ASEDock-docking based on alpha spheres and excluded volumes

ASEDock is a novel docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. We have introduced two novel concepts into ASEDock. One is an ASE model, which is defined by the combination of alpha spheres generated at a concavity in a protein and the excluded volumes around the concavity. The other is an ASE score, which evaluates the shape similarity between the ligand and the ASE model. The ASE score selects and refines the initial pose by maximizing the overlap between the alpha spheres and the ligand, and minimizing the overlap between the excluded volume and the ligand. Because the ASE score makes good use of the Gaussian-type function for evaluating and optimizing the overlap between the ligand and the site model, it can pose a ligand onto the docking site relatively faster and more effectively than using potential energy functions. The posing stage through the use of the ASE score is followed by full atomistic energy minimization. Because the posing algorithm of ASEDock is free from any bias except for shape, it is a very robust docking method. A validation study using 59 high-quality X-ray structures of the complexes between drug-like molecules and the target proteins has demonstrated that ASEDock can faithfully reproduce experimentally determined docking modes of various druglike molecules in their target proteins. Almost 80% of the structures were reconstructed within the estimated experimental error. The success rate of approximately 98% was attained based on the docking criterion of the root-mean-square deviation (RMSD) of non-hydrogen atoms (< or = 2.0 A). The markedly high success of ASEDock in redocking experiments clearly indicates that the most important factor governing the docking process is shape complementarity.     

A novel route for the construction of Taxol ABC-ring framework: skeletal rearrangement approach to AB-ring and intramolecular aldol approach to C-ring

We report here on the construction of the ABC-ring framework of (±)-Taxol using an intramolecular aldol reaction as a key step. AB-ring compound 8 was converted to ketoaldehyde 25 as a precursor of an aldol reaction via introduction of oxygen-functionalities and a methoxycarbonyl group, which can be converted to a methyl group, in the proper positions of the B-ring. An aldol reaction of ketoaldehyde with LDA led to the formation of the desired product 27, which corresponds to the ABC-ring framework of (±)-Taxol.     

Studies on neurosteroids XXII. Liquid chromatography-tandem mass spectrometric method for profiling rat brain 3-oxo-4-ene-neuroactive steroids

A sensitive liquid chromatography-electrospray ionization-tandem mass spectrometric (LC-ESI-MS/MS) method for the simultaneous determination of five 3-oxo-4-ene-neuroactive steroids, i.e. androstenedione, testosterone (T), progesterone (PROG), 20alpha-dihydroprogesterone and 20beta-dihydroprogesterone, in rat brain has been developed and validated. The brain steroids were extracted with methanol-acetic acid, purified using solid-phase extraction cartridges and subjected to LC-ESI-MS/MS. The method does not require derivatization. Deuterium-labeled T and PROG were used as the internal standards, and quantification was based on the selected reaction monitoring mode. This method allowed the reproducible and accurate quantification of the brain neuroactive steroids using 100 mg of tissue; the intra- and inter-assay relative standard deviations were below 4.7 and 4.3%, respectively, and the accuracy values were 97.6-103.2% for all the steroids. The limits of quantitation were 0.1 ng/g tissue for all the steroids. The application of this developed method for the analysis of changes in the brain neuroactive steroid levels by immobilization stress is also presented.     

Characterization of in vivo metabolites of toad venom using liquid chromatography-mass spectrometry

The structures of in vivo metabolites of marinobufotoxin (marinobufagin 3-suberoylarginine ester), marinobufagin, or bufalin which are typical components of toad venom widely used as the traditional Chinese drug, Ch'an Su, are confirmed using authentic samples based on their liquid chromatography-mass spectrometric behavior. A rat is orally administered 2 mg of the previously mentioned components of toad venom, the serum is collected 30 min after the administration, extracted, and then characterized. Marinobufotoxin is hydrolyzed and further epimerized into 3-epimarinobufagin, but marinobufagin 3-hemisuberate is not detected. After the administration of marinobufagin, 3-epimarinobufagin is detected in both the male and female rats, but marinobufagin 3-sulfate is formed only in the female rats. Bufalin is metabolized to 3-epibufalin, which is found to undergo further conjugation resulting in its 3-glucuronide. Furthermore, 3-epibufalin 3-sulfate is formed only in the female rats.     

In situ Observation of Evolving H2 and Solid Electrolyte Interphase Development at Potassium Insertion Materials within Highly Concentrated Aqueous Electrolytes

The solid-electrolyte interphase (SEI) is key to stable, high voltage lithium-ion batteries (LIBs) as a protective barrier that prevents electrolyte decomposition. The SEI is thought to play a similar role in highly concentrated water-in-salt electrolytes (WISEs) for emerging aqueous batteries, but its properties remain unknown. In this work, we utilized advanced scanning electrochemical microscopy (SECM) and operando electrochemical mass spectrometry (OEMS) techniques to gain deeper insight into the SEI that occurs within highly concentrated WISEs. As a model, we focus on a 55 mol/kg K(FSA)_0.6(OTf)_0.4 electrolyte and a 3,4,9,10-perylenetetracarboxylic diimide negative electrode. For the first time, our work showed distinctly passivating structures with slow apparent electron transfer rates alike to the SEI found in LIBs. In situ analyses indicated stable passivating structures when PTCDI was stepped to low potentials (≈−1.3 V vs. Ag/AgCl). However, the observed SEI was discontinuous at the surface and H₂ evolution occurred as the electrode reached more extreme potentials. OEMS measurements further confirmed a shift in the evolution of detectable H₂ from −0.9 V to <−1.4 V vs. Ag/AgCl when changing from dilute to concentrated electrolytes. In all, our work shows a combined approach of traditional battery measurements with in situ analyses for improving characterization of other unknown SEI structures.     

Liposome modified with Mn-porphyrin complex can simultaneously induce antioxidative enzyme-like activity of both superoxide dismutase and peroxidase

An antioxidative liposome catalysis that mimics both superoxide dismutase (SOD) and peroxidase (POD) activities has been developed by using the liposomes modified with lipophilic Mn-(5,10,15,20-tetrakis[1-hexadecylpyridium-4-yl]-21H,23H-porphyrin) (Mn-HPyP). The SOD- and POD-like activities of the Mn-HPyP-modified liposome were first investigated by varying the type of phospholipid, such as 1,2-distearyl-sn-glycero-3-phosphocholine (DSPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC). Higher SOD-like activity was obtained in the case of DLPC and DMPC liposomes, in which the ligands were well-dispersed on the membrane in the liquid crystalline phase. The POD-like activity was maximal in the case of DMPC liposome, in which the Mn-HPyP complex was appropriately clustered on the membrane in the gel phase. On the basis of the above results, the co-induction of the SOD and POD activities to eliminate the superoxide and also hydrogen peroxide as a one-pot reaction was finally performed by using the Mn-HPyP-modified DMPC liposome, resulting in an increase in the efficiency of the elimination of both superoxide and hydrogen peroxide.     

Preparation of nano-sized Pt metal particles by photo-assisted deposition (PAD) on transparent Ti-containing mesoporous silica thin film

We have investigated a novel technique for the preparation of nano-sized Pt metals on Ti-containing mesoporous silica (TMS) thin film by photo-assisted deposition (PAD). The transparent TMS thin film was prepared on a quartz plate through sol—gel/spin coating. XRD, UV-Vis and Ti K-edge XAFS measurements revealed the formation of isolated Ti oxide species with a tetrahedral-coordination geometry in the silica framework. Deposition of Pt metal precursor on TMS thin film under UV-light irradiation, followed by reduction with molecular hydrogen, afforded a transparent thin film (Pt/TMS). The formation of highly dispersed nano-sized Pt metals having narrow size distributions was determined by Pd L_III-edge XANES and TEM analysis. The TMS and Pt/TMS thin films have been demonstrated to exhibit a strong hydrophilic property, even before UV irradiation, compared to the common mesoporous silica and TiO₂ thin films. After UV-light irradiation, the contact angle of water droplet on the TMS and Pt/TMS thin films became extremely lower, indicating the appearance of the photo-induced super-hydrophilic property.     

Palladium-catalyzed dehydrogenative cis double phosphorylation of alkynes with H-phosphonate leading to (Z)-bisphosphoryl-1-alkenes

Dehydrogenative cis double phosphorylation of terminal alkynes with H-phosphonate took place efficiently in the presence of a divalent palladium catalyst to afford (Z)-bisphosphoryl-1-alkenes selectively.