Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues

Conformationally restricted diastereomeric homoarabinofuranosylpyrimidines (AZT analogue), i.e., (5′R)-3′-azido-3′-deoxy-2′-O,5′-C-bridged-β-ᴅ-homoarabinofuranosylthymine and -uracil had been synthesized starting from diacetone ᴅ-glucofuranose following chemoenzymatic and chemical routes in 34–35% and 24–25% overall yields, respectively. The quantitative and diastereoselective acetylation of primary hydroxy over two secondary hydroxy groups present in the key nucleoside precursor was mediated with Lipozyme® TL IM in 2-methyltetrahydrofuran following a chemoenzymatic pathway. Whereas, the protection of the primary hydroxy over the lone secondary hydroxy group in the key azido sugar precursor was achieved using bulky tert-butyldiphenylsilyl chloride (TBDPS-Cl) in pyridine in 92% yield following a chemical synthetic pathway. The chemoenzymatic method was found to be superior over the chemical method in respect of the number of synthetic steps and overall yield of the final product.

Robust organic cages prepared using hydrazone condensation display sulfate/hydrogenphosphate selectivity in water

Two robust hexacationic cages incorporating either urea or isophthalamide motifs were synthesized via a short and high-yielding synthetic pathway using hydrazone condensation reactions in water for the cage forming step. Stability testing revealed that the cages are stable to a range of stimuli in water and in organic solvents. The urea containing cage can bind anions in pure water, and displays strong and selective binding of SO42– over HPO42–. The isophthalamide containing cage binds SO42– only weakly in 1:1 D2O:d6-DMSO but displays strong and cooperative binding of two HPO42– anions. Combined quantum mechanical/annealed molecular dynamics simulations suggest that the remarkable differences in anion selectivity are largely a result of the differing flexibilities of the two cages.

From Far West to East: Joining the Molecular Architecture of Imidazole-like Ligands in HO-1 Complexes

HO-1 overexpression has been reported in several cases/types of human malignancies. Unfortunately, poor clinical outcomes are reported in most of these cases, and the inhibition of HO-1 is considered a valuable and proven anticancer approach. To identify novel hit compounds suitable as HO-1 inhibitors, we report here a fragment-based approach where ligand joining experiments were used. The two most important parts of the classical structure of the HO-1 inhibitors were used as a starting point, and 1000 novel compounds were generated and then virtually evaluated by structure and ligand-based approaches. The joining experiments led us to a novel series of indole-based compounds. A synthetic pathway for eight selected molecules was designed, and the compounds were synthesized. The biological activity revealed that some molecules reach the micromolar activity, whereas molecule 4d inhibits the HO-1 with an IC50 of 1.03 μM. This study suggested that our joining approach was successful, and a novel hit compound was generated. These results are ongoing for further development.

Cobalt-Catalyzed Cyclization of 2-Bromobenzamides with Carbodiimides: A New Route for the Synthesis of 3-(Imino)isoindolin-1-ones

A novel synthetic pathway to approach 3-(imino)isoindolin-1-ones by the Co-catalyzed cyclization reaction of 2-bromobenzamides with carbodiimides has been developed. This catalytic reaction can tolerate a variety of substituents and provide corresponding products in moderate yields for most cases. According to the literature, the reaction mechanism is proposed through the formation of a five-membered aza-cobalacycle complex, which carries out the following reaction subsequence, including nucleophilic addition and substitution, to furnish the desired structures.

RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model

Background Despite proven therapeutic effects in inflammatory conditions, the specific mechanisms of phytochemical therapies are not well understood. The transcriptome effects of Traumeel (Tr14), a multicomponent natural product, and diclofenac, a non-selective cyclooxygenase (COX) inhibitor, were compared in a mouse cutaneous wound healing model to identify both known and novel pathways for the anti-inflammatory effect of plant-derived natural products. Methods Skin samples from abraded mice were analyzed by single-molecule, amplification-free RNAseq transcript profiling at 7 points between 12 and 192 h after injury. Immediately after injury, the wounds were treated with either diclofenac, Tr14, or placebo control (n = 7 per group/time). RNAseq levels were compared between treatment and control at each time point using a systems biology approach. Results At early time points (12–36 h), both control and Tr14-treated wounds showed marked increase in the inducible COX2 enzyme mRNA, while diclofenac-treated wounds did not. Tr14, in contrast, modulated lipoxygenase transcripts, especially ALOX12/15, and phospholipases involved in arachidonate metabolism. Notably, Tr14 modulated a group of cell-type specific markers, including the T cell receptor, that could be explained by an overarching effect on the type of cells that were recruited into the wound tissue. Conclusions Tr14 and diclofenac had very different effects on the COX/LOX synthetic pathway after cutaneous wounding. Tr14 allowed normal autoinduction of COX2 mRNA, but suppressed mRNA levels for key enzymes in the leukotriene synthetic pathway. Tr14 appeared to have a broad ‘phytocellular’ effect on the wound transcriptome by altering the balance of cell types present in the wound.

Analysis of Primary Metabolites of Morchella Fruit Bodies And Mycelium Based On Widely Targeted Metabolomics

Morchella is a kind of medicinal and edible homologous fungia that is rich in multiple metabolites. The metabolites from Morchella are a kind of essential substance because of their biological activities. In this study, Morchella fruit bodies and mycelium were selected to identify their metabolites. The primary metabolites of the two experimental group were analyzed using a method of widely targeted metabolome based on UPLC-ESI-MS/MS. A total of 354 different metabolites, including 188 upregulated metabolites and 166 downregulated metabolites, were characterized. Further, the main 20 metabolic pathways of the metabolites were analyzed. The first 9 ones are tyrosine metabolites, thyroid hormone biosynthetic pathway, phenylalanine metabolites, linoleic metabolites synthetic pathway, glycerophosphate metabolic pathway, choline in tumors, methyl butyl metabolites, arginine synthetic pathway, arginine, arginine and proline metabolites. This study provides theoretical basis for the analysis of metabolic pathway of Morchella fruit bodies and mycelium that serving for further research of their medicinal mechanism and effective components.

Optimization of Synthesis of the Amino Lipid ECO for Effective Delivery of Nucleic Acids

Nucleic acids are promising for a variety of therapies, such as cancer therapy and the gene therapy of genetic disorders. The therapeutic efficacy of nucleic acids is reliant on the ability of their efficient delivery to the cytosol of the target cells. Amino lipids have been developed to aid in the cytosolic delivery of nucleic acids. This work reports a new and efficient synthetic pathway for the lipid carrier, (1−aminoethyl) iminobis [N−(oleicylcysteinyl−1−amino−ethyl)propionamide] (ECO). The previous synthesis of the ECO was inefficient and presented poor product quality control. A solution−phase synthesis of the ECO was explored, and each intermediate product was characterized with better quality control. The ECO was synthesized with a relatively high yield and high purity. The formulations of the ECO nanoparticles were made with siRNA, miRNA, or plasmid DNA, and characterized. The transfection efficiency of the nanoparticles was evaluated in vitro over a range of N/P ratios. The nanoparticles were consistent in size with previous formulations and had primarily a positive zeta potential. The ECO/siLuc nanoparticles resulted in potent luciferase silencing with minimal cytotoxicity. The ECO/miR−200c nanoparticles mediated the efficient delivery of miR−200c into the target cells. The ECO/pCMV−GFP nanoparticles resulted in substantial GFP expression upon transfection. These results demonstrate that the solution−phase synthetic pathway produced pure ECO for the efficient intracellular delivery of nucleic acids without size limitation.

Resurrecting essential amino acid biosynthesis in a mammalian cell

Major genomic deletions in independent eukaryotic lineages have led to repeated ancestral loss of biosynthesis pathways for nine of the twenty canonical amino acids1. While the evolutionary forces driving these polyphyletic deletion events are not well understood, the consequence is that extant metazoans are unable to produce nine essential amino acids (EAAs). Previous studies have highlighted that EAA biosynthesis tends to be more energetically costly2,3, raising the possibility that these pathways were lost from organisms with access to abundant EAAs in the environment4,5. It is unclear whether present-day metazoans can reaccept these pathways to resurrect biosynthetic capabilities that were lost long ago or whether evolution has rendered EAA pathways incompatible with metazoan metabolism. Here, we report progress on a large-scale synthetic genomics effort to reestablish EAA biosynthetic functionality in a mammalian cell. We designed codon-optimized biosynthesis pathways based on genes mined from Escherichia coli. These pathways were de novo synthesized in 3 kilobase chunks, assembled in yeasto and genomically integrated into a Chinese Hamster Ovary (CHO) cell line. One synthetic pathway produced valine at a sufficient level for cell viability and proliferation, and thus represents a successful example of metazoan EAA biosynthesis restoration. This prototrophic CHO line grows in valine-free medium, and metabolomics using labeled precursors verified de novo biosynthesis of valine. RNA-seq profiling of the valine prototrophic CHO line showed that the synthetic pathway minimally disrupted the cellular transcriptome. Furthermore, valine prototrophic cells exhibited transcriptional signatures associated with rescue from nutritional starvation. This work demonstrates that mammalian metabolism is amenable to restoration of ancient core pathways, thus paving a path for genome-scale efforts to synthetically restore metabolic functions to the metazoan lineage.