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.     

Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a “plug–plug” technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan‐X, β‐endorphin, and oxytocin, as candidates for calmodulin‐binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug–plug technique, the ACE–MS screening methodology successfully selected calmodulin‐binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with K_d values between 8–147 μM for calmodulin were obtained from a Glu‐C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE–MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.     

Thermoreversible sol-gel transition of an aqueous solution of polyrotaxane composed of highly methylated alpha-cyclodextrin and polyethylene glycol

Novel thermo-gelling aqueous solution systems are developed with a polyrotaxane, consisting of methylated alpha-cyclodextrin and polyethylene glycol, based on the slide-ring properties of the macrocycles along the linear chain.     

Charge‐Conversional Polyionic Complex Micelles—Efficient Nanocarriers for Protein Delivery into Cytoplasm

Special delivery! Polyionic complex (PIC) micelles that contain the charge‐conversional moieties citaconic amide or cis‐aconitic amide were developed for cytoplasmic protein delivery. The increase of the charge density on the protein cargo helped the stability of the PIC micelles without cross‐linking, and the charge‐conversion in endosomes induced the dissociation of the PIC micelles to result in efficient endosomal release (see picture).

     

Construction of Helically Stacked π‐Electron Systems in Poly(quinolylene‐2,3‐methylene) Stabilized by Intramolecular Hydrogen Bonds

π‐Stacked polymers, which consist of layered π‐electron systems in a polymer, can be expected to be used in molecular electronic devices. However, the construction of a stable π‐stacked structure in a polymer is considerably challenging because it requires sophisticated designs and precise synthetic methods. Herein, we present a novel π‐stacked architecture based on poly(quinolylene‐2,3‐methylene) bearing alanine derivatives as the side chain, obtained through the living cyclo‐copolymerization of an o‐allenylaryl isocyanide. In the resulting polymer, the neighboring quinoline rings of the main chain form a layered structure with π–π interactions, which is stabilized by intramolecular hydrogen bonds. The vicinal quinoline units form two independent helices and the whole molecule is a twisted‐tape structure. This structure is established on the basis of UV/CD spectra, theoretical calculations, and atomic‐force microscopy.     

Syntheses and biological activities of renin inhibitors containing statine analogues

Syntheses and biological activities of dipeptide renin inhibitors that contain statine analogues are described. The key steps of the synthetic approach to dipeptide renin inhibitors are the asymmetric synthesis of 2(R)-substituted-3-aminocarbonylpropionic acids and the diastereoselective syntheses of (3S,4S)-statine analogues. These inhibitors (2,14-40) inhibited human renin in the 3-140 nM range. Inhibitor ES 6864 (2) was found to be a highly potent inhibitor of human renin (IC50: 4.6 x 10(-9) M) and showed high enzyme specificity. Oral administration of ES 6864 at 3 mg/kg to conscious, sodium-depleted marmosets inhibited plasma renin activity (PRA) more than 80% after 1 h.     

Selective cross-catenation of Pd(II) and Pt(II) coordination rings

The reversible cross-catenation of two different coordination rings (Pd(II)- and Pt(II)-linked rings) has been achieved by using the labile nature of the Pd-N interaction and efficient hydrophobic contact between the rings.     

Effect of poly(butylene succinate) crystals on spherulitic growth of poly(ethylene oxide) in binary blends of the two substances

The effects of the lamellar growth direction, extinction rings, and spherulitic boundaries of poly(butylene succinate) (PBSU) on the spherulitic growth of poly(ethylene oxide) (PEO) were investigated in miscible blends of the two crystalline polymers. In the crystallization process from a homogeneous melt, PBSU first developed volume‐filling spherulites, and then PEO spherulites nucleated and grew inside the PBSU spherulites. The lamellar growth direction of PEO was identical with that of PBSU even when the PBSU content was about 5 wt %. PEO, which intrinsically does not exhibit banded spherulites, showed apparent extinction rings inside the banded spherulites of PBSU. The growth rate of a PEO spherulite, G_PEO, was influenced not only by the blend composition and the crystallization temperature of PEO, but also by the growth direction with respect to PBSU lamellae, the boundaries of PBSU spherulites, and the crystallization temperature of PBSU, T_PBSU. The value of G_PEO first increased with decreasing T_PBSU when a PEO spherulite grew inside a single PBSU spherulite. Then, G_PEO decreased when T_PBSU was further decreased and a PEO spherulite grew through many tiny PBSU spherulites. This behavior was discussed based on the aforementioned factors affecting G_PEO. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 539–547, 2009     

On mean flow generation due to oblique reflection of internal waves at a slope

Small‐amplitude expansions are utilized to discuss the mean flow induced by the reflection of a weakly nonlinear internal gravity wave beam at a uniform rigid slope, in the case where the beam planes of constant phase meet the slope at an arbitrary direction, not necessarily parallel to the isobaths, and the flow cannot be taken as two dimensional. Along the vertical, the Eulerian mean flow, due to such an oblique reflection, is equal and opposite to the Stokes drift so the Lagrangian mean flow vanishes, similar to a two‐dimensional reflection. The horizontal Eulerian mean flow, however, is controlled by the mean potential vorticity (PV) and the corresponding Lagrangian mean flow is generally nonzero, in contrast to two‐dimensional flow where PV identically vanishes. For an oblique reflection, furthermore, viscous dissipation can trigger generation of horizontal mean flow via irreversible production of mean PV, a phenomenon akin to streaming.