Insights into E. coli cyclopropane fatty acid synthase (CFAS) towards enantioselective carbene free biocatalytic cyclopropanation.

Cyclopropane fatty acid synthases (CFAS) are a class of S-adenosylmethionine (SAM) dependent methyltransferase enzymes able to catalyse the cyclopropanation of unsaturated phospholipids. Since CFAS enzymes employ SAM as a methylene source to cyclopropanate alkene substrates, they have the potential to be mild and more sustainable biocatalysts for cyclopropanation transformations than current carbene based approaches. This work describes the characterisation of E. coli CFAS enzyme (ecCFAS) and its exploitation in the stereoselective biocatalytic synthesis of cyclopropyl lipids.  ecCFAS was found to convert phosphatidylglycerol (PG) to methyl dihydrosterculate 1 from  in up to 58% conversion and 73% ee and the absolute configuration (9S,10R) was established. Substrate tolerance of ecCFAS was found to be correlated with the electronic properties of phospholipid headgroups  and for the first time ecCFAS was found to catalyse cyclopropanation of both phospholipid chains to form dicyclopropanated products. In addition, mutagenesis and in-silico experiments were carried out to identify the enzyme residues with key roles in catalysis and to provide structural insights into the lipid substrate preference of ecCFAS. Finally, the biocatalytic synthesis of methyl dihydrosterculate 1 and its deuterated analogue was also accomplished combining pure ecCFAS with the SAM regenerating AtHMT enzyme in presence of CH3I and CD3I.

Phytosterols in human serum as measured using a liquid chromatography tandem mass spectrometry.

Phytosterols are lipophilic compounds found in plants with structural similarity to mammalian cholesterol. They cannot be endogenously produced by mammals and therefore always originate from diet. There has been increased interest in dietary phytosterols over the last few decades due to their association with a variety of beneficial health effects including low-density lipoprotein cholesterol lowering, anti-inflammatory and anti-cancerous effects. They are proposed as potential moderators for diseases associated with the central nervous system where cholesterol homeostasis is found to be imperative (multiple sclerosis, dementia, etc.) due to their ability to reach the brain. Here we utilised an enzyme-assisted derivatisation for sterol analysis (EADSA) in combination with a liquid chromatography tandem mass spectrometry (LC-MSn) to characterise phytosterol content in human serum. As little as 100 fg of plant sterol was injected on a reversed phase LC column. The method allows semi-quantitative measurements of phytosterols and their derivatives simultaneously with measurement of cholesterol metabolites. The identification of phytosterols in human serum was based on comparison of their LC retention times and MS2, MS3 spectra with a library of authentic standards. Free campesterol serum concentration was in the range from 0.30-4.10 µg/mL, ß-sitosterol 0.16-3.37 µg/mL and fucosterol was at lowest concentration range from 0.05-0.38 µg/mL in ten individuals. This analytical methodology could be applied to the analysis of other biological fluids and tissues.

Antibiotic Residues in UK Foods: Exploring the Exposure Pathways and Associated Health Risks.

While the use of antibiotics has been reported as extensive in the rearing of agricultural animals, insufficient information is available on the antibiotic residues in animal products and the adverse impact that consistent low-level exposure to antibiotics might have on the human body and its microbiome. The aim of this study was to estimate the antibiotic concentrations that humans are exposed to via their diet using the concentration of antibiotics in animal food products and water and an online survey on dietary intake. A total of 131 participants completed the dietary intake survey, with the majority belonging to the omnivorous diet group (76.3%). Distinct dietary trends were observed in the omnivorous and unknown groups eating animal products, with specific food types dominating each meal: pork (e.g., ham) and dairy products (e.g., milk, yoghurt) during breakfast, beef (e.g., burgers) and chicken (e.g., chicken breast) products during lunch, and fish (e.g., salmon fillet) during dinner. In total, 34 different animal-based food and drink products were tested for the presence of ten different antibiotics. Of all the products tested, over 35% exceeded the acceptable daily antibiotic intake for amoxicillin, ampicillin, and enrofloxacin.

Two-substrate enzyme engineering using small libraries that combine the substrate preferences from two different variant lineages.

Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in kcat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.

The Nitrile Bis-Thiol Bioconjugation Reaction.

Electron-poor aryl nitriles are promising reagents for bioconjugation due to their high electrophilicity and selectivity for reaction with thiols, albeit generally in a reversible manner. A transient species has previously been observed in such reactions, involving the addition of two thiols to the nitrile functional group, forming a tetrahedral amino dithioacetal (ADTA). In this work, the reaction of heteroaryl nitriles with bis-thiols is explored in an attempt to generate stable ADTAs, which could facilitate new bioconjugation protocols. By use of a 1,2-dithiol, or the incorporation of an electrophilic trap into the aryl nitrile design, the formation of stable products is achieved. The resultant "nitrile bis-thiol" (NBT) reaction is then explored in the context of protein modification, specifically to carry out antibody conjugation. By addition of these nitriles to the reduced disulfide bond of an antibody fragment, it is shown that, depending on the reagent design, cysteine-to-lysine transfer or disulfide bridged NBT products can be generated. Both represent site-selective conjugates and are shown to be stable when challenged with glutathione under physiological conditions and upon incubation in serum. Furthermore, the NBT reaction is tested in the more challenging context of a full antibody, and all four disulfide bonds are effectively modified by these new one-carbon bridging reagents. Overall, this reaction of heteroaryl-nitriles with bis-thiols is shown to be highly efficient and versatile, of tunable reversibility, and offers enticing prospects as a new addition to the toolbox of biocompatible "click"-type reactions.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration.

The granular activated carbon (GAC) sandwich modification to slow sand filtration could be considered as a promising technology for improved drinking water quality. Biofilms developed on sand and GAC surfaces are expected to show a functional diversity during the biofiltration. Bench-scale GAC sandwich biofilters were set-up and run continuously with and without antibiotic exposure. Surface sand (the schmutzdecke) and GAC biofilms were sampled and subject to high-throughput qPCR for antibiotic resistance gene (ARG) analysis and 16 S rRNA amplicon sequencing. Similar diversity of ARG profile was found in both types of biofilms, suggesting that all ARG categories decreased in richness along the filter bed. In general, surface sand biofilm remained the most active layer with regards to the richness and abundance of ARGs, where GAC biofilms showed slightly lower ARG risks. Network analysis suggested that 10 taxonomic genera were implicated as possible ARG hosts, among which Nitrospira, Methyloversatilis and Methylotenera showed the highest correlation. Overall, this study was the first attempt to consider the whole structure of the GAC sandwich biofilter and results from this study could help to further understand the persistence of ARGs and their association with the microbial community in drinking water biofiltration system.

Antibacterial Properties of Honey Nanocomposite Fibrous Meshes.

Natural substances are increasingly being developed for use in health-related applications. Honey has attracted significant interest, not only for its physical and chemical properties, but also for its antibacterial activity. For the first time, suspensions of Black Forest honeydew honey and manuka honey UMF 20+ were examined for their antibacterial properties against Escherichia coli and Staphylococcus epidermidis using flow cytometry. The inhibitory effect of honey on bacterial growth was evident at concentrations of 10, 20 and 30 v/v%. The minimum inhibitory effects of both honey types against each bacterium were also investigated and reported. Electrospray ionisation (ESI) mass spectrometry was performed on both Black Forest honeydew honey and manuka honey UMF 20+. Manuka honey had a gluconic concentration of 2519 mg/kg, whilst Black Forest honeydew honey had a concentration of 2195 mg/kg. Manuka honey demonstrated the strongest potency when compared to Black Forest honeydew honey; therefore, it was incorporated into nanofiber scaffolds using pressurised gyration and 10, 20 and 30 v/v% manuka honey-polycaprolactone solutions. Composite fibres were analysed for their morphology and topography using scanning electron microscopy. The average fibre diameter of the manuka honey-polycaprolactone scaffolds was found to range from 437 to 815 nm. The antibacterial activity of the 30 v/v% scaffolds was studied using S. epidermidis. Strong antibacterial activity was observed with a bacterial reduction rate of over 90%. The results show that honey composite fibres formed using pressurised gyration can be considered a natural therapeutic agent for various medicinal purposes, including wound-healing applications.

Unearthing the unique stability of thiophosphonium-C-terminal cysteine adducts on peptides and proteins.

Herein we report a fundamental discovery on the use of tris(dialkylamino)phosphine reagents for peptide and protein modification. We discovered that C-terminal thiophosphonium species, which are uniquely stable, could be selectively and rapidly generated from their disulfide counterparts. In sharp and direct contrast, internal thiophosphonium species rapidly degrade to dehydroalanine. We demonstrate this remarkable chemoselectivity on a bis-cysteine model peptide, and the formation of a stable C-terminal-thiophosphonium adduct on an antibody fragment, as well as characterise the species in various small molecule/peptide studies.

Identification of diverse lipid-binding modes in the groove of zinc α2 glycoprotein reveals its functional versatility.

ZAG is a multifunctional glycoprotein with a class I MHC-like protein fold and an α1-α2 lipid-binding groove. The intrinsic ZAG ligand is unknown. Our previous studies showed that ZAG binds the dansylated C11 fatty acid, DAUDA, differently to the boron dipyrromethane C16 fatty acid, C16 -BODIPY. Here, the molecular basis for this difference was elucidated. Multi-wavelength analytical ultracentrifugation confirmed that DAUDA and C16 -BODIPY individually bind to ZAG and compete for the same binding site. Molecular docking of lipid-binding in the structurally related Cluster of differentiation 1 proteins predicted nine conserved ligand contact residues in ZAG. Twelve mutants were accordingly created by alanine scanning site directed mutagenesis for characterisation. Mutation of Y12 caused ZAG to misfold. Mutation of K147, R157 and A158 abrogated C16 -BODIPY but not DAUDA binding. L69 and T169 increased the fluorescence emission intensity of C16 -BODIPY but not of DAUDA compared to wild-type ZAG and showed that C16 -BODIPY binds close to T169 and L69. Distance measurements of the crystal structure revealed K147 forms a salt bridge with D83. A range of bioactive bulky lipids including phospholipids and sphingolipids displaced DAUDA from the ZAG binding site but unexpectedly did not displace C16 -BODIPY. We conclude that the ZAG α1-α2 groove contains separate but overlapping sites for DAUDA and C16 -BODIPY and is involved in binding to a bulkier and wider repertoire of lipids than previously reported. This work suggested that the in vivo activity of ZAG may be dictated by its lipid ligand.

Probing cytochrome P450 (CYP) bioactivation with chloromethylindoline bioprecursors derived from the duocarmycin family of compounds.

The duocarmycins belong to a class of agent which has great potential for use in cancer therapy. Their exquisite potency means they are too toxic for systemic use, and targeted approaches are required to unlock their clinical potential. In this study, we have explored seco-OH-chloromethylindoline (CI) duocarmycin-based bioprecursors for their potential for cytochrome P450 (CYP)-mediated cancer cell kill. We report on synthetic and biological explorations of racemic seco-CI-MI, where MI is a 5-methoxy indole motif, and dehydroxylated analogues. We show up to a 10-fold bioactivation of de-OH CI-MI and a fluoro bioprecursor analogue in CYP1A1-transfected cells. Using CYP bactosomes, we also demonstrate that CYP1A2 but not CYP1B1 or CYP3A4 has propensity for potentiating these compounds, indicating preference for CYP1A bioactivation.

Correction: Optimisation of the dibromomaleimide (DBM) platform for native antibody conjugation by accelerated post-conjugation hydrolysis.

Correction for 'Optimisation of the dibromomaleimide (DBM) platform for native antibody conjugation by accelerated post-conjugation hydrolysis' by Maurício Morais et al., Org. Biomol. Chem., 2017, 15, 2947-2952, DOI: .

Simultaneous measurement of free and conjugated estrogens in surface water using capillary liquid chromatography tandem mass spectrometry.

Given detrimental impacts induced by estrogens at trace level, determination of them is significant but challenging due to their low content in environmental samples and inherent weak ionisation. A modified derivatisation-based methodology was applied for the first time to detect estrogen in free and conjugated forms including some isomers simultaneously using liquid chromatography tandem mass spectrometry (LC-MSn). Derivatisation reaction with previously used 1,2-dimethyl-1H-imidazole-5-sulphonyl chloride allowed significant increase of mass spectrometric signal of analytes and also provided distinctive fragmentation for their confirmation even in complicated matrix. Then satisfactory recovery (>75%) for the majority of analytes was achieved following optimisation of solid phase extraction (SPE) factors. The linearity was validated over a wide concentration with the correlation coefficient around 0.995. The repeatability of this methodology was also confirmed via the intra-day and inter-day precision and was less than 11.73%. Validation of method quantification limits (MQLs) for all chosen estrogens was conducted using 1000 mL surface water, ranging from 7.0 to 132.3 pg L-1. The established methodology was applied to profile presence of targeted estrogens in natural surface water samples. Out of the ten compounds of interest, three free estrogens (E1, E2, E3) and two sulphate estrogens (E1-3S and E2-3S) were found over their MQLs, being in the range of 0.05-0.32 ng L-1.

Removal of antibiotics in sand, GAC, GAC sandwich and anthracite/sand biofiltration systems.

Drinking water biofiltration offers the possibility of the removal of trace level micropollutants from source water. Sand, granular activated carbon (GAC), GAC sandwich (a layer of GAC loaded in the middle of sand bed), and anthracite-sand dual biofilters were set-up in duplicate at bench-scale to mimic the filtration process in real drinking water treatment works. During the 3-month system operation, removal of five antibiotics (amoxicillin, clarithromycin, oxytetracycline, sulfamethoxazole, and trimethoprim) and overall biofilter performance were evaluated. Natural surface water spiked with a mixture of the target antibiotics was used as feedwater to the biofilters. Results showed that the target antibiotics were substantially removed (>90%) by GAC-associated biofilters and partially removed (≤20%) by sand alone and anthracite-sand biofilters. In particular, the GAC sandwich biofilter exhibited superior performance compared to sand/anthracite biofilter, and the comparisons among all biofilters indicated that both adsorption and biodegradation contributed to the removal of the target antibiotics in the GAC-associated biofilters. Adsorption kinetics showed that sulfamethoxazole fitted with pseudo-first-order adsorption model, while trimethoprim, amoxicillin, oxytetracycline and clarithromycin fitted the pseudo-second-order model. All antibiotics fitted the Langmuir model according to the isotherm experiment. To date, this is the first study evaluating the removal of antibiotics by GAC sandwich biofilters. Overall, this research will provide useful information which can be used for optimising or updating existing biofiltration processes in industry to reduce antibiotic residues from source water.

Continuous Single-Phase Synthesis of [Au25(Cys)18] Nanoclusters and their Photobactericidal Enhancement.

Thiolate-gold nanoclusters have various applications. However, most of the synthesis methods require prolonged synthesis times from several hours to days. In the present study, we report a rapid synthesis method for [Au25(Cys)18] nanoclusters and their application for photobactericidal enhancement. For [Au25(Cys)18] synthesis, we employed a tube-in-tube membrane reactor using CO as a reducing agent at elevated temperatures. This approach allows continuous generation of high-quality [Au25(Cys)18] within 3 min. Photobactericidal tests against Staphylococcus aureus showed that crystal violet-treated polymer did not have photobactericidal activity, but addition of [Au25(Cys)18] in the treated polymer demonstrated a potent photobactericidal activity at a low white light flux, resulting in >4.29 log reduction in viable bacteria numbers. Steady-state and time-resolved photoluminescence spectroscopies demonstrated that after light irradiation, photoexcited electrons in crystal violet flowed to [Au25(Cys)18] in the silicone, suggesting that redox reaction from [Au25(Cys)18] enhanced the photobactericidal activity. Stability tests revealed that leaching of crystal violet and [Au25(Cys)18] from the treated silicone was negligible and cyclic testing showed that the silicone maintained a strong photobactericidal activity after repeated use.

Photobactericidal activity activated by thiolated gold nanoclusters at low flux levels of white light.

The emergence of antibiotic resistant bacteria is a major threat to the practice of modern medicine. Photobactericidal agents have obtained significant attention as promising candidates to kill bacteria, and they have been extensively studied. However, to obtain photobactericidal activity, an intense white light source or UV-activation is usually required. Here we report a photobactericidal polymer containing crystal violet (CV) and thiolated gold nanocluster ([Au25(Cys)18]) activated at a low flux levels of white light. It was shown that the polymer encapsulated with CV do not have photobactericidal activity under white light illumination of an average 312 lux. However, encapsulation of [Au25(Cys)18] and CV into the polymer activates potent photobactericidal activity. The study of the photobactericidal mechanism shows that additional encapsulation of [Au25(Cys)18] into the CV treated polymer promotes redox reactions through generation of alternative electron transfer pathways, while it reduces photochemical reaction type-ІІ pathways resulting in promotion of hydrogen peroxide (H2O2) production.

Quantitative Proteomic Analysis of the Central Amygdala in Neuropathic Pain Model Rats.

Pain and emotional distress have a reciprocal relation. The amygdala has been implicated in emotional processing. The central nucleus of the amygdala (CeA) receives nociceptive information from the dorsal horn of spinal cord and is responsible for the central plasticity in chronic pain. Neuropathic pain is a type of severe chronic pain and can be strongly influenced by emotional components. Plastic changes in the CeA may play a key role in the development or maintenance or both of neuropathic pain. We studied the expression levels of proteins in the CeA of spinal nerve transection (SNT) model rats. Total tissue lysate proteins were separated by two-dimensional-gel electrophoresis (2D-PAGE). Gels from different time points were compared using Progenesis SameSpot software, and the spots with Fold Change greater than 2 were excised for protein identification by mass spectrometry. We identified more than 50 cytosolic proteins as significantly altered in their expression levels in the CeA of SNT rats, and most of these changes have been validated at mRNA levels by qRT-PCR. We also identified more than 40 membrane proteins as notably up- or down-regulated in the CeA of SNT model rats relative to a control using stable isotope dimethyl labeling nano-LC-MS/MS based proteomics and found that one such protein, doublecortin (DCX), a microtubule-associated protein expressed by neuronal precursor cells during development, is specifically localized in the membrane fraction without changes in total amount of the protein. Immunohistochemistry showed that doublecortin is expressed in processes in the CeA of rats 7 and 21 days after SNT surgery, suggesting that doublecortin is one of the proteins that may contribute to the plastic changes, namely, redevelopment or rewiring of neural networks, in the CeA in the neuropathic pain model. These dysregulated proteins may play roles in reciprocal relationships between pain and psychological distress in the amygdala and contribute to central sensitization. Data are available via ProteomeXchange with identifier PXD017473.

Optimised approach to albumin-drug conjugates using monobromomaleimide-C-2 linkers.

Conjugation of therapeutics to human serum albumin (HSA) using bromomaleimides represents a promising platform for half-life extension. We show here that the Cys-34 crevice substantially reduces the rate of serum stabilising maleimide hydrolysis in these conjugates, necessitating reagent optimisation. This improved reagent design is applied to the construction of an HSA-paclitaxel conjugate, preventing drug loss during maleimide hydrolysis.

Cysteine-to-lysine transfer antibody fragment conjugation.

The modification of lysine residues with acylating agents has represented a ubiquitous approach to the construction of antibody conjugates, with the resulting amide bonds being robustly stable and clinically validated. However, the conjugates are highly heterogeneous, due to the presence of numerous lysines on the surface of the protein, and greater control of the sites of conjugation are keenly sought. Here we present a novel approach to achieve the targeted modification of lysines distal to an antibody fragment's binding site, using a disulfide bond as a temporary 'hook' to deliver the acylating agent. This cysteine-to-lysine transfer (CLT) methodology offers greatly improved homogeneity of lysine conjugates, whilst retaining the advantages offered by the formation of amide linkages.

LC-MS analysis to determine the biodistribution of a polymer coated ilomastat ocular implant.

Ilomastat is a matrix metalloproteinase inhibitor (MMPi) that has shown the potential to inhibit scarring (fibrosis) by mediating healing after injury or surgery. A long lasting ocular implantable pharmaceutical formulation of ilomastat is being developed to mediate the healing process to prevent scarring after glaucoma filtration surgery. The ilomastat implant was coated with water permeable and biocompatible phosphoryl choline polymer (PC1059) displayed extended slow release of ilomastat in vitro and in vivo. The ocular distribution of ilomastat from the implant in rabbits at day 30 post surgery was determined by the extraction of ilomastat and its internal standard marimastat from the ocular tissues, plasma, aqueous humour and vitreous fluid followed by capillary-flow liquid chromatography (cap-LC), the column effluent was directed into a triple quadrupole mass spectrometer operating in product scan mode. The lower limits of quantification (LLOQs) were 0.3 pg/µL for ocular fluids and plasma, and 3 pg/mg for ocular tissues. The extraction recoveries were 90-95% for ilomastat and its internal standard from ocular tissues. Ilomastat was found in ocular fluids and tissues at day 30 after surgery. The level of ilomastat was 18 times higher in the aqueous humour than vitreous humour. The concentration ranking of ilomastat in the ocular tissues was sclera > bleb conjunctiva > conjunctiva (rest of the eye) > cornea. Mass spectrometry analysis to confirm the presence of ilomastat in the ocular tissues and fluids at day 30 post-surgery establishes the extended release of ilomastat can be achieved in vivo, which is crucial information for optimisation of the ilomastat coated implant.

Effect of Flavin-Containing Monooxygenase Genotype, Mouse Strain, and Gender on Trimethylamine N-oxide Production, Plasma Cholesterol Concentration, and an Index of Atherosclerosis.

The objectives of the study were to determine the contribution, in mice, of members of the flavin-containing monooxygenase (FMO) family to the production of trimethylamine (TMA) N-oxide (TMAO), a potential proatherogenic molecule, and whether under normal dietary conditions differences in TMAO production were associated with changes in plasma cholesterol concentration or with an index of atherosclerosis (Als). Concentrations of urinary TMA and TMAO and plasma cholesterol were measured in 10-week-old male and female C57BL/6J and CD-1 mice and in mouse lines deficient in various Fmo genes (Fmo1-/- , 2-/- , 4-/- , and Fmo5-/- ). In female mice most TMA N-oxygenation was catalyzed by FMO3, but in both genders 11%-12% of TMA was converted to TMAO by FMO1. Gender-, Fmo genotype-, and strain-related differences in TMAO production were accompanied by opposite effects on plasma cholesterol concentration. Plasma cholesterol was negatively, but weakly, correlated with TMAO production and urinary TMAO concentration. Fmo genotype had no effect on Als. There was no correlation between Als and either TMAO production or urinary TMAO concentration. Our results indicate that under normal dietary conditions TMAO does not increase plasma cholesterol or act as a proatherogenic molecule.