Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples

Liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is currently the method of choice for untargeted metabolomic analysis. The availability of established protocols to achieve a high confidence identification of metabolites is crucial. The aim of this work is to describe the workflow that we have applied to build an Accurate Mass Retention Time (AMRT) database using a commercial metabolite library of standards. LC-HRMS analysis was carried out using a Vanquish Horizon UHPLC system coupled to a Q-Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Milan, Italy). The fragmentation spectra, obtained with 12 collision energies, were acquired for each metabolite, in both polarities, through flow injection analysis. Several chromatographic conditions were tested to obtain a protocol that yielded stable retention times. The adopted chromatographic protocol included a gradient separation using a reversed phase (Waters Acquity BEH C18) and a HILIC (Waters Acquity BEH Amide) column. An AMRT database of 518 compounds was obtained and tested on real plasma and urine samples analyzed in data-dependent acquisition mode. Our AMRT library allowed a level 1 identification, according to the Metabolomics Standards Initiative, of 132 and 124 metabolites in human pediatric plasma and urine samples, respectively. This library represents a starting point for future metabolomic studies in pediatric settings.     

Minimisation of palladium content in Suzuki cross-coupling reactions

A protocol for conducting Suzuki reactions in a plate format amenable to use in library synthesis of biaryl compounds has been developed. A key objective was to determine reaction conditions which give biaryl products containing <10 ppm of Pd for a wide variety of building blocks. A Design of Experiments (DoE) approach for the identification of an optimised set of reaction conditions was successfully applied. The utility of the protocol developed has been demonstrated by preparation of an array of 96 biaryl compounds in a parallel fashion.     

Synthesis of catechins via thiourea/AuCl(3)-catalyzed cycloalkylation of aryl epoxides

A diversity-oriented approach for the synthesis of structurally diverse catechins was achieved in good yields via thiourea/AuCl(3)/AgOTf-catalyzed annulations of aryl epoxides under mild conditions. This new protocol provides a highly efficient entry to a library of catechins-derived natural products, notably anti-HIV agent 8-C-ascorbyl-(-)-epigallocatechin.     

Novel Dual Use of Formamide-POCl3 Mixture for the Efficient,One-Pot Synthesis of Condensed 2H-Pyrimidin-4-amine Libraries Under Microwave Irradiation

The novel dual use of formamide-POCl₃ mixture for the incorporation of a C-N fragment to form the pyrimidine nucleus and its subsequent chlorination in an efficient, one-pot synthesis of potentially bioactive condensed 2H-pyrimidin-4-amine libraries under microwave irradiation (MWI) is reported. The one-pot microwave-assisted synthetic protocol is high-yielding, ecofriendly, rapid, and novel as well as eliminates intermittent workups. The protocol can be adapted for the library synthesis of series of a condensed pyrimidines.     

Palladium-catalyzed intramolecular C-H activation/C-C bond formation: a straightforward synthesis of phenanthridines

The palladium-catalyzed intramolecular C-H activation/C-C cross-coupling has been developed for a straightforward and efficient synthesis of phenanthridines. With Pd(OAc)(2) (4 mol %) as the catalyst, PCy(3) (8 mol %) as the ligand, and Cs(2)CO(3) as the base, this protocol was applied to synthesize a small library of phenanthridine derivatives in good yields in THF.     

A cross-metathesis route to the 5-F(2)-isoprostanes

A library of eight 5-F(2)-isoprostanes was prepared through a ring-opening metathesis/cross-metathesis protocol between functionalized bicyclo[3.2.0]heptenes, ethylene, and alpha,beta-unsaturated ketones. This sequence provided racemic enones in a regio- and stereoselective fashion that could be converted to enantiomerically enriched allylic alcohols through a catalyst-controlled asymmetric reduction. Completion of the sidechains, followed by global deprotection, resulted in a stereodivergent route to eight enantiomerically enriched 5-F(2)-isoprostanes. Overall, the synthesis of this library of known and anticipated lipid oxidation metabolites was achieved in 10 steps from commercially available 4-hydroxy-2-cyclopentenone.     

Parallel solution-phase synthesis of acrylonitrile scaffolds carrying L-alpha-amino acidic or D-glycosyl residues

A practical and straightforward protocol for the preparation of a solution-phase library of acrylonitrile scaffolds is reported. Target compounds were obtained in high yield, stereoselectivity, and purity by two simple and practical steps from cyanoacetic acid. Moreover, our study proposes a synthetic approach starting from the constructed library to obtain three-membered heterocycles.     

Rapid synthesis and zebrafish evaluation of a phenanthridine-based small molecule library

A Heck cyclisation approach is described for the rapid synthesis of a library of natural product-like small molecules, based on the phenanthridine core. The synthesis of a range of substituted benzylamine building blocks and their incorporation into the library is reported, together with a highly selective cis-dihydroxylation protocol that enables access to the target compounds in an efficient manner. Biological evaluation of the library using zebrafish phenotyping has led to the discovery of compound 20c, a novel inhibitor of early-stage zebrafish embryo development.     

A green,isocyanide-based three-component reaction approach for the synthesis of multisubstituted ureas and thioureas

A one-pot, isocyanide based multicomponent protocol was presented starting from secondary amines towards (thio)urea derivatives and utilized for the construction of a diverse 27-membered chemical library. Following a green compatible microwave assisted condition, the formed N,N′-multisubstituted (thio)ureas were obtained in up to 85% yield.     

Cascade reaction of isatins with heterocyclic ketene aminals: synthesis of imidazopyrroloquinoline derivatives

A concise and efficient route for the synthesis of highly substituted imidazopyrroloquinoline derivatives by simply refluxing a reaction mixture of different types of isatins and heterocyclic ketene aminals (HKAs) by acetic acid was developed. This method is suitable for combinatorial and parallel syntheses in drug discovery; consequently, a library of highly substituted imidazopyrroloquinoline derivatives was rapidly constructed using the present protocol.     

Achieving functional group diversity in parallel synthesis: solution-phase synthesis of a library of ureas, carbamates, thiocarbamates, and amides using carbamoylimidazolium salts

A convenient protocol for the parallel solution-phase synthesis of a library of thiocarbamates, ureas, carbamates, and amides from carbamoylimidazolium salts has been developed. The crystalline carbamoylimidazolium salts are readily synthesized from secondary amines, CDI and iodomethane, and act as stable carbamoylation reagents. A common set of reaction conditions and a straightforward non-chromatographic liquid-liquid extraction purification protocol were developed for reactions with thiols, amines, phenols, and carboxylic acids, giving the products with high purities and yields. The resultant library incorporates diversity arising from the choice of reaction partners and the functional group linkage generated in the couplings.     

Fully automated flow-through synthesis of secondary sulfonamides in a binary reactor system

A fully automated flow-through process for the production of secondary sulfonamides is presented. Primary sulfonamides were monoalkylated using a two-step "catch and release" protocol to generate library products of high purity. The automated flow synthesis platform incorporates four independent reactor columns and is able to perform automated column regeneration. A 48-member sulfonamide library was prepared as two 24-member sublibraries, affording library compounds in good yields and high purities without the need for further column chromatographic purification.     

A statistical-based approach to assessing the fidelity of combinatorial libraries encoded with electrophoric molecular tags. Development and application of tag decode-assisted single bead LC/MS analysis

A statistical sampling protocol is described to assess the fidelity of libraries encoded with molecular tags. The methodology, termed library QA, is based on the combined application of tag decode analysis and single bead LC/MS. The physical existence of library compounds eluted from beads is established by comparing the molecular weight predicted by tag decode with empirical measurement. The goal of sampling is to provide information on overall library fidelity and an indication of the performance of individual library synthons. The minimal sampling size n for library QA is l0 x the largest synthon set. Data are reported as proportion (p) +/- lower and upper boundary (lb-ub) computed at the 95% confidence level (alpha = 0.05). As a practical demonstration, library QA was performed on a 25,200-member library of statine amides (size = 40 x 63 x 10). Sampling was conducted three times at n approximately 630 beads per run for a total of 1902 beads. The overall proportions found for the three runs were consistent with one another: p = 84.4%, lb-ub = 81.5-87.2%; p = 83.1%, lb-ub = 80.2-85.95; and p = 84.5%, lb-ub = 81.8-87.3%, suggesting the true value of p is close to 84% compound confirmation. The performance pi of individual synthons was also computed. Corroboration of QA data with biological screening results obtained from assaying the library against cathepsin D and plasmepsin II is discussed.     

Syntheses of oxazabicycle library via one-pot tandem reactions

A practical protocol for the preparation of a parallel solution-phase library of oxazabicycle is reported. Target compounds were obtained in moderate to good yields by a Yb(OTf)3-catalyzed one-pot tandem reaction from various anisidines, aromatic aldehydes, isobutyraldehyde, and 4-hydroxycoumarins/dimedone. Purification of the final products by either recrystallization in ethyl acetate/methylene chloride or column chromatography allowed easy isolation of the 18 components of the array.     

Combining C-H functionalisation and flow photochemical heterocyclic metamorphosis (FP-HM) for the synthesis of benzo[1,3]oxazepines

C-H Activation/functionalisation and Flow Photochemical Heterocyclic Metamorphosis (FP-HM) have been combined to synthesize a library of benzo [1,3]oxazepines, a rarely described heterocyclic family. This combined protocol allows a range of arylated products to be made from simple starting materials, and the cheap flow photochemical system has proven effective for rapid synthesis of gram-quantities of benzo [1,3]oxazepines.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Comparison of negative ion electrospray mass spectra measured by seven tandem mass analyzers towards library formation

A library of negative ion electrospray ionization mass spectra and tandem mass spectra (MS/MS) of sulfonated dyes has been developed for fast identification purposes. The uniform protocol has been elaborated and applied to the measurements of more than 50 anionic dyes. Three collision energies are selected in our protocol which ensures that at least one of them provides a suitable ratio of product ions to the precursor ion. The robustness is investigated with altered values of tuning parameters (e.g. the pressure of the nebulizing gas, the temperature and the flow rate of drying gas, and the mobile phase composition). The results of the inter-laboratory comparison of product ion mass spectra recorded on seven different tandem mass spectrometers (three ion traps, two triple quadrupoles and two hybrid quadrupole time of flight instruments) are presented for four representative anionic dyes--azo dye Acid Red 118, anthraquinone dye Acid Violet 43, triphenylmethane dye Acid Blue 1 and Al(III) metal-complex azo dye. The fragmentation patterns are almost identical for all tandem mass analyzers, only the ratios of product ions differ somewhat which confirms the possibility of spectra transfer among different mass analyzers with the goal of library formation.     

Instant ligand libraries. Parallel synthesis of monodentate phosphoramidites and in situ screening in asymmetric hydrogenation

Chiral phosphoramidites have been identified as excellent ligands for various metal-catalyzed enantioselective transformations. Taking advantage of their easy preparation and modular nature, we designed a fully automated protocol for the parallel preparation of a library of 32 phosphoramidites and its screening in asymmetric hydrogenation of amino acid precursors. This initial study led to the discovery of a new ligand for the preparation of an enantiopure beta(3)-homoalanine precursor. [structure--see text]