Synthesis of C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation, especially biological effect on bone by modification at the C-2 position

In order to obtain vitamin D derivatives, which have strong activity for enhancing bone growth, we designed vitamin D derivatives with various substitutions at the C-2 position. Novel 2 α-substituted vitamin D derivatives were synthesized starting from d-glucose as a chiral template of the A-ring with a CD-ring bromoolefin unit using the Trost coupling method. We evaluated these compounds by two in vitro assays, affinity to VDR and transactivation assays, using human osteosarcoma (Hos) cells, and demonstrated the SAR of the C-2 position of VD(3). Furthermore, by using the OVX model, we found that compound 5c, which has a hydroxypropoxy side chain at C-2 and 2,2-dimethyl cyclopentanone in the CD-ring side chain, has a strong activity for enhancing bone growth, same as the reported compound, 2α-(3-hydroxypropoxy)-1α,25-dihydroxyvitamin D(3)1d, and this derivative shows a possibility that calcemic activity is less than 1d in vivo.     

Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes

We developed a new protocol for in silico drug screening for G-protein-coupled receptors (GPCRs) using a set of "universal active probes" (UAPs) with an ensemble docking procedure. UAPs are drug-like compounds, which are actual active compounds of a variety of known proteins. The current targets were nine human GPCRs whose three-dimensional (3D) structures are unknown, plus three GPCRs, namely β(2)-adrenergic receptor (ADRB2), A(2A) adenosine receptor (A(2A)), and dopamine D3 receptor (D(3)), whose 3D structures are known. Homology-based models of the GPCRs were constructed based on the crystal structures with careful sequence inspection. After subsequent molecular dynamics (MD) simulation taking into account the explicit lipid membrane molecules with periodic boundary conditions, we obtained multiple model structures of the GPCRs. For each target structure, docking-screening calculations were carried out via the ensemble docking procedure, using both true active compounds of the target proteins and the UAPs with the multiple target screening (MTS) method. Consequently, the multiple model structures showed various screening results with both poor and high hit ratios, the latter of which could be identified as promising for use in in silico screening to find candidate compounds to interact with the proteins. We found that the hit ratio of true active compounds showed a positive correlation to that of the UAPs. Thus, we could retrieve appropriate target structures from the GPCR models by applying the UAPs, even if no active compound is known for the GPCRs. Namely, the screening result that showed a high hit ratio for the UAPs could be used to identify actual hit compounds for the target GPCRs.     

Cooperative Catalysis of an Alcohol Dehydrogenase and Rhodium‐Modified Periodic Mesoporous Organosilica

The combined use of a metal‐complex catalyst and an enzyme is attractive, but typically results in mutual inactivation. A rhodium (Rh) complex immobilized in a bipyridine‐based periodic mesoporous organosilica (BPy‐PMO) shows high catalytic activity during transfer hydrogenation, even in the presence of bovine serum albumin (BSA), while a homogeneous Rh complex exhibits reduced activity due to direct interaction with BSA. The use of a smaller protein or an amino acid revealed a clear size‐sieving effect of the BPy‐PMO that protected the Rh catalyst from direct interactions. A combination of Rh‐immobilized BPy‐PMO and an enzyme (horse liver alcohol dehydrogenase; HLADH) promoted sequential reactions involving the transfer hydrogenation of NAD⁺ to give NADH followed by the asymmetric hydrogenation of 4‐phenyl‐2‐butanone with high enantioselectivity. The use of BPy‐PMO as a support for metal complexes could be applied to other systems consisting of a metal‐complex catalyst and an enzyme.     

A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations

The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) domain of mSin3. An NMR experiment revealed that the minimal binding unit of NRSF is a 15-residue segment that adopts a helical structure upon binding to a cleft of mSin3. We computed a free-energy landscape of this system by an enhanced conformational sampling method, all-atom multicanonical molecular dynamics. The simulation started from a configuration where the NRSF segment was fully disordered and distant from mSin3 in explicit solvent. In the absence of mSin3, the disordered NRSF segment thermally fluctuated between hairpins, helices, and bent structures. In the presence of mSin3, the segment bound to mSin3 by adopting the structures involved in the isolated state, and non-native and native complexes were formed. The free-energy landscape comprised three superclusters, and free-energy barriers separated the superclusters. The native complex was located at the center of the lowest free-energy cluster. When NRSF landed in the largest supercluster, the generated non-native complex moved on the landscape to fold into the native complex, by increasing the interfacial hydrophobic contacts and the helix content. When NRSF landed in other superclusters, the non-native complex overcame the free-energy barriers between the various segment orientations in the binding cleft of mSin3. Both population-shift and induced-fit (or induced-folding) mechanisms work cooperatively in the coupled folding and binding. The diverse structural adaptability of NRSF may be related to the hub properties of the IDP.     

Development of Divide‐and‐Conquer Density‐Functional Tight‐Binding Method for Theoretical Research on Li‐Ion Battery

The density‐functional tight‐binding (DFTB) method is one of the useful quantum chemical methods, which provides a good balance between accuracy and computational efficiency. In this account, we reviewed the basis of the DFTB method, the linear‐scaling divide‐and‐conquer (DC) technique, as well as the parameterization process. We also provide some refinement, modifications, and extension of the existing parameters that can be applicable for lithium‐ion battery systems. The diffusion constants of common electrolyte molecules and LiTFSA salt in solution have been estimated using DC‐DFTB molecular dynamics simulation with our new parameters. The resulting diffusion constants have good agreement to the experimental diffusion constants.     

Heterogeneous Catalysis for Water Oxidation by an Iridium Complex Immobilized on Bipyridine‐Periodic Mesoporous Organosilica

Heterogenization of metal‐complex catalysts for water oxidation without loss of their catalytic activity is important for the development of devices simulating photosynthesis. In this study, efficient heterogeneous iridium complexes for water oxidation were prepared using bipyridine‐bridged periodic mesoporous organosilica (BPy‐PMO) as a solid chelating ligand. The BPy‐PMO‐based iridium catalysts (Ir‐BPy‐PMO) were prepared by postsynthetic metalation of BPy‐PMO and characterized through physicochemical analyses. The Ir‐BPy‐PMOs showed high catalytic activity for water oxidation. The turnover frequency (TOF) values for Ir‐BPy‐PMOs were one order of magnitude higher than those of conventional heterogeneous iridium catalysts. The reusability and stability of Ir‐BPy‐PMO were also examined, and detailed characterization was conducted using powder X‐ray diffraction, nitrogen adsorption, ¹³C DD MAS NMR spectroscopy, TEM, and XAFS methods.     

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Preconcentration of indium with 1-phenyl-3-methyl-4-stearoyl-5-pyrazolone on silica gel

Indium was quantitatively retained at pH > 2.8, and could be removed by treatment with 1 M hydrochloric acid. The adsorption capacity of the material was 32 μmol In g^?1. Nickel, cobalt and zinc had no effect on the retention of indium.     

Phase-Drift-Suppression in Heterodyne Detection Using Coherent Light Source

The validity of the phase-drift-suppression method (PDSM) using coherent light sources of a single-mode laser diode (LD) or multimode Nd:YAG laser has been experimentally shown. PDSM can enhance the stability of an output signal in heterodyne detection using higher order harmonics. In the Michelson interferometer, the fundamental and second harmonics in heterodyne beat signals were detected by two lock-in amplifiers, and the computed signal intensity (CSI) was obtained in the computer as an output signal. Relations between the stability of CSI and modulation indexes in sinusoidal phase modulations were measured. The CSI stability was enhanced about twice by PDSM using a single-mode laser diode, and from 4 times to 9 times using a multimode laser.     

Nonclassical Abramov Products Formed on Orifices of Cage-Opened C60 Derivatives

By nucleophilic addition of phosphite P(OMe)₃ to a cage-opened C₆₀ derivative, α-hydrophosphate and enol phosphate were obtained as kinetic and thermodynamic products, respectively. Different from classical Abramov products bearing a phosphorus–carbon bond, these products have a phosphorus–oxygen bond. The observed anomaly originates from the fully conjugated π system, which significantly stabilizes zwitterionic intermediates bearing a phosphorus–oxygen bond. The thus formed enol phosphate was found to exhibit an intense absorption band that extended to 730 nm, reflecting the intramolecular charge-transfer transitions. We also report domino phosphorylation reactions, which gave a cage-opened C₆₀ derivative bearing a direct P−C bond.