Scaffold-based molecular design with a graph generative model

Searching for new molecules in areas like drug discovery often starts from the core structures of known molecules. Such a method has called for a strategy of designing derivative compounds retaining a particular scaffold as a substructure. On this account, our present work proposes a graph generative model that targets its use in scaffold-based molecular design. Our model accepts a molecular scaffold as input and extends it by sequentially adding atoms and bonds. The generated molecules are then guaranteed to contain the scaffold with certainty, and their properties can be controlled by conditioning the generation process on desired properties. The learned rule of extending molecules can well generalize to arbitrary kinds of scaffolds, including those unseen during learning. In the conditional generation of molecules, our model can simultaneously control multiple chemical properties despite the search space constrained by fixing the substructure. As a demonstration, we applied our model to designing inhibitors of the epidermal growth factor receptor and show that our model can employ a simple semi-supervised extension to broaden its applicability to situations where only a small amount of data is available.

We propose a scaffold-based graph generative model for designing novel drug candidates that include the desired scaffold as a substructure.     

A polymer-based microfluidic device for immunosensing biochips

This paper describes the design, fabrication, and test of a PDMS/PMMA-laminated microfluidic device for an immunosensing biochip. A poly(dimethyl siloxane)(PDMS) top substrate molded by polymer casting and a poly(methyl methacrylate)(PMMA) bottom substrate fabricated by hot embossing are bonded with pressure and hermetically sealed. Two inlet ports and an air vent are opened through the PDMS top substrate, while gold electrodes for electrochemical biosensing are patterned onto the PMMA bottom substrate. The analyte sample is loaded from the sample inlet port to the detection chamber by capillary force, without any external intervening forces. For this and to control the time duration of sample fluid in each compartment of the device, including the inlet port, diffusion barrier, reaction chamber, flow-delay neck, and detection chamber, the fluid conduit has been designed with various geometries of channel width, depth, and shape. Especially, the fluid path has been designed so that the sample flow naturally stops after filling the detection chamber to allow sufficient time for biochemical reaction and subsequent washing steps. As model immunosensing tests for the microfluidic device, functionalizations of ferritin and biotin to the sensing surfaces on gold electrodes and their biospecific interactions with antiferritin antiserum and streptavidin have been investigated. An electrochemical detection method for immunosensing by biocatalyzed precipitation has been developed and applied for signal registration. With the biochip, the whole immunosensing processes could be completed within 30 min.     

A theoretical investigation of the gas-phase oxidation reaction of the saturated tert-butyl radical.

The radical-radical reaction mechanisms and dynamics of ground-state atomic oxygen [O(3P)] with the saturated tert-butyl radical (t-C4H9) are investigated using the density functional method and the complete basis set model. Two distinctive reaction pathways are predicted to be in competition: addition and abstraction. The barrierless addition of O(3P) to t-C4H9 leads to the formation of an energy-rich intermediate (OC4H9) on the lowest doublet potential energy surface, which undergoes subsequent direct elimination or isomerization-elimination leading to various products: C3H6O + CH3, iso-C4H8O + H, C3H7O + CH2, and iso-C4H8 + OH. The respective microscopic reaction processes examined with the aid of statistical calculations, predict that the major addition pathway is the formation of acetone (C3H6O) + CH3 through a low-barrier, single-step cleavage. For the direct, barrierless H-atom abstraction mechanism producing iso-C4H8 (isobutene) + OH, which was recently reported in gas-phase crossed-beam investigations, the reaction is described in terms of both an abstraction process (major) and a short-lived addition dynamic complex (minor).     

Resveratrol derivatives potently induce apoptosis in human promyelocytic leukemia cells

Resveratrol has been shown to possess antioxidant and anticancer activities, but little is known on the effect of resveratrol derivatives. Recently we have isolated resveratrol and its dimers and trimers from peony (Paeonia lactiflora) seeds, and reported their strong antioxidant and cytotoxic activity. In the present study, we have evaluated cellular effects of resveratrol derivatives; viniferin, gnetin H, and suffruticosol B on the proliferation and apoptosis in HL-60 cells in vitro. All resveratrol and its derivatives reduced viability of HL-60 cells in a dose-dependent manner with their IC(50) values of 20-90 microM. Ascending orders of IC(50) values were suffruticosol B, gnetin H, viniferin and resveratrol respectively. HL-60 cells treated with the four stilbenes exhibited the distinct morphological changes characteristics of cell apoptosis such as chromatin condensation, apoptotic bodies, and DNA fragmentations. A time-dependent histogram of the cellular DNA analyzed by flow cytometry revealed a rapid increase in subdiploid cells and a concomitant decrease in diploid cells exposed to 100 microM resveratrol for 0-24 h. Cells treated with 25 microM of resveratrol, viniferin, gnetin H, and suffruticosol B for 24 h resulted in increment of sub-G1 population by 51, 5, 11 and 59%, respectively. Treatment of cells with 0-20 microM resveratrol for 5 h produced a concentration-dependent decrease in cytochrome P450 (CYP) 1B1 mRNA levels. Suffruticosol B also suppressed CYP1B1 gene expression. These results demonstrated that resveratrol oligomers also strongly suppressed HL-60 cell proliferation, and induced DNA damage. In addition, CYP1B1 gene supression may suggest an involvement in the resveratrol-induced apoptosis in HL-60 cells.     

Comparison of Fatty Acid Contents and MMP-1 Inhibitory Effects of the Two Antarctic Fish,Notothenia rossii and Champsocephalus gunnari

Total fatty-acid (FA) contents of different organs (stomach, liver, brain, and skin) of two Antarctic fish, marbled rockcod (Notothenia rossii) and mackerel icefish (Champsocephalus gunnari), were examined using gas chromatography–mass spectrometry (GC–MS). N. rossii possessed higher contents of total omega-3, where eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), the most represented omega-3 FAs, were distributed throughout all parts of the fish. The highest level of EPA was observed in the skin and that of DHA was observed in the brain of N. rossii. C. gunnari showed organ peculiarity in that most of the omega-3 FAs were found in stomach and skin. Specifically, the highest levels of EPA and DHA were both observed in the stomach. Although N. rossii and C. gunnari both inhabit the Antarctic Southern Oceans, their characteristics in terms of the composition of fatty acids were shown to vary. The extracts were also evaluated for matrix metalloproteinase-1 (MMP-1)-inhibitory activities in UVB-induced human dermal fibroblasts, where extracts of the skin and liver of N. rossii showed the most significant inhibition upon MMP-1 production. These findings provide experimental evidence that the extracts of the Antarctic fish could be utilized as bioactive nutrients, particularly in the enhancement of skin health.     

New Cyclization Route to the Skeletons of Lennoxamine and Chilenine

A new cyclization route, triggered by epoxide opening, has been performed to provide the key intermediates for isoindolobenzapine alkaloids, lennoxamine and chilenine. The epoxide was prepared by the Stille reaction using vinyltributylstannane and the following dioxirane treatment. Cyclization under the treatment of BF₃ · OEt₂ provided an azepine moiety, and the oxidative cyclization toward the known precursor for the alkaloids has been achieved by reaction with a stoichiometric amount of Pd(OAc)₂. This formal synthesis suggests a new route to the alkaloids.     

Reaction Behaviors of S-, O-, and N-containing Aliphatic Molecules with a Propyl Moiety on Ge(100) Surface

The reaction pathways of 1-propanethiol, 1-propanol, and propylamine molecules, containing a propyl moiety, on a Ge(100) surface were investigated using high-resolution photoemission spectroscopy (HRPES) experiments and density functional theory (DFT) calculations. Upon analysis of the HRPES data, the adsorption of 1-propanethiol and 1-propanol was found to occur through a dissociation reaction, whereas that of propylamine took place via N dative bonding at room temperature. On the basis of our DFT results, adsorption geometries and transition states for each of these molecules on the Ge(100) surface were confirmed. Systematic studies of S-, O-, and N-containing molecules, composed of an identical propyl moiety, on the Ge(100) surface provide insight into the adsorption mechanism of aliphatic molecules containing alkyl chains on the Ge(100) surface.     

Electro‐optic switching with liquid crystal graphene

Graphene oxide (GO) particles in aqueous dispersions can form liquid crystal (LC) phases at extremely low concentrations due to the extremely high aspect ratio of the flakes and noticeably, they possess an extremely large Kerr coefficient attractive for low power consumption electro‐optic devices. Reduced graphene does not easily form LC phases in water due to its hydrophobic nature but here we show that stable dispersions of reduced graphene oxide can be realized with surfactants and that they exhibit birefringence upon shearing as well as under application of electric fields. The performance of the system is largely superior to GO LC possessing longer time stability and drastically improved electro‐optic properties with an induced birefringence twice as large at the same field strength thanks to the almost recovery of graphene properties upon reduction. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)