Copper(I)-Dioxygen Adducts and Copper Enzyme Mechanisms

Primary copper(I)-dioxygen (O₂) adducts, cupric-superoxide complexes, have been proposed intermediates in copper-containing dioxygen-activating monooxygenase and oxidase enzymes. Here, mechanisms of C−H activation by reactive copper-(di)oxygen intermediates are discussed, with an emphasis on cupric-superoxide species. Over the past 25 years, many synthetically derived cupric-superoxide model complexes have been reported. Due to the thermal instability of these intermediates, early studies focused on increasing their stability and obtaining physical characterization. More recently, in an effort to gain insight into the possible substrate oxidation step in some copper monooxygenases, several cupric-superoxide complexes have been used as surrogates to probe substrate scope and reaction mechanisms. These cupric superoxides are capable of oxidizing substrates containing weak O−H and C−H bonds. Mechanistic studies for some enzymes and model systems have supported an initial hydrogen-atom abstraction via the cupric-superoxide complex as the first step of substrate oxidation.     

A Bayesian adaptive dose-finding algorithm for balancing individual- and population-level ethics in Phase I clinical trials

Multiple Bayesian adaptive designs have been proposed for Phase I clinical trials since the continual reassessment method (CRM) was proposed by O’Quigley et al. (1990). Focused on dose-finding in cancer studies, the CRM seeks to allocate new patients to an estimated maximum tolerable dose (MTD). Later, Whitehead and Brunier (1995 Whitehead, J. and Brunier, H. (1995). Continual Reassessment Method: Bayesian Decision Procedures for Dose Determining Experiments, Statistics in Medicine 14: 885–893.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) applied Bayesian decision theory to maximize statistical information for the MTD when allocating new patients. The two allocation rules reflect conflicting perspectives. The CRM emphasizes individual-level ethics, whereas the method of Whitehead and Brunier (1995 Whitehead, J. and Brunier, H. (1995). Continual Reassessment Method: Bayesian Decision Procedures for Dose Determining Experiments, Statistics in Medicine 14: 885–893.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) emphasizes population-level ethics. In the design of a Phase I clinical trial to investigate hyperthermic intraperitoneal chemotherapy (HIPEC) we sought to compromise the two perspectives. To this end, we propose a novel dose allocation design referred to as the balanced information gain method. We first decompose the loss function used by Whitehead and Brunier and then modify it with a tuning parameter that allows a trialist to differentially weigh individual- and population-level ethics based on their particular clinical setting. Simulation studies show that the proposed design provides a reasonable compromise between the distribution of the estimated MTD and the distribution of the number of observed adverse events per trial when compared to the two existing methods.     

Evaluating p97 Inhibitor Analogues for Potency against p97–p37 and p97–Npl4–Ufd1 Complexes

We previously found that the p97 cofactor, p47, significantly decreased the potency of some ATP‐competitive p97 inhibitors such as ML240 [2‐(2‐amino‐1H‐benzo[d]imidazol‐1‐yl)‐N‐benzyl‐8‐methoxyquinazolin‐4‐amine] and ML241 [2‐(2H‐benzo[b][1,4]oxazin‐4(3H)‐yl)‐N‐benzyl‐5,6,7,8 tetrahydroquinazolin‐4‐amine]. In this study, we aimed to evaluate inhibitor potencies against two additional p97 cofactor complexes, p97–p37 and p97–Npl4–Ufd1. We focused on these two cofactor complexes, because the protein sequence of p37 is 50 % identical to that of p47, and the Npl4–Ufd1 heterodimer (NU) is the most‐studied p97 cofactor complex. We screened 200 p97 inhibitor analogues for their ability to inhibit the ATPase activity of p97 alone and of p97–p37 and p97–NU complexes. In contrast to the effect of p47, p37 and NU did not significantly change the potencies of most of the compounds. These results highlight differences among p97 cofactors in influencing p97 conformation and effects of inhibitors on p97 complexes, as compared to p97 alone. Continued efforts are needed to advance the development of complex‐specific p97 inhibitors.     

Structure–Activity Relationships of JMV4463, a Vectorized Cathepsin D Inhibitor with Antiproliferative Properties: The Unique Role of the AMPA‐Based Vector

Cathepsin D (CathD) is overexpressed and secreted by several solid tumors and stimulates their growth, the mechanism of which is still not understood. In this context, the pepstatin bioconjugate JMV4463 [Ac‐arg‐O₂Oc‐(Val)₃‐Sta‐Ala‐Sta‐(AMPA)₄‐NH₂; O₂Oc=8‐amino‐3,6‐dioxaoctanoyl, Sta=statine, AMPA=ortho‐aminomethylphenylacetyl], containing a new kind of cell‐penetrating vector, was previously shown to exhibit potent antiproliferative effects in vitro and to delay the onset of tumors in vivo. In this study, we performed a structure–activity relationship analysis to evaluate the significance of the inhibitor and vector moieties of JMV4463. By modifying both statine residues of pepstatin we found that the antiproliferative activity is correlated with CathD inhibition, supporting a major role of the catalytic activity of intracellular CathD in cancer cell proliferation. Replacing the vector composed of four AMPA units with other vectors was found to abolish cytotoxicity, although all of the conjugates enabled pepstatin transport into cells. In addition, the AMPA₄ vector must be localized at the C terminus of the bioconjugate. The unexpected importance of the vector structure and position for cytotoxic action suggests that AMPA₄ enables pepstatin to inhibit the proteolysis of critical CathD substrates involved in cell proliferation via a unique mechanism of action.     

Improved fallow: growth and nitrogen accumulation of five native tree species in Brazil

Nitrogen (N) is the most important yield-limiting factor in agricultural systems, however, N application can lead to emissions and environmental problems such as global warming (N₂O) and groundwater contamination (NO₃ ^?). This study analyses the N balance, nitrogen-use efficiency, and N loss potential of conventional farming systems (arable farming, improved arable farming, and agroforestry) and organic farming systems (mixed farming, arable farming, and agroforestry) based on long-term field experiments in southern Germany. The effects of the conversion of farm structure and N management are identified. The conventional farming systems in this study were high N-input and high N-output systems. The conventional arable farming system had the lowest nitrogen-use efficiency and the highest N surplus. An optimised N management and the use of high-yielding crop varieties improved its nitrogen-use efficiency. The establishment of conventional agroforestry resulted in the reduction of N input, N output and N surplus, while maintaining high yields. The organic mixed farming system is characterised by a relatively high N input and N output, the accumulation of soil organic nitrogen, the highest nitrogen-use efficiency, and the lowest N surplus of all analysed systems. These good results can be attributed to the intensive farm N cycle between soil–plant–animal. The shift from organic mixed farming to organic arable farming system extensified the N cycle, reduced N input, crop yield and N output. The change from organic arable farming to organic agroforestry reduced the N input, increased the biomass yield, and remained the N surplus within an optimal range.     

Phylogenetic-Derived Insights into the Evolution of Sialylation in Eukaryotes: Comprehensive Analysis of Vertebrate β-Galactoside α2,3/6-Sialyltransferases (ST3Gal and ST6Gal)

Cell surface of eukaryotic cells is covered with a wide variety of sialylated molecules involved in diverse biological processes and taking part in cell–cell interactions. Although the physiological relevance of these sialylated glycoconjugates in vertebrates begins to be deciphered, the origin and evolution of the genetic machinery implicated in their biosynthetic pathway are poorly understood. Among the variety of actors involved in the sialylation machinery, sialyltransferases are key enzymes for the biosynthesis of sialylated molecules. This review focus on β-galactoside α2,3/6-sialyltransferases belonging to the ST3Gal and ST6Gal families. We propose here an outline of the evolutionary history of these two major ST families. Comparative genomics, molecular phylogeny and structural bioinformatics provided insights into the functional innovations in sialic acid metabolism and enabled to explore how ST-gene function evolved in vertebrates.     

An Iterative O‐Methyltransferase Catalyzes 1,11‐Dimethylation of Aspergillus fumigatus Fumaric Acid Amides

S‐adenosyl‐l ‐methionine (SAM)‐dependent methyltransfer is a common biosynthetic strategy to modify natural products. We investigated the previously uncharacterized Aspergillus fumigatus methyltransferase FtpM, which is encoded next to the bimodular fumaric acid amide synthetase FtpA. Structure elucidation of two new A. fumigatus natural products, the 1,11‐dimethyl esters of fumaryl‐l ‐tyrosine and fumaryl‐l ‐phenylalanine, together with ftpM gene disruption suggested that FtpM catalyzes iterative methylation. Final evidence that a single enzyme repeatedly acts on fumaric acid amides came from an in vitro biochemical investigation with recombinantly produced FtpM. Size‐exclusion chromatography indicated that this methyltransferase is active as a dimer. As ftpA and ftpM homologues are found clustered in other fungi, we expect our work will help to identify and annotate natural product biosynthesis genes in various species.     

Design of New Cardanol Derivative: Synthesis and Application as Potential Biobased Plasticizer for Poly(lactide)

A novel biobased plasticizer made of cardanol is designed for poly(lactide) (PLA). This cardanol‐derived plasticizer, i.e., methoxylated hydroxyethyl cardanol (MeCard), is synthesized through methoxylation of the double bonds on the side chain of cardanol, and characterized by ¹H NMR and mass spectrometry. The plasticization effect of MeCard on the molecular structure, morphology, thermal and mechanical properties of PLA is evaluated and compared to that of a commercial cardanol, i.e., hydroxyethyl cardanol (pCard). The plasticization efficiency of MeCard is demonstrated by a substantial decrease of the glass transition temperature and storage modulus together with a significant increase of the elongation at break as compared to neat PLA. Moreover, MeCard exhibits higher plasticization performance than pCard toward PLA. Such behavior is related to a higher miscibility and compatibility between PLA and MeCard thanks to the methoxylation of the double bonds on the side chain of cardanol as shown by SEM micrographs.