Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design.

Computational molecular generation methods that generate chemical structures from gene expression profiles have been actively developed for de novo drug design. However, most omics-based methods involve complex models consisting of multiple neural networks, which require pretraining. In this study, we propose a straightforward molecular generation method called GxRNN (gene expression profile-based recurrent neural network), employing a single recurrent neural network (RNN) that necessitates no pretraining for omics-based drug design.

EMBER multidimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

In neurodegenerative diseases, proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations in situ. Here, we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid-binding dyes to identify six distinct different conformational strains in vitro, as well as amyloid-β (Aβ) deposits in different transgenic mouse models.

EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

Unlabelled: In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains , as well as Aβ deposits in different transgenic mouse models.

Simultaneous Inhibition of PGE2 and PGI2 Signals Is Necessary to Suppress Hyperalgesia in Rat Inflammatory Pain Models.

Prostaglandin E2 (PGE2) is well known as a mediator of inflammatory symptoms such as fever, arthritis, and inflammatory pain. In the present study, we evaluated the analgesic effect of our selective PGE2 synthesis inhibitor, compound I, 2-methyl-2-[cis-4-([1-(6-methyl-3-phenylquinolin-2-yl)piperidin-4-yl]carbonyl amino)cyclohexyl] propanoic acid, in rat yeast-induced acute and adjuvant-induced chronic inflammatory pain models. Although this compound suppressed the synthesis of PGE2 selectively, no analgesic effect was shown in both inflammatory pain models.

A Novel Selective Prostaglandin E2 Synthesis Inhibitor Relieves Pyrexia and Chronic Inflammation in Rats.

Prostaglandin E2 (PGE2) is a terminal prostaglandin in the cyclooxygenase (COX) pathway. Inhibition of PGE2 production may relieve inflammatory symptoms such as fever, arthritis, and inflammatory pain. We report here the profile of a novel selective PGE2 synthesis inhibitor, compound A [N-[(1S,3S)-3-carbamoylcyclohexyl]-1-(6-methyl-3-phenylquinolin-2-yl)piperidine-4-carboxamide], in animal models of pyrexia and inflammation.

A new method for production of chiral 2-aryl-2-fluoropropanoic acids using an effective kinetic resolution of racemic 2-aryl-2-fluoropropanoic acids.

We report a new method for the preparation of chiral 2-aryl-2-fluoropropanoic acids, including 2-fluoroibuprofen, a fluorinated analogue of non-steroidal anti-inflammatory drugs (NSAIDs), by the kinetic resolution of racemic 2-aryl-2-fluoropropanoic acids using enantioselective esterification. By applying pivalic anhydride (Piv2O) as a coupling agent, bis(α-naphthyl)methanol [(α-Np)2CHOH] as an achiral alcohol, and (+)-benzotetramisole (BTM) as a chiral acyl-transfer catalyst, a series of racemic 2-aryl-2-fluoropropanoic acids were kinetically separated to afford the optically active carboxylic acids and the corresponding esters with good to high enantiomeric excesses. This technology can provide a convenient approach to furnish the chiral α-fluorinated drugs containing quaternary carbons at the α-positions in the 2-aryl-2-fluoropropanoic acid structure.

Artificial metallo-DNA: structural control and discrete metal assembly.

To array Cu2+ ions within a double-stranded DNA along the helix axis in a controllable manner, a series of artificial oligonucleotides, d(5'-GHnC-3') (n = 1-5), were synthesized, where H is a hydroxypyridone nucleobase. Right-handed double helices of the oligonucleotides, nCu2+ x d(5'-GHnC-3')2 (n = 1-5), were quantitatively formed through Cu2+-mediated metallo-base pairing (H-Cu2+-H). The Cu2+ ions incorporated into each duplex were aligned along the helix axes with the Cu2+-Cu2+ distance of 3.

Role of a non-natural beta-C-nucleotide unit in DNA as a template for DNA and RNA syntheses and as a substrate for nucleolytic digestion.

A non-natural beta-C-nucleoside bearing a 3,4-dibenzyloxyphenyl group as a nucleobase (X) was synthesized and incorporated into a 34-mer oligomer with the sequence 5'-dTTTTTAAAAAAXATATAGCAGCGACATGTCACCG-3'. This synthetic oligonucleotide was examined for template activity in the enzymatic syntheses of DNA by the Klenow fragments of Escherichia coli DNA polymerase I and the recombinant DNA polymerase I, and in the synthesis of RNA by the E. coli RNA polymerase core enzyme.

A discrete self-assembled metal array in artificial DNA.

DNA has a structural basis to array functionalized building blocks. Here we report the synthesis of a series of artificial oligonucleotides, d(5'-GH(n)C-3') (n = 1 to 5), with hydroxypyridone nucleobases (H) as flat bidentate ligands. Right-handed double helices of the oligonucleotides, nCu2+.

Syntheses and structure-activity relationships of nonnatural beta-C-nucleoside 5'-triphosphates bearing an aromatic nucleobase with phenolic hydroxy groups: inhibitory activities against DNA polymerases.

Five nonnatural beta-C-nucleoside 5'-triphosphates bearing a 3,4-dihydroxyphenyl (1TP), a 2-hydroxyphenyl (2TP), a 3-hydroxyphenyl (3TP), a 4-hydroxyphenyl (4TP), or a phenyl (5TP) group were synthesized, and their structure-activity relationships were examined for a series of DNA polymerase reactions in vitro under typical polymerase chain reaction conditions. We found that the 5'-triphosphates (1TP-5TP) are not incorporated into DNA strands but inhibit the DNA polymerase reactions in the presence of natural nucleoside 5'-triphosphates (dNTPs). 1TP having two phenolic hydroxy groups at the nucleobase moiety showed the most potent inhibitory effect against DNA synthesis by Ex Taq polymerase (IC(50) = 30 microM).

Efficient incorporation of a copper hydroxypyridone base pair in DNA.

Recently, we reported the first artificial nucleoside for alternative DNA base pairing through metal complexation (J. Org. Chem.