A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Identification of metabolites in humans remains challenging. Here, we present synthesis-based reverse metabolomics as a strategy for structure elucidation that aims to also find phenotypic associations. In this approach, MS/MS spectra are acquired from newly synthesized compounds, and searched against public metabolomics data to uncover their phenotypic associations. To demonstrate the concept, we used combinatorial amide coupling reactions to synthesize an array of amino acid conjugated bile acids. A total of 16,587 spectral matches were found for 145 amidates synthesized, representing the single largest expansion of structures in the 170+ year history of bile acids. Furthermore, some new bile acids were associated with health-related phenotypes such as inflammatory bowel diseases and obesity. Using independent human cohorts for validation revealed that some cholic and chenodeoxycholic acid conjugates were elevated in Crohn’s disease, of which some were also potent PXR agonists. Bacteria belonging to bifidobacterium, clostridium, and enterococci genera were the main producers of these new conjugated bile acids. Because searching repositories with MS/MS spectra has only recently become possible, this synthesis-based reverse metabolomics approach can now be employed as a general strategy to elucidate structures and discover other new molecules from human and animal ecosystems.

Surface Modification of a Graphite Felt Cathode with Amide-Coupling Enhances the Electron Uptake of Rhodobacter sphaeroides

Microbial electrosynthesis (MES) is a promising technology platform for the production of chemicals and fuels from CO2 and external conducting materials (i.e., electrodes). In this system, electroactive microorganisms, called electrotrophs, serve as biocatalysts for cathodic reaction. While several CO2-fixing microorganisms can reduce CO2 to a variety of organic compounds by utilizing electricity as reducing energy, direct extracellular electron uptake is indispensable to achieve highly energy-efficient reaction. In the work reported here, Rhodobacter sphaeroides, a CO2-fixing chemoautotroph and a potential electroactive bacterium, was adopted to perform a cathodic CO2 reduction reaction via MES. To promote direct electron uptake, the graphite felt cathode was modified with a combination of chitosan and carbodiimide compound. Robust biofilm formation promoted by amide functionality between R. sphaeroides and a graphite felt cathode showed significantly higher faradaic efficiency (98.0%) for coulomb to biomass and succinic acid production than those of the bare (34%) and chitosan-modified graphite cathode (77.8%), respectively. The results suggest that cathode modification using a chitosan/carbodiimide composite may facilitate electron utilization by improving direct contact between an electrode and R. sphaeroides.

Racemization-free synthesis of Nα-2-thiophenoyl-phenylalanine-2-morpholinoanilide enantiomers and their antimycobacterial activity

Nα-2-thiophenoyl-d-phenylalanine-2-morpholinoanilide (MMV688845, IUPAC: N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide) from the Pathogen Box® library (Medicines for Malaria Ventures, MMV) is a promising lead compound for antimycobacterial drug development. Two straightforward synthetic routes to the title compound starting from phenylalanine or its Boc-protected derivative are reported. Employing Boc-phenylalanine as starting material and the T3P® and PyBOP® amide coupling reagents enables racemization-free synthesis, avoiding the need for subsequent separation of the enantiomers. The crystal structure of the racemic counterpart gives insight into the molecular structure and hydrogen bonding interactions in the solid state. The R-enantiomer of the title compound (derived from d-phenylalanine) exhibits activity against non-pathogenic and pathogenic mycobacterial strains, whereas the S-enantiomer is inactive. Neither of the enantiomers and the racemate of the title compound shows cytotoxicity against various mammalian cells.

Towards the synthesis of photobactin: methodology and metal binding aspects

Siderophores are metal-typically iron-chelating compounds that have received countless attention in research, as they can play a role in medicine intended for drug delivery and iron overload treatment. The synthesis of Photobactin has been of interest as it has been previously isolated (<10 mg) from Photorhabdus luminescence and has not once been synthesized. This thesis examined the preparation of Photobactin using a multi-step approach: synthesizing two building blocks individually and coupling them together with an amide coupling reagent. Both building blocks were synthesized successfully. However, the deprotection of the ester group on one of the building blocks has been uncooperative, and therefore the total synthesis of Photobactin was not achieved. Moreover, DFT computation calculations were performed to study Photobactin binding properties with Fe3+. According to the results, iron (Fe3+) is likely to form a hexadentate (6-coordinate ligand) or a tetradentate (4-coordinate ligand) complex with Photobactin. Each of the compounds leading to Photobactin was characterized using 1H and 13C-NMR. Some compounds were characterized using elemental analysis and performing 2D-NMR (COSY, HMBC, and HSQC) to make final assignments.

Towards the synthesis of photobactin: methodology and metal binding aspects

Siderophores are metal-typically iron-chelating compounds that have received countless attention in research, as they can play a role in medicine intended for drug delivery and iron overload treatment. The synthesis of Photobactin has been of interest as it has been previously isolated (<10 mg) from Photorhabdus luminescence and has not once been synthesized. This thesis examined the preparation of Photobactin using a multi-step approach: synthesizing two building blocks individually and coupling them together with an amide coupling reagent. Both building blocks were synthesized successfully. However, the deprotection of the ester group on one of the building blocks has been uncooperative, and therefore the total synthesis of Photobactin was not achieved. Moreover, DFT computation calculations were performed to study Photobactin binding properties with Fe3+. According to the results, iron (Fe3+) is likely to form a hexadentate (6-coordinate ligand) or a tetradentate (4-coordinate ligand) complex with Photobactin. Each of the compounds leading to Photobactin was characterized using 1H and 13C-NMR. Some compounds were characterized using elemental analysis and performing 2D-NMR (COSY, HMBC, and HSQC) to make final assignments.

Efficient and accessible silane-mediated direct amide coupling of carboxylic acids and amines

A highly practical method for the direct coupling of amines and unactivated carboxylic acids to form amides.

Terpyridine-Functionalized Calixarenes: Synthesis, Characterization and Anion Sensing Applications

Lanthanide complexes have been developed and are reported herein. These complexes were derived from a terpyridine-functionalized calix[4]arene ligand, chelated with Tb3+ and Eu3+. Synthesis of these complexes was achieved in two steps from a calix[4]arene derivative: (1) amide coupling of a calix[4]arene bearing carboxylic acid functionalities and (2) metallation with a lanthanide triflate salt. The ligand and its complexes were characterized by NMR (1H and 13C), fluorescence and UV-vis spectroscopy as well as MS. The photophysical properties of these complexes were studied; high molar absorptivity values, modest quantum yields and luminescence lifetimes on the ms timescale were obtained. Anion binding results in a change in the photophysical properties of the complexes. The anion sensing ability of the Tb(III) complex was evaluated via visual detection, UV-vis and fluorescence studies. The sensor was found to be responsive towards a variety of anions, and large binding constants were obtained for the coordination of anions to the sensor.

Rapid Mechanochemical Synthesis of Amides with Uronium-Based Coupling Reagents, a Method for Hexa-amidation of Biotin[6]uril

<p>Solid-state reactions using mechanochemical activation have emerged as solvent-free atom-efficient strategies for sustainable chemistry. Herein we report a new mechanochemical approach for the amide coupling of carboxylic acids and amines, mediated by combination of (1-сyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylaminomorpholinocarbenium hexafluorophosphate (COMU) or <i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylchloroformamidinium hexafluorophosphate (TCFH) and K₂HPO₄. The method delivers a range of amides in high 70–96% yields and fast reaction rates. The reaction protocol is mild, maintains the integrity of the adjacent to carbonyl stereocenters, and streamlines isolation procedure for solid amide products. Minimal waste is generated due to the absence of bulk solvent. We show that K₂HPO₄ plays a dual role, acting as a base and a precursor of reactive acyl phosphate species. Amide bonds from hindered carboxylic acids and low-nucleophilic amines can be assembled within 90 min by using TCFH in combination with K₂HPO₄ or <i>N</i>-methylimidazole. The developed mechanochemical liquid-assisted amidation protocols were successfully applied to the challenging couplings of all six carboxylate functions of biotin[6]uril macrocycle with phenylalanine methyl ester, resulting in an 80% yield of highly pure hexa-amide-biotin[6]uril. In addition, fast and high-yielding synthesis of peptides and versatile amide compounds can be performed in a safe and environmentally benign manner, as verified by green metrics.<b></b></p>