Synthesis of the Human Milk Oligosaccharide Lacto‐N‐Tetraose in Metabolically Engineered,Plasmid‐Free E. coli

Human milk oligosaccharides (HMOs) constitute the third most abundant solid component of human milk. HMOs have been demonstrated to show positive effects on the infant’s well‐being. Despite numerous studies, more physiological analyses of single compounds are needed to fully elucidate these effects. Although being one of the most abundant core structures in human milk, the HMO lacto‐N‐tetraose (LNT) is not available at reasonable prices. In this study, we demonstrate the construction of the first E. coli strain capable of producing LNT in vivo. The strain was constructed by chromosomally integrating the genes lgtA and wbgO, encoding β‐1,3‐N‐acetylglucosaminyltransferase and β‐1,3‐galactosyltransferase. In shake‐flask cultivations, the strain yielded a total concentration of 219.1±3.5 mg L^?1 LNT (LNT in culture broth and the cell pellet). After recovery of LNT, structural analysis by NMR spectroscopy confirmed the molecule structure.     

The Development of Selective Inhibitors of NagZ: Increased Susceptibility of Gram‐Negative Bacteria to β‐Lactams

The increasing incidence of inducible chromosomal AmpC β‐lactamases within the clinic is a growing concern because these enzymes deactivate a broad range of even the most recently developed β‐lactam antibiotics. As a result, new strategies are needed to block the action of this antibiotic resistance enzyme. Presented here is a strategy to combat the action of inducible AmpC by inhibiting the β‐glucosaminidase NagZ, which is an enzyme involved in regulating the induction of AmpC expression. A divergent route facilitating the rapid synthesis of a series of N‐acyl analogues of 2‐acetamido‐2‐deoxynojirimycin is reported here. Among these compounds are potent NagZ inhibitors that are selective against functionally related human enzymes. These compounds reduce minimum inhibitory concentration values for β‐lactams against a clinically relevant Gram‐negative bacterium bearing inducible chromosomal AmpC β‐lactamase, Pseudomonas aeruginosa. The structure of a NagZ–inhibitor complex provides insight into the molecular basis for inhibition by these compounds.     

Synthesis of N-acetyllactosamine derivatives with variation in the aglycon moiety for the study of inhibition of sialyl Lewis x expression

Herein we describe an inhibition study of the sialyl Lewis x (sLe(x)) expression on a human monocytic cell line (U937), using a series of peracetylated N-Acetyllactosamine (LacNAc) analogues with variation at the aglycon moiety. It was found that the extent of inhibition was related to the hydrophobicity and structure of the aglycon. In general, peracetylated LacNAc analogues with a naphthyl or biphenyl aglycon (3, 4, 6, and 7) were better in suppression of sLe(x) expression than a benzyl derivative (2). Steady-state kinetic experiments with human alpha-1,3-fucosyltransferases IV and VI (FucT IV and VI, EC 2.4.1.65) revealed that the deacetylated LacNAc-aglycons with naphthyl (18, 19, and 20) or biphenyl (17) moieties exhibited higher affinity to the fucosyltransferases than aglycon moieties with smaller hydrophobic groups (14, 15, and 16). These results are in agreement with the findings of the U937 cell-based experiments, and suggest that the higher enzyme affinity LacNAc-aglycons make better acceptor decoys and, hence, the observed differences in LacNAc-aglycon inhihitory effects on sLe(x) expression.     

Disulfiram is an inhibitor of human purified monoacylglycerol lipase, the enzyme regulating 2-arachidonoylglycerol signaling

Monoacylglycerol lipase (MAGL) is a key enzyme responsible for the termination of endocannabinoid signaling. Its crucial role in 2-arachidonoylglycerol (2-AG) metabolism, together with the numerous pharmacological properties mediated by this endocannabinoid, emphasize the interest in MAGL as therapeutic target, along with the need to design potent and selective inhibitors. Meanwhile, the complexity of 2-AG degradation pathways underscores the need to use a purified source of enzyme in evaluation studies of new inhibitors. We report here the first heterologous expression and purification of human MAGL. A highly pure protein was obtained and allowed us to measure the affinity of several MAGL inhibitors for the human enzyme. Importantly, disulfiram (tetraethylthiuram disulfide), a compound used to treat alcoholism, and other disulfide-containing compounds were shown to inhibit MAGL with good potency, likely through an interaction with cysteine residues.     

Poly(ADP-ribose)-polymerase-catalyzed hydrolysis of NAD+: QM/MM simulation of the enzyme reaction

Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme which uses NAD+ as substrate and catalyzes the transfer of multiple units of ADP-ribose to target proteins. PARP is an attractive target for the discovery of novel therapeutic agents and PARP inhibitors are currently evaluated for the treatment of a variety of pathological conditions such as brain ischemia, inflammation, and cancer. Herein, we use the PARP-catalyzed reaction of NAD+ hydrolysis as a model for gaining insight into the molecular details of the catalytic mechanism of PARP. The reaction has been studied in both the gas-phase and in the enzyme environment through a QM/MM approach. Our results indicate that the cleavage reaction of the nicotinamide-ribosyl bond proceeds through an SN2 dissociative mechanism via an oxacarbenium transition structure. These results confirm the importance of the structural water molecule in the active site and may constitute the basis for the design of transition-state-based PARP inhibitors.     

From human skin to Nano-Skin: an experimental study on human skin temperature measurement

The human state in human–machine systems should be monitored to improve system performance. In monitoring it is preferable to use physiological cues such as skin temperature. The sensing capabilities of human skin were analyzed. The sensing system of human skin was modeled, and inspired the design of a Nano-Skin for physiological measurement in dynamic human–machine contact for human state recognition. The Nano-Skin involves a flexible bottom layer, sensors, special integrated circuit, interconnection between sensors and special integrated circuit, and flexible top layer. The requirements for the sensors of a Nano-Skin are summarized, and compared with common sensors, MEMS sensors, and nano sensors. A Nano-Skin with deposited platinum was manufactured. The manufacturing process is shown to be feasible and repeatable. The Nano-Skin with deposited platinum was used to measure skin temperature. Its performance was investigated using experiments. The results verified that the accuracy of the Nano-Skin sensors will not be lower than Pt1000Ω. Smaller sensors in a Nano-Skin generally have better performance.     

Spray and freeze drying of human milk on the retention of immunoglobulins (IgA,IgG, IgM)

Several freeze-drying and spray-drying methods were investigated in relation to the retention of immunoglobulins (Ig) A, IgG, and IgM. Spray drying produced human milk powders with 2% humidity and a good retention of IgG (>88%) and IgM (～70%). However, only 38% of IgA remained after spray drying. For freeze drying, only the highest heating plate temperature used in this study (40°C) brought IgA content down to 55% in powder with 1.75% residual humidity, whereas milk samples undergoing lower temperatures had higher preservation rates (75% for IgA and 80% for IgG and IgM) and higher residual moisture contents. From these results, it can be concluded that IgA is the most sensitive Ig lost during drying processing of human milk. The best method to generate human milk powders without a significant loss of Ig was thus freeze drying at 30°C heating plate temperature, which accelerated the process compared to lower processing temperatures, but still had good overall Ig retention.     

Crystal Structure of the Human Monoacylglycerol Lipase,a Key Actor in Endocannabinoid Signaling

2‐Arachidonoylglycerol plays a major role in endocannabinoid signaling, and is tightly regulated by the monoacylglycerol lipase (MAGL). Here we report the crystal structure of human MAGL. The protein crystallizes as a dimer, and despite structural homologies to haloperoxidases and esterases, it distinguishes itself by a wide and hydrophobic access to the catalytic site. An apolar helix covering the active site also gives structural insight into the amphitropic character of MAGL, and likely explains how MAGL interacts with membranes to recruit its substrate. Docking of 2‐arachidonoylglycerol highlights a hydrophobic and a hydrophilic cavity that accommodate the lipid into the catalytic site. Moreover, we identified Cys201 as the crucial residue in MAGL inhibition by N‐arachidonylmaleimide, a sulfhydryl‐reactive compound. Beside the advance in the knowledge of endocannabinoids degradation routes, the structure of MAGL paves the way for future medicinal chemistry works aimed at the design of new drugs exploiting 2‐arachidonoylglycerol transmission.     

Docosahexaenoic acid and arachidonic acid levels are correlated in human milk: Implications for new European infant formula regulations

From February 2022, all infant formula sold in the European Union must contain docosahexaenoic acid (DHA) at ~0.33%–1.14% of total fat with no minimum requirement for arachidonic acid (ARA). This work examines the association between DHA and ARA levels in human milk, the gold standard for infant feeding. Human milk (n = 470) was collected over 12-weeks postpartum from lactating mothers (n = 100) of infants born weighing <1250 g (NCT02137473). Fatty acids were analyzed by gas chromatography. ARA and DHA concentrations were associated in human milk (β = 0.47 [95% confidence interval 0.38–0.56] mol%), including transitional and mature milk, but not colostrum. This remained significant upon adjustment for percentages of other saturated, monounsaturated, n-3, or n-6 fatty acids, day of sample collection, or maternal characteristics (body mass index, ethnicity, education, and income). Infant formulas containing relatively high concentrations of DHA without ARA, as permitted by the new regulations, would not reflect the balance of these fatty acids in human milk.     

Facile purification and characterization of recombinant human antithrombin III from transgenic goat milk

BACKGROUND: Antithrombin III (AT III) is a serine protease inhibitor that inhibits thrombin and the activated forms of factors X, VII, IX, XI and XII. Transgenic expression of therapeutic proteins in animal systems has gradually matured from laboratory scale to industrial practice, demanding efficient and scalable purification processes. The purification and characterization of recombinant human antithrombin III (rhAT III) from transgenic goat milk are described here. RESULTS: The rhAT III was purified by isoelectric precipitation, heparin affinity chromatography, and size exclusion chromatography, resulting in a 90.6% yield and > 99% purity. The goat β‐casein secretion peptide introduced to the rhAT III was cut off using enterokinase and removed by size exclusion chromatography using a Superdex 75 column. The primary structure, disulfide linkages, glycosylation sites, secondary structure and tertiary structure of the rhAT III were measured and found to be the same as those of the plasma‐derived AT III (phAT III). CONCLUSION: A facile process is introduced for the purification of rhAT III from transgenic goat milk. The rhAT III with high purity was achieved after an initial isoelectric precipitation step in which most of the bulk protein impurities are removed, followed by affinity chromatography and size exclusion chromatography. The rhAT III was demonstrated to have the same structure as phAT III. Copyright © 2011 Society of Chemical Industry     

Glucose 1‐Phosphate Thymidylyltransferase in the Synthesis of Uridine 5′‐Diphosphate Galactose and its Application in the Synthesis of N‐Acetyllactosamine

In this study, we describe the direct synthesis of uridine 5′‐diphosphate galactose (UDP‐Gal) by a wild‐type bacterial thymidylyltransferase (RmlA), which is used to synthesize thymidine 5′‐diphosphate glucose (TDP‐glucose) in nature. By using magnesium (Mg²⁺) as a cofactor and a reaction temperature of 55 °C, a one hundred milligram‐scale synthesis of UDP‐Gal was achieved by RmlA. In addition, RmlA was site‐specifically and covalently immobilized on magnetic nanoparticles (MNPa) The resulting RmlA‐MNP complex retained almost 95% of its activity after reuse in ten consecutive enzyme assays. Furthermore, β‐1,4‐galactosyltransferase (GalT) from Neisseria meningitides was successfully overexpressed and purified by using an intein‐mediated protein expression system. GalT was relatively stable at 25 °C, and its activity was enhanced in the presence of DTT and BSA. Thus, it was feasible to synthesize N‐acetyllactosamine (LacNAc) using RmlA and GalT in a sequential addition of enzyme and adjustment of thereaction temperature. These results demonstrate the potential applications of bacterial RmlA in carbohydrate synthesis.     

Design of different bioreactor configurations: application to ligninolytic enzyme production in semi‐solid‐state cultivation

The production of ligninolytic enzymes by Phanerochaete chrysosporium BKM‐F‐1767 (ATCC 24725) in laboratory‐scale bioreactors was studied. The cultivations were carried out in semi‐solid‐state conditions, employing corncob as carrier, which functioned both as a place of attachment and as a source of nutrients. Several bioreactor configurations were investigated in order to determine the most suitable one for ligninolytic enzyme production: a 1‐dm³‐static‐bed bioreactor, a 1‐dm³‐static‐bed bioreactor with air diffusers into the bed, a 0.5‐dm³‐static‐bed bioreactor with air diffusers into the bed and a tray bioreactor. Although the static‐bed configurations produced maximum individual lignin peroxidase (LiP) activities about 400 U dm⁻³ (1.0‐dm³ bioreactor) and about 700 U dm⁻³ (0.5‐dm³ bioreactor), manganese‐dependent peroxidase (MnP) was not detected throughout the cultures. Nevertheless, the tray configuration led to maximum individual MnP and LiP activities of about 200 U dm⁻³ and 300 U dm⁻³, respectively. Therefore, this configuration is the most adequate of the different bioreactor configurations tested in the present work, since the ligninolytic complex formed by MnP and LiP is more efficient for its application to bio‐processing systems. In addition, the results indicated the influence of the oxygen in ligninolytic enzyme production. © 2001 Society of Chemical Industry     

Enhancing the thermal robustness of an enzyme by directed evolution: least favorable starting points and inferior mutants can map superior evolutionary pathways

In a previous directed evolution study, the B-FIT approach to increasing the thermal robustness of proteins was introduced and applied to the lipase from Bacillus subtilis. It is based on the general concept of iterative saturation mutagenesis (ISM), according to which sites in an enzyme are subjected to saturation mutagenesis, the best hit of a given library is then used as a template for randomization at other sites, and the process is continued until the desired catalyst improvement has been achieved. The appropriate choice of the ISM sites is crucial; in the B-FIT method the criterion is residues characterized by highest B factors available from X-ray crystallography data. In the present study, B-FIT was employed in order to increase the thermal robustness of the epoxide hydrolase from Aspergillus niger. Several rounds of ISM resulted in the best variant showing a 21 °C increase in the T(60)(50) value, an 80-fold improvement in half-life at 60 °C, and a 44 kcal mol(-1) improvement in inactivation energy. Seven other variants were also evolved with moderate yet significant improvements; these were characterized by 10-14 °C increases in T(60)(50), 20-30-fold improvement in half-lives at 60 °C and 15-20 kcal mol(-1) elevations in activation energy. Unexpectedly, in the ISM process the best variants were obtained from essentially neutral or even inferior mutant parents, that is, when a given library contains no improved mutants. This constitutes a practical way to escape from what appear to be local minima ("dead ends") in the fitness landscape-a finding of notable significance in directed evolution.     

Molecular weight distribution and regioisomeric structure of triacylglycerols in some common human milk substitutes

Triacylglycerol (TAG) molecular weight distribution and regioisomeric structure of selected molecular weight species in human milk and in 32 human milk substitutes was determined. Negative ion chemical ionization mass spectrometry was used to determine the molecular weight distribution and collisionally induced dissociation tandem mass spectrometry applied to identify the sn-2 and sn-1/3 positions of fatty acids in TAG. The main molecular weight species of human milk TAG in decreasing order of abundance were 52∶2, 52∶3, 52∶1, 54∶3, 50∶2, 50∶1, 54∶4, 48∶1, 54∶2, 48∶2, 46∶1, 52∶4, and 50∶3 (acyl carbon number/number of double bonds), constituting 83 mol% of total TAG molecular species. In human milk substitutes, the proportion of the corresponding molecular weight species varied from 33 to 87 mol%. The main TAG regioisomers within the molecular weight species 52∶2, 52∶3, and 50∶1 in human milk were 18∶1-16∶0-18∶1 (83 mol%), 18∶1-16∶0-18∶2 (83 mol%), and 18∶1-16∶0-16∶0 (80 mol%), respectively. In human milk substitutes, the corresponding proportions varied in a wide range of 0–82 mol%, 0–100 mol%, and 0–73 mol%, respectively. Although TAG structures in some human milk substitutes closely resembled those in human milk, the great variation among samples leads to the conclusion that it is still possible to improve the TAG composition in human milk substitutes by applying novel methods to synthesize structured TAG.     

Novel Function of CtXyn5A from Acetivibrio thermocellus: Dual Arabinoxylanase and Feruloyl Esterase Activity in the Same Active Site**

Enzymes’ uncharacterised side activities can have significant effects on reaction products and yields. Hence, their identification and characterisation are crucial for the development of successful reaction systems. Here, we report the presence of feruloyl esterase activity in CtXyn5A from Acetivibrio thermocellus, besides its well-known arabinoxylanase activity, for the first time. Activity analysis of enzyme variants mutated in the catalytic nucleophile, Glu279, confirmed removal of all activity for E279A and E279L, and increased esterase activity while removing xylanase activity for E279S, thus allowing the proposal that both reaction types are catalysed in the same active site in two subsequential steps. The ferulic acid substituent is cleaved off first, followed by hydrolysis of the xylan backbone. The esterase activity on complex carbohydrates was found to be higher than that of a designated ferulic acid esterase (E-FAERU). Therefore, we conclude that the enzyme exhibits a dual function rather than an esterase side activity.     

Synergistic Inhibitor Binding to the Papain‐Like Protease of Human SARS Coronavirus: Mechanistic and Inhibitor Design Implications

We previously developed two potent chemical classes that inhibit the essential papain‐like protease (PLpro) of severe acute respiratory syndrome coronavirus. In this study, we applied a novel approach to identify small fragments that act synergistically with these inhibitors. A fragment library was screened in combination with four previously developed lead inhibitors by fluorescence‐based enzymatic assays. Several fragment compounds synergistically enhanced the inhibitory activity of the lead inhibitors by approximately an order of magnitude. Surface plasmon resonance measurements showed that three fragments bind specifically to the PLpro enzyme. Mode of inhibition, computational solvent mapping, and molecular docking studies suggest that these fragments bind adjacent to the binding site of the lead inhibitors and further stabilize the inhibitor‐bound state. We propose potential next‐generation compounds based on a computational fragment‐merging approach. This approach provides an alternative strategy for lead optimization for cases in which direct co‐crystallization is difficult.