Targeting the Water Network in Cyclin G-Associated Kinase (GAK) with 4-Anilino-quin(az)oline Inhibitors

Water networks within kinase inhibitor design and more widely within drug discovery are generally poorly understood. The successful targeting of these networks prospectively has great promise for all facets of inhibitor design, including potency and selectivity for the target. Herein, we describe the design and testing of a targeted library of 4-anilinoquin(az)olines for use as inhibitors of cyclin G-associated kinase (GAK). GAK cellular target engagement assays, ATP binding-site modelling and extensive water mapping provide a clear route to access potent inhibitors for GAK and beyond.     

Targeting an EGFR Water Network with 4-Anilinoquin(az)oline Inhibitors for Chordoma

Quinoline- and quinazoline-based kinase inhibitors of the epidermal growth factor receptor (EGFR) have been used to target non-small cell lung cancer (NSCLC) and chordomas with varying amounts of success. We designed and prepared compounds to probe several key structural features including an interaction with Asp855 within the EGFR DGF motif and interactions with the active site water network. EGFR target engagement was then evaluated in a cellular assay, with the inhibitors then profiled in representative cellular models of NSCLC and chordomas. In addition, structure–activity relationship insight into EGFR inhibitor design with potent dimethoxyquin(az)olines identified compounds 1 [N-(3-ethynylphenyl)-6,7-dimethoxyquinolin-4-amine], 4 [N-(3-ethynylphenyl)-6,7-dimethoxyquinazolin-4-amine], and 7 [4-((3-ethynylphenyl)amino)-6,7-dimethoxyquinoline-3-carbonitrile]. We also identified 6,7-dimethoxy-N-(4-((4-methylbenzyl)oxy)phenyl)quinolin-4-amine (compound 18 ), which is the most potent inhibitor (IC₅₀=310 nm ) of the UCH-2 chordoma cell line to date.     

Distinct Fatty Acid Compositions of HDL Phospholipids Are Characteristic of Metabolic Syndrome and Premature Coronary Heart Disease—Family Study

HDL particles can be structurally modified in atherosclerotic disorders associated with low HDL cholesterol level (HDL-C). We studied whether the lipidome of the main phosphatidylcholine (PC), lysophosphatidylcholine (LPC) and sphingomyelin (SM) species of HDL2 and HDL3 subfractions is associated with premature coronary heart disease (CHD) or metabolic syndrome (MetS) in families where common low HDL-C predisposes to premature CHD. The lipidome was analyzed by LC-MS. Lysophosphatidylcholines were depleted of linoleic acid relative to more saturated and shorter-chained acids containing species in MetS compared with non-affected subjects: the ratio of palmitic to linoleic acid was elevated by more than 30%. A minor PC (16:0/16:1) was elevated (28–40%) in MetS. The contents of oleic acid containing PCs were elevated relative to linoleic acid containing PCs in MetS; the ratio of PC (16:0/18:1) to PC (16:0/18:2) was elevated by 11–16%. Certain PC and SM ratios, e.g., PC (18:0/20:3) to PC (16:0/18:2) and a minor SM 36:2 to an abundant SM 34:1, were higher (11–36%) in MetS and CHD. The fatty acid composition of certain LPCs and PCs displayed a characteristic pattern in MetS, enriched with palmitic, palmitoleic or oleic acids relative to linoleic acid. Certain PC and SM ratios related consistently to CHD and MetS.     

Acid hydrolysis of glycosidic bonds in oat β‐glucan and development of a structured kinetic model

Homogeneous acid‐catalyzed hydrolysis of oat β‐glucan, which contains β‐(1,4) and β‐(1,3) glycosidic bonds in a nonrandom order, was studied at 353 K using HCl and H₂SO₄. A new structured kinetic model was developed that takes into account the difference in the reactivity of β‐(1,4) and β‐(1,3) glycosidic bonds as well as their positions in the polysaccharide chain. To minimize the correlation of adjustable parameters in the new model, the reactivities of these bonds were studied independently (T = 313…363 K; c_H+ = 0.1…2 mol/L) using cellobiose and laminaribiose. The difference in kinetic parameters (e.g., T = 338 K: k_β‐(1,4) = 0.693 × 10^?3 L/mol/min, k_β‐(1,3) = 1.027 × 10^?3 L/mol/min) was found to be statistically significant (P < 0.0001), which emphasizes the need for the structured model for oat β‐glucan hydrolysis. The simulation of β‐glucan hydrolysis with the new model was in good agreement with the experimental data and shows improvement over existing nonstructured models. © 2018 American Institute of Chemical Engineers AIChE J, 64: 2570–2580, 2018     

Towards a standard methodology for greenhouse gas balances of bioenergy systems in comparison with fossil energy systems

In this paper, which was prepared as part of IEA Bioenergy Task XV (“Greenhouse Gas Balances of Bioenergy Systems”), we outline a standard methodology for comparing the greenhouse gas balances of bioenergy systems with those of fossil energy systems. Emphasis is on a careful definition of system boundaries. The following issues are dealt with in detail: time interval analysed and changes of carbon stocks; reference energy systems; energy inputs required to produce, process and transport fuels; mass and energy losses along the entire fuel chain; energy embodied in facility infrastructure; distribution systems; cogeneration systems; by-products; waste wood and other biomass waste for energy; reference land use; and other environmental issues. For each of these areas recommendations are given on how analyses of greenhouse gas balances should be performed. In some cases we also point out alternative ways of doing the greenhouse gas accounting. Finally, the paper gives some recommendations on how bioenergy systems should be optimized from a greenhouse-gas-emissions point of view.     

Greenhouse impact assessment of peat-based Fischer–Tropsch diesel life-cycle

New raw materials for transportation fuels need to be introduced, in order to fight against climate change and also to cope with increasing risks of availability and price of oil. Peat has been recognised suitable raw material option for diesel produced by gasification and Fischer–Tropsch (FT) synthesis. The energy content of Finnish peat reserves is remarkable. In this study, the greenhouse impact of peat-based FT diesel production and utilisation in Finland was assessed from the life-cycle point of view. In 100 year's time horizon the greenhouse impact of peat-based FT diesel is likely larger than the impact of fossil diesel. The impact can somewhat be lowered by producing peat from the agricultural peatland (strong greenhouse gas emissions from the decaying peatlayer are avoided) with new peat production technique, and utilising the produced biomass from the after-treatment area for diesel also. If diesel production is integrated with pulp and paper mill to achieve energy efficiency benefits and if the electricity demand can be covered by zero emission electricity, the greenhouse impact of peat-based FT diesel reduces to the level of fossil diesel when agricultural peatland is used, and is somewhat higher when forestry-drained peatland is used as raw material source.     

Temperature optimisation of a diesel engine using exhaust gas heat recovery and thermal energy storage (diesel engine with thermal energy storage)

Modern automotive diesel engines are so energy efficient that they are heating up slowly and tend to run rather cold at subzero temperatures. The problem is especially severe in mail delivery operations where the average speed is low and the drive cycle includes plenty of idling. The problem is typically solved by adding a diesel fuelled additional engine heater which is used for the preheating of the engine during cold start and additional heating of the engine if the coolant temperature falls below a thermostat set point during the drive cycle. However, this additional heater may drastically increase the total fuel consumption and exhaust gas emissions of the vehicle. In this study the additional heater was replaced by a combination of exhaust gas heat recovery system and latent heat accumulator for thermal energy storage. The system was evaluated on a laboratory dynamometer using a simulated drive cycle and in field testing in the city of Oulu (65°N), Finland in February 2009.     

Use of life cycle assessments to evaluate the environmental footprint of contaminated sediment remediation

Ecological and human risks often drive the selection of remedial alternatives for contaminated sediments. Traditional human and ecological risk assessment (HERA) includes assessing risk for benthic organisms and aquatic fauna associated with exposure to contaminated sediments before and after remediation as well as risk for human exposure but does not consider the environmental footprint associated with implementing remedial alternatives. Assessment of environmental effects over the whole life cycle (i.e., Life Cycle Assessment, LCA) could complement HERA and help in selecting the most appropriate sediment management alternative. Even though LCA has been developed and applied in multiple environmental management cases, applications to contaminated sediments and marine ecosystems are in general less frequent. This paper implements LCA methodology for the case of the polychlorinated dibenzo-p-dioxins and -furans (PCDD/F)-contaminated Grenland fjord in Norway. LCA was applied to investigate the environmental footprint of different active and passive thin-layer capping alternatives as compared to natural recovery. The results showed that capping was preferable to natural recovery when analysis is limited to effects related to the site contamination. Incorporation of impacts related to the use of resources and energy during the implementation of a thin layer cap increase the environmental footprint by over 1 order of magnitude, making capping inferior to the natural recovery alternative. Use of biomass-derived activated carbon, where carbon dioxide is sequestered during the production process, reduces the overall environmental impact to that of natural recovery. The results from this study show that LCA may be a valuable tool for assessing the environmental footprint of sediment remediation projects and for sustainable sediment management.