated cells demonstrated enhanced degradation of tyrosinase, the rate-limiting enzyme of melanin synthesis, following endoplasmic reticulum (ER) and Golgi maturation. Protein levels of GS28, a member of an ER/cis-Golgi SNARE protein complex, were also diminished in 25HC-treated melanocytes, however levels of the ER chaperone calnexin and the cis-Golgi matrix protein GM130 were unaffected. Effects of 25HC on tyrosinase were completely reversed by 4 alpha-allylcholestan-3 alpha-ol, a sterol identified by its ability to reverse effects of 25HC on cholesterol homeostasis. Finally, the addition of 25HC to lipid deficient serum inhibited correct processing of tyrosinase. We conclude that 25HC acts in the Golgi compartment to regulate pigmentation by a mechanism shared with cholesterol homeostasis.     

In vitro and in silico investigation of caprylic acid effect on multi drug resistant (MDR) Klebsiella pneumoniae biofilm

Abstract

Communicated by Ramaswamy H. Sarma