Design of a tripartite network for the prediction of drug targets

Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred. The tripartite network was found to have a stable structure and simulated network growth was accompanied by a steady increase in assortativity, reflecting increasing correlation between degrees of connected nodes leading to even network connectivity. Local drug environments in the tripartite network typically contained neighbor targets and revealed interesting drug-compound-target relationships for further analysis. Candidate targets were prioritized. The tripartite network design extends standard drug-target networks and provides additional opportunities for drug target prediction.     

Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Skeletal Transformation Triggered by C−F Bond Activation after Photochemical Rearrangement of Fluorinated [7]Helicenes

Tri- and tetra-fluorinated [7]helicenes are photolabile and undergo a double fluorine atom transfer. Herein, we show that the transferred product further undergoes a skeletal transformation on silica gel. The transformation begins with activation of the allylic C−F bond on the silanol surface. Then, the resulting carbocation readily undergoes a regioselective nucleophilic aromatic substitution with water, depending on the position of the fluorine substituents. Hexafluoro-2-propanol also activated the allylic C−F bond and acted as a nucleophile. These findings support the generation of a highly reactive cationic electrophilic intermediate in the successive transformations involving fluorine atoms.     

Detailed Analysis of the Crystal Structures and Magnetic Properties of a Dysprosium(III) Phthalocyaninato Sextuple-Decker Complex: Weak f–f Interactions Suppress Magnetic Relaxation

In the research field of single-molecule magnets (SMMs), lanthanoid–lanthanoid interactions, so-called f–f interactions, are known to affect the SMM properties, although their magnitudes are small. In this article, an SMM with very weak f–f interactions is reported, and the effects of the interactions on the SMM properties are discussed. X-ray structural analysis of the Dy^III-Cd^II-phthalocyaninato sextuple-decker complex (Dy₂Cd₃) reveals that the intramolecular Dy−Dy length in Dy₂Cd₃ is more than 13 Å, which is longer than the intermolecular Dy−Dy length. Even though the two Dy^III ions are far apart, intermolecular ferromagnetic dipole–dipole interactions are observed in Dy₂Cd₃. From detailed analysis of ac magnetic susceptibilities, quantum tunneling of the magnetization (QTM) in Dy₂Cd₃ is partially suppressed owing to the existence of very weak Dy−Dy interactions. Our results show that even very weak Dy−Dy interactions act as a dipolar bias, suppressing QTM.     

Controlled Reduction of Carboxamides to Alcohols or Amines by Zinc Hydrides

New protocols for controlled reduction of carboxamides to either alcohols or amines were established using a combination of sodium hydride (NaH) and zinc halides (ZnX₂). Use of a different halide on ZnX₂ dictates the selectivity, wherein the NaH‐ZnI₂ system delivers alcohols and NaH‐ZnCl₂ gives amines. Extensive mechanistic studies by experimental and theoretical approaches imply that polymeric zinc hydride (ZnH₂)_∞ is responsible for alcohol formation, whereas dimeric zinc chloride hydride (H?Zn?Cl)₂ is the key species for the production of amines.     

Radical polymerization of trifluoromethyl‐substituted methyl methacrylates and their application for use in pressure‐sensitive paint

Three CF₃‐substituted methyl methacrylates (MMAs), 2,2,2‐trifluoroethyl methacrylate (TFEMA), 1,1,1,3,3,3‐hexafluoroisopropyl methacrylate (HFIPMA) and nonafluoro‐tert‐butyl methacrylate (NFTBMA), were polymerized by conventional radical polymerization to give oxygen‐permeable polymers for application in pressure‐sensitive paint (PSP). The radical copolymerizations of styrene with TFEMA, HFIPMA, or NFTBMA were carried out to examine the effect of CF₃ groups on the polymerizability. The e values increased in the order of MMA (0.40) < TFEMA (0.76) < HFIPMA (1.19) < NFTBMA (1.31). The homopolymers of TFEMA, HFIPMA and NFTBMA (PTFEMA, PHFIPMA, and PNFTBM, respectively) were examined as polymers for use in PSP using 5,10,15,20‐tetrakis(pentafluorophenyl)porphinato platinum(II) (PtTFPP). The PSP consisting of PNFTBMA and PtTFPP exerted very high pressure sensitivity and very low temperature sensitivity. In the absence of oxygen, the temperature sensitivity decreased in the order of PTFEMA > PHFIPMA > PNFTBMA = PMMA, which corresponds to the order of glass transition temperatures (T_g). However, the activation energies of the overall process of the luminescence quenching by oxygen were found to be 16.8 (PMMA), 13.0 (PTFEMA), 6.8 (PHFIPMA), and 4.3 kJ mol^?1 (PNFTBMA). Therefore, the low temperature sensitivity of PNFTBMA was attributed to its high degree of substitution with CF₃ groups and to its relatively high T_g value. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 963–972     

Polymerization-induced self-assembly of amino-acid-based nano-objects by reversible addition–fragmentation chain-transfer dispersion polymerization

A series of amino-acid-based amphiphilic diblock copolymer nano-objects having different morphologies were developed by reversible addition–fragmentation chain-transfer (RAFT) dispersion polymerization of styrene (St) in methanol. This was mediated by six different hydrophilic poly(N-acryloyl amino acid) macro-chain transfer agents (CTAs), including three carboxylic-acid-containing ones, poly(N-acryloyl-l -proline) (PAProOH), poly(N-acryloyl-4-trans-hydroxy-l -proline) (PAHypOH), and poly(N-acryloyl-l -threonine) (PAThrOH) prepared by RAFT polymerization, and their methyl ester forms, PAProOMe, PAHypOMe, and PAThrOMe. The effects of polymerization conditions on RAFT dispersion polymerization of St using a dithiocarbamate-terminated PAProOH was investigated. A systematic study of the effects of monomer conversion and concentration afforded the formation of various morphologies (i.e., spheres, worms, and vesicles). The effects of hydrogen-bonding and ionic interactions of the macro-CTAs on the assembled structures of the nano-objects were evaluated using six different macro-CTAs. Transforming the products from methanol to water via dialysis produced amino-acid-based block copolymer nano-objects, exhibiting pH-responsive morphological change, in aqueous solution.