Oxygen permeability of regenerated cellulose films with different water regains.

The effect of water regain on the oxygen permeability coefficient (OP) of regenerated cellulose film was investigated. The OP of the dry film was extremely low, which was classified as a "very high" performance gas barrier; however, the OP increased with increasing water regain, and reached to the OP similar to that of low-density polyethylene film, which was categorized as a "poor" gas barrier. The film thickness increased with increasing water regain, and edge-view small-angle X-ray scattering revealed widening of the space between microcrystals in the thickness direction. Oxygen molecules likely passed through the space between cellulose molecules, which was widened with increasing water regain. The viscoelastic measurements indicated that regenerated cellulose existed in a rubbery state under wet conditions. Overall, the OP of regenerated cellulose was increased because of the widening and micro-Brownian motion of cellulose main chains caused by water.

Geometrically programmed self-limited assembly of tubules using DNA origami colloids.

Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.

Tiling a tubule: how increasing complexity improves the yield of self-limited assembly.

The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of systems with self-limited length scales is that thermal fluctuations can lead to the assembly of nearby, off-target states. We investigate strategies for limiting off-target assembly by using multiple types of subunits. Using simulations and energetics calculations, we explore this concept by considering the assembly of tubules built from triangular subunits that bind edge to edge. While in principle, a single type of triangle can assemble into tubules with a monodisperse width distribution, in practice, the finite bending rigidity of the binding sites leads to the formation of off-target structures. To increase the assembly specificity, we introduce tiling rules for assembling tubules from multiple species of triangles. We show that the selectivity of the target structure can be dramatically improved by using multiple species of subunits, and provide a prescription for choosing the minimum number of subunit species required for near-perfect yield. Our approach of increasing the system's complexity to reduce the accessibility of neighboring structures should be generalizable to other systems beyond the self-assembly of tubules.

Effects of N-Substituents on the Functional Activities of Naltrindole Derivatives for the δ Opioid Receptor: Synthesis and Evaluation of Sulfonamide Derivatives.

We have recently reported that N-alkyl and N-acyl naltrindole (NTI) derivatives showed activities for the δ opioid receptor (DOR) ranging widely from full inverse agonists to full agonists. We newly designed sulfonamide-type NTI derivatives in order to investigate the effects of the N-substituent on the functional activities because the side chain and S=O part in the sulfonamide moiety located in spatially different positions compared with those in the alkylamine and amide moieties. Among the tested compounds, cyclopropylsulfonamide 9f (SYK-839) was the most potent full inverse agonist for the DOR, whereas phenethylsulfonamide 9e (SYK-901) showed full DOR agonist activity with moderate potency. These NTI derivatives are expected to be useful compounds for investigation of the molecular mechanism inducing these functional activities.

A molecular interaction field describing nonconventional intermolecular interactions and its application to protein-ligand interaction prediction.

Nonconventional noncovalent interactions such as CH/O, CH/π, and halogen bonds play important roles in molecular recognition in biological systems and have been increasingly exploited in structure-based drug design. In silico approaches that consider these interactions would be an effective strategy for drug discovery. The computation of the molecular interaction field (MIF), which is a three-dimensional (3D) potential map describing the interactions formed around a target compound, would assist the design of molecules that bind to the target biomolecule via nonconventional interactions. In this study, we developed a novel MIF calculation method that describes nonconventional interactions. This method evaluates the MIF as the interaction energy between the target ligand molecule and probe molecule. To describe the nonconventional interactions, our method employs quantum chemical calculations with four types of probe molecules. The calculated MIFs for casein kinase 2 (CK2) inhibitors correctly identify the halogen bond, CH/π, and CH/O interactions formed in the CK2/inhibitor complexes. Additionally, we have developed a method for calculating the protein-ligand interaction energy (Eint) based on the MIF and a coarse-grained protein model. The calculated interaction energies for CK2 inhibitors correlate with the experimental log(Ki) values. Thus, MIF and Eint obtained by our method show promise as descriptors for protein-ligand interaction prediction by considering nonconventional noncovalent interactions.

Synthesis of a novel and potent small-molecule antagonist of PAC1 receptor for the treatment of neuropathic pain.

We recently identified novel small-molecule antagonists of the PACAP type I (PAC1) receptor using docking-based in silico screening followed by in vitro/vivo pharmacological assays. In the present study, we synthesized 18 novel derivatives based on the structure of PA-9, a recently developed antagonist of the PAC1 receptor, with a view to obtain a panel of compounds with more potent antagonistic and analgesic activities. Among them, compound 3d showed improved antagonistic activities. Intrathecal injection of 3d inhibited both pituitary adenylate cyclase-activating polypeptide (PACAP) and spinal nerve ligation-induced mechanical allodynia. The effects were more potent than PA-9. Compound 3d also showed anti-allodynic effects following oral administration. Hence, our results suggest that 3d may become an orally available analgesic in the treatment of the neuropathic pain.

Formal Syntheses of (-)-Lepadiformines A, C, and (-)-Fasicularin.

Marine tricyclic alkaloids lepadiformine and fasicularin, with a unique perhydropyrrolo[2,1- j]quinoline or perhydropyrido[2,1- j]quinoline framework, were synthesized starting from the B ring of the tricyclic system. This approach includes a highly stereocontrolled diallylation of a cyclic enaminoester and subsequent ring-closing metathesis to construct the A/B ring system, which was transformed into key lactams 32 and 33, and amino alcohol 37. Thus, we achieved formal syntheses of (-)-lepadiformines A, C, and (-)-fasicularin in a divergent manner.

Essential structure of orexin 1 receptor antagonist YNT-707, part III: Role of the 14-hydroxy and the 3-methoxy groups in antagonistic activity toward the orexin 1 receptor in YNT-707 derivatives lacking the 4,5-epoxy ring.

Morphinan derivatives lacking the 4,5-epoxy ring were synthesized to examine the participation of the 14-OH group, the 3-OMe group, and the aromaticity of the A-ring in the activity and selectivity for the orexin 1 receptor (OX1R). The assay results and the conformational analyses of the 14-dehydrated and 14-H derivatives suggested that the orientations of the 6-amide side chain and the 17-benzenesulfonyl group would play important roles in the activity for OX1R. In the 6ß-derivatives, removal of the 3-OMe group and the reduction of the A-ring significantly decreased the activity toward the OX1R, but these changes did not affect the 6α-derivatives. These results indicate that the 3-OMe group and the A-ring would be essential structural moieties for the 6ß-derivatives.

DFT study of the influence of acetyl groups of cellulose acetate on its intrinsic birefringence and wavelength dependence.

The effect of the acetyl groups of cellulose acetate (CA) on its intrinsic birefringence and its wavelength dependence was investigated using density functional theory (DFT). Seven types of CA repeating-unit models that differ in their degree of substitution (DS) and substitution sites were used in the calculations. The results suggested that the intrinsic birefringence (Δn°) and its wavelength dependence significantly depended on the conformations of the acetyl group at C6. Additionally, the intrinsic birefringence of CA films was estimated as the ensemble average of the calculated Δn° values of the conformers. The increase in the DS of CA led to a more negative intrinsic birefringence and a larger wavelength dependence. The computational results were in good qualitative agreement with the experimental results and suggested that conformational variety and/or its control would be important factors for the design of optical films containing CA.

In Silico Screening Identified Novel Small-molecule Antagonists of PAC1 Receptor.

Pituitary adenylate cyclase-activating polypeptide (PACAP) and its receptors are present in the spinal dorsal horn and dorsal root ganglia, suggesting an important role of PACAP signaling systems in the modulation of spinal nociceptive transmission. Previously, we found that intrathecal injection of PACAP or maxadilan, a selective PACAP type I (PAC1) receptor agonist, induced transient aversive responses followed by a long-lasting mechanical allodynia in mice, suggesting that PACAP-PAC1 receptor systems are involved in chronic pain and that selective PAC1 antagonists may become a new class of analgesics. Although several PAC1 antagonists, such as PACAP 6-38, have been reported, all of them are peptide compounds. In the present study, we identified new small-molecule antagonists of the PAC1 receptor using in silico screening and in vitro/vivo pharmacological assays. The identified small-molecule compounds, named PA-8 and PA-9, dose dependently inhibited the phosphorylation of CREB induced by PACAP in PAC1-, but not VPAC1- or VPAC2-receptor-expressing CHO cells. PA-8 and PA-9 also dose dependently inhibited PACAP-induced cAMP elevation with an IC50 of 2.0 and 5.6 nM, respectively. In vivo pharmacological assays showed that intrathecal injection of these compounds blocked the induction of PACAP-induced aversive responses and mechanical allodynia in mice. In contrast, the compounds when administered alone exerted neither agonistic nor algesic actions in the in vitro/vivo assays. The compounds identified in the present study are new and the first small-molecule antagonists of the PAC1 receptor; they may become seed compounds for developing novel analgesics.

Essential structure of orexin 1 receptor antagonist YNT-707, Part II: Drastic effect of the 14-hydroxy group on the orexin 1 receptor antagonistic activity.

The 14-dehydration- and 14-H derivatives of the orexin 1 receptor (OX1R) antagonist YNT-707 (2) were synthesized. The obtained derivatives showed higher affinities for OX1R than the corresponding 14-hydroxy derivatives. The conformational analysis suggested that the 17-sulfonamide groups in the derivatives without the 14-hydroxy group have a greater tendency to be oriented toward the upper side of the D-ring compared with the 14-hydroxy derivatives. Additionally, the 14-dehydration-derivative with 6α-amide side chain showed significantly higher affinity than the 14-hydroxy derivative, while the corresponding 14-H derivative showed only slightly higher affinity. Thus, the 14-hydroxy group strongly affects the affinity of the antagonist for the OX1R.

Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase.

Most of the endogenous free d-serine (about 90%) in the brain is produced by serine racemase (SR). d-Serine in the brain is involved in neurodegenerative disorders and epileptic states as an endogenous co-agonist of the NMDA-type glutamate receptor. Thus, SR inhibitors are expected to be novel therapeutic candidates for the treatment of these disorders. In this study, we solved the crystal structure of wild-type SR, and tried to identify a new inhibitor of SR by in silico screening using the structural information. As a result, we identified two hit compounds by their in vitro evaluations using wild-type SR. Based on the structure of the more potent hit compound 1, we synthesized 15 derivatives and evaluated their inhibitory activities against wild-type SR. Among them, the compound 9C showed relatively high inhibitory potency for wild-type SR. Compound 9C was a more potent inhibitor than compound 24, which was synthesized by our group based upon the structural information of the mutant-type SR.

Evaluation of hydrogen bond networks in cellulose Iß and II crystals using density functional theory and Car-Parrinello molecular dynamics.

Crystal models of cellulose Iß and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iß allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).

In silico analyses of the effects of a point mutation and a pharmacological chaperone on the thermal fluctuation of phenylalanine hydroxylase.

Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism due to mutations in phenylalanine hydroxylase (PAH). Recently, small compounds, known as pharmacological chaperones (PhCs), have been identified that restore the enzymatic activity of mutant PAHs. Understanding the mechanism of the reduction in enzymatic activity due to a point mutation in PAH and its restoration by PhC binding is important for the design of more effective PhC drugs. Thermal fluctuations of an enzyme can alter its activity. Here, molecular dynamics simulation show the thermal fluctuation of PAH is increased by introduction of the A313T mutation. Moreover, a simulation using the A313T-PhC complex model was also performed. Thermal fluctuation of the mutant was found to be reduced upon PhC binding, which contributes to restoring its enzymatic activity.

Essential structure of orexin 1 receptor antagonist YNT-707, Part I: Role of the 4,5-epoxy ring for binding with orexin 1 receptor.

The essential structure of the orexin 1 receptor (OX1R) antagonist YNT-707 (2) was clarified, particularly the roles to OX1R antagonist activities of the 3-OMe, the 4,5-epoxy ring, the 14-hydroxy group, and the orientation of the 6-amide side chain. The 3-OMe and 17-sulfonamide group were shown to be essential for the OX1R antagonistic activity. The 4,5-epoxy ring plays an important role for the active orientation of the 6-amide group. The 14-hydroxy group could lower the activity of the 6ß-amide isomer by the interaction of the 14-hydroxy group with the 6-amide group, which could orient the 6-amide group toward the upper side of the C-ring. Finally, we proposed the difference in the active conformation between OX1R and κ opioid receptor (KOR), especially in the orientation of the 6-amide group which is expected to be a useful guide for medicinal chemists to design OX1R ligands.

Multi-step virtual screening to develop selective DYRK1A inhibitors.

Developing selective inhibitors for a particular kinase remains a major challenge in kinase-targeted drug discovery. Here we performed a multi-step virtual screening for dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) inhibitors by focusing on the selectivity for DYRK1A over cyclin-dependent kinase 5 (CDK5). To examine the key factors contributing to the selectivity, we constructed logistic regression models to discriminate between actives and inactives for DYRK1A and CDK5, respectively, using residue-based binding free energies. The residue-based parameters were calculated by molecular mechanics-generalized Born surface area (MM-GBSA) decomposition methods for kinase-ligand complexes modeled by computer ligand docking. Based on the findings from the logistic regression models, we built a three-dimensional (3D) pharmacophore model and chose filter criteria for the multi-step virtual screening. The virtual hit compounds obtained from the screening were assessed for their inhibitory activities against DYRK1A and CDK5 by in vitro assay. Our screening identified two novel selective DYRK1A inhibitors with IC50 values of several µM for DYRK1A and >100µM for CDK5, which can be further optimized to develop more potent selective DYRK1A inhibitors.

Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

Electric-field control of magnetic moment in Pd.

Several magnetic properties have recently become tunable with an applied electric field. Particularly, electrically controlled magnetic phase transitions and/or magnetic moments have attracted attention because they are the most fundamental parameters in ferromagnetic materials. In this study, we showed that an electric field can be used to control the magnetic moment in films made of Pd, usually a non-magnetic element. Pd ultra-thin films were deposited on ferromagnetic Pt/Co layers. In the Pd layer, a ferromagnetically ordered magnetic moment was induced by the ferromagnetic proximity effect. By applying an electric field to the ferromagnetic surface of this Pd layer, a clear change was observed in the magnetic moment, which was measured directly using a superconducting quantum interference device magnetometer. The results indicate that magnetic moments extrinsically induced in non-magnetic elements by the proximity effect, as well as an intrinsically induced magnetic moments in ferromagnetic elements, as reported previously, are electrically tunable. The results of this study suggest a new avenue for answering the fundamental question of "can an electric field make naturally non-magnetic materials ferromagnetic?".

Computational study to evaluate the birefringence of uniaxially oriented film of cellulose triacetate.

The intrinsic birefringence of a cellulose triacetate (CTA) film is evaluated using the polarizability of the monomer model of the CTA repeating unit, which is calculated using the density functional theory (DFT). Since the CTA monomer is known to have three rotational isomers, referred to as gg, gt, and tg, the intrinsic birefringence of these isomers is evaluated separately. The calculation indicates that the monomer CTA with gg and gt structures shows a negative intrinsic birefringence, whereas the monomer unit with a tg structure shows a positive intrinsic birefringence. By using these values, a model of the uniaxially elongated CTA film is constructed with a molecular dynamics simulation, and the orientation birefringence of the film model was evaluated. The result indicates that the film has negative orientation birefringence and that its value is in good agreement with experimental results.