Use of a large Stokes-shift fluorophore to increase the multiplexing capacity of a point-of-care DNA diagnostic device.

The intense demand for fluorescence-based point of care (POC) DNA diagnostics is driving developments to reduce the size of instrumentation, imposing limitations on the optical hardware that can be included. Here we describe a combination of instrumentation and fluorogenic probes to detect three fluorophores using two excitation and two detection channels.

Fuel Properties of Pongamia (Milletia pinnata) Seeds and Pods Grown in Hawaii.

Pongamia, a leguminous, oilseed-bearing tree, is a potential resource for renewable fuels in general and sustainable aviation fuel in particular. The present work characterizes physicochemical properties of reproductive materials (seeds and pods) from pongamia trees grown in different environments at five locations on the island of Oahu, Hawaii, USA. Proximate and ultimate analyses, heating value, and elemental composition of the seeds, pods, and de-oiled seed cake were determined. The oil content of the seeds and the properties of the oil were determined using American Society for Testing and Materials and American Oil Chemist's Society methods. The seed oil content ranged from 19 to 33 wt % across the trees and locations. Oleic (C18:1) was the fatty acid present in the greatest abundance (47 to 60 wt %), and unsaturated fatty acids accounted for 77 to 83 wt % of the oil. Pongamia oil was found to have similar characteristics as other plant seed oils (canola and jatropha) and would be expected to be well suited for hydroprocessed production of sustainable aviation fuel. Nitrogen-containing species is retained in the solid phase during oil extraction, and the de-oiled seed cake exhibited enrichment in the N content, ∼5 to 6%, in comparison with the parent seed. The pods would need further treatment before being used as fuel for combustion or gasification owing to the high potassium and chlorine contents.

Pyrolysis of waste polypropylene and characterisation of tar.

Waste polypropylene (PP) has been pyrolysed to obtain mainly a liquid tar product of high yield (83.5%) with the balance as gas (15.5%) and a little residue (1.0%). The elemental composition of the PP tar was: C: 87.1%, H: 12.6% and O+others: 0.4% (by difference). The tar samples have been characterised by gas chromatography/mass spectrometry, heated-probe mass spectrometry and laser -desorption mass spectrometry (LD- MS), to give molecular mass distributions for comparison with molecular mass ranges indicated by size-exclusion chromatography (SEC). About 50% of the tar was soluble in 1-methyl-2-pyrrolidinone, the solvent used for SEC. It appeared to consist mostly of low molecular mass materials with elution time at 20-27 min. Mass ranges from SEC and LD-MS agreed approximately in showing the upper mass limit of the tar to be about 1200 u, consisting of aromatics, alkenes, dialkenes and only minor quantities of alkanes.

Selective Phenylimidazole-Based Inhibitors of the Mycobacterium tuberculosis Proteasome.

Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.

IRAK-4 inhibitors. Part II: a structure-based assessment of imidazo[1,2-a]pyridine binding.

A potent IRAK-4 inhibitor was identified through routine project cross screening. The binding mode was inferred using a combination of in silico docking into an IRAK-4 homology model, surrogate crystal structure analysis and chemical analogue SAR.

IRAK-4 inhibitors. Part 1: a series of amides.

The synthesis and profile of a series of amides are described. Some of these compounds were potent IRAK-4 inhibitors and two examples were evaluated in vivo.

IRAK-4 inhibitors. Part III: a series of imidazo[1,2-a]pyridines.

Following the identification of a potent IRAK inhibitor through routine project cross screening, a novel class of IRAK-4 inhibitor was established. The SAR of imidazo[1,2-a]pyridino-pyridines and benzimidazolo-pyridines was explored.

Achieving multi-isoform PI3K inhibition in a series of substituted 3,4-dihydro-2H-benzo[1,4]oxazines.

The SAR and pharmacokinetic profiles of a series of multi-isoform PI3K inhibitors based on a 3,4-dihydro-2H-benzo[1,4]oxazine scaffold are disclosed.

Fast Pyrolysis of Tropical Biomass Species and Influence of Water Pretreatment on Product Distributions.

The fast pyrolysis behaviour of pretreated banagrass was examined at four temperatures (between 400 and 600 C) and four residence times (between ~1.2 and 12 s). The pretreatment used water washing/leaching to reduce the inorganic content of the banagrass. Yields of bio-oil, permanent gases and char were determined at each reaction condition and compared to previously published results from untreated banagrass. Comparing the bio-oil yields from the untreated and pretreated banagrass shows that the yields were greater from the pretreated banagrass by 4 to 11 wt% (absolute) at all reaction conditions. The effect of pretreatment (i.e. reducing the amount of ash, and alkali and alkali earth metals) on pyrolysis products is: 1) to increase the dry bio-oil yield, 2) to decrease the amount of undetected material, 3) to produce a slight increase in CO yield or no change, 4) to slightly decrease CO2 yield or no change, and 5) to produce a more stable bio-oil (less aging). Char yield and total gas yield were unaffected by feedstock pretreatment. Four other tropical biomass species were also pyrolyzed under one condition (450°C and 1.4 s residence time) for comparison to the banagrass results. The samples include two hardwoods: leucaena and eucalyptus, and two grasses: sugarcane bagasse and energy-cane. A sample of pretreated energy-cane was also pyrolyzed. Of the materials tested, the best feedstocks for fast pyrolysis were sugarcane bagasse, pretreated energy cane and eucalyptus based on the yields of 'dry bio-oil', CO and CO2. On the same basis, the least productive feedstocks are untreated banagrass followed by pretreated banagrass and leucaena.

Fast Pyrolysis Behavior of Banagrass as a Function of Temperature and Volatiles Residence Time in a Fluidized Bed Reactor.

A reactor was designed and commissioned to study the fast pyrolysis behavior of banagrass as a function of temperature and volatiles residence time. Four temperatures between 400 and 600°C were examined as well as four residence times between ~1.0 and 10 seconds. Pyrolysis product distributions of bio-oil, char and permanent gases were determined at each reaction condition. The elemental composition of the bio-oils and chars was also assessed. The greatest bio-oil yield was recorded when working at 450°C with a volatiles residence time of 1.4 s, ~37 wt% relative to the dry ash free feedstock (excluding pyrolysis water). The amounts of char (organic fraction) and permanent gases under these conditions are ~4 wt% and 8 wt% respectively. The bio-oil yield stated above is for 'dry' bio-oil after rotary evaporation to remove solvent, which results in volatiles and pyrolysis water being removed from the bio-oil. The material removed during drying accounts for the remainder of the pyrolysis products. The 'dry' bio-oil produced under these conditions contains ~56 wt% carbon which is ~40 wt% of the carbon present in the feedstock. The oxygen content of the 450°C, 1.4 s 'dry' bio-oil is ~38 wt%, which accounts for ~33 wt% of the oxygen in the feedstock. At higher temperature or longer residence time less bio-oil and char is recovered and more gas and light volatiles are produced. Increasing the temperature has a more significant effect on product yields and composition than increasing the volatiles residence time. At 600°C and a volatiles residence time of 1.2 seconds the bio-oil yield is ~21 wt% of the daf feedstock, with a carbon content of 64 wt% of the bio-oil. The bio-oil yield from banagrass is significantly lower than from woody biomass or grasses such as switchgrass or miscanthus, but is similar to barley straw. The reason for the low bio-oil yield from banagrass is thought to be related to its high ash content (8.5 wt% dry basis) and high concentration of alkali and alkali earth metals (totaling ~2.8 wt% relative to the dry feedstock) which are catalytic and increase cracking reactions during pyrolysis.

A solid-phase route to N-cyanoamides.

[reaction: see text] A new method for the solid-phase synthesis of cyanamides is described. The attachment of a secondary amine to solid support is accomplished using Merrifield resin. After functionalization, cleavage is readily achieved with cyanogen bromide to afford the desired cyanamide.

The background, discovery and clinical development of BCR-ABL inhibitors.

The story of the inhibition of BCR-ABL as a treatment for chronic myelogenous leukaemia serves to illustrate key aspects of the kinase drug discovery and development process. Firstly, elucidation of the disease mechanism enabled identification of the molecular target(s) which catalysed pharmaceutical research and resulted in Gleevec(®) (Novartis) as the first FDA approved BCR-ABL inhibitor. However, clinical success was soon tempered by the emergence of drug resistance through various mechanisms. Using rational drug design, several hypotheses were devised to overcome resistance issues leading to the development of second generation inhibitors, providing clinicians and patients with greater therapeutic choice.

Integrated Synthesis and Testing of Substituted Xanthine Based DPP4 Inhibitors: Application to Drug Discovery.

A novel integrated discovery platform has been used to synthesize and biologically assay a series of xanthine-derived dipeptidyl peptidase 4 (DPP4) antagonists. Design, synthesis, purification, quantitation, dilution, and bioassay have all been fully integrated to allow continuous automated operation. The system has been validated against a set of known DPP4 inhibitors and shown to give excellent correlation between traditional medicinal chemistry generated biological data and platform data. Each iterative loop of synthesis through biological assay took two hours in total, demonstrating rapid iterative structure-activity relationship generation.

Rapid discovery of a novel series of Abl kinase inhibitors by application of an integrated microfluidic synthesis and screening platform.

Drug discovery faces economic and scientific imperatives to deliver lead molecules rapidly and efficiently. Using traditional paradigms the molecular design, synthesis, and screening loops enforce a significant time delay leading to inefficient use of data in the iterative molecular design process. Here, we report the application of a flow technology platform integrating the key elements of structure-activity relationship (SAR) generation to the discovery of novel Abl kinase inhibitors. The platform utilizes flow chemistry for rapid in-line synthesis, automated purification, and analysis coupled with bioassay. The combination of activity prediction using Random-Forest regression with chemical space sampling algorithms allows the construction of an activity model that refines itself after every iteration of synthesis and biological result. Within just 21 compounds, the automated process identified a novel template and hinge binding motif with pIC50 > 8 against Abl kinase--both wild type and clinically relevant mutants. Integrated microfluidic synthesis and screening coupled with machine learning design have the potential to greatly reduce the time and cost of drug discovery within the hit-to-lead and lead optimization phases.

The high-mass component (>m/z 10 000) of coal tar pitch by matrix-assisted laser desorption/ionisation mass spectrometry and size-exclusion chromatography.

The size-exclusion chromatography (SEC) of acetone-soluble, pyridine-soluble and pyridine-insoluble fractions of a coal tar pitch indicates a bimodal distribution in each fraction. The proportion of high-mass material excluded from the SEC column porosity increases with solvent polarity. The polymer calibration of SEC shows the mass range of the small molecules to be from approximately 100 u to approximately 6000 u, with the mass range of the large excluded molecules above 200 000 u and up to several million u. In contrast, matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) shows a similar low-mass range of ion abundances (< m/z 6000), but with a smaller range of high-mass ion abundances, from approximately m/z 10 000 to 100 000. The large molecules may have three-dimensional structures to allow molecules of relatively low mass to behave as if they are of large size in SEC. Laser desorption mass spectrometry of the acetone- and pyridine-soluble fractions produced molecular ions of polycyclic aromatics that can be related to the known compositions from gas chromatography (GC) mass spectrometry. The experimental conditions used to generate the bimodal distribution by MALDI-MS involve reducing the ion signal intensities to avoid overload of the detector and enable detection of the high-mass ions, by reducing the high-mass detector voltage (i.e. sensitivity) and increasing the laser power.

Novel 7-methoxy-6-oxazol-5-yl-2,3-dihydro-1H-quinazolin-4-ones as IMPDH inhibitors.

The synthesis and biological activity of a novel series of 7-methoxy-6-oxazol-5-yl-2,3-dihydro-1H-quinazolin-4-ones are described. Some of these compounds were found to be potent inhibitors of inosine 5'-monophosphate dehydrogenase type II (IMPDH II).