NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein–protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus–cell and cell–cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein–protein interaction surface.     

Sieving properties of end group‐halogenated Pluronic polymer matrix in DNA separation under nondenaturing CE analysis

CE‐SSCP analysis is a well‐established DNA separation method that is based on variations in mobility caused by sequence‐induced differences in the conformation of single‐stranded DNA. The resolution of CE‐SSCP analysis was improved by using a Pluronic polymer matrix, and it has been successfully applied in various genetic analyses. Because the Pluronic polymer forms a micellar cubic structure in the capillary, it provides a stable internal structure for high‐resolution CE‐SSCP analysis. We hypothesized that formation of micellar cubic structure is influenced by the end hydroxyl group of the Pluronic polymer, which affords structural stability through hydrogen bonding. To test this hypothesis, the hydroxyl group was halogenated to eliminate the hydrogen bonding without disturbing the polarity of polymer matrix. CE‐SSCP resolution of two DNA fragments with a single base difference was significantly worse in the halogenated polymer matrices due to band broadening. The viscoelastic properties of control (which has hydroxyl group), chlorinated, and brominated F108 solution upon heating were also investigated by rheological experiments, and we found that gelation was significantly associated with resolution. In this series of experiments, the effect of the hydroxyl group in Pluronic polymer matrix on separation resolution of CE‐SSCP analysis was demonstrated.     

Studies on the metabolism and the detectability of 4-methyl-amphetamine and its isomers 2-methyl-amphetamine and 3-methyl-amphetamine in rat urine using GC-MS and LC-(high-resolution)-MS n

4-Methyl-amphetamine (1-(4-methylphenyl)propane-2-amine; 4-MA) and its isomers 2-methyl-amphetamine (2-MA) and 3-methyl-amphetamine (3-MA) belong to the group of amphetamine-type stimulants and of new psychoactive substances. Several studies showed similar potencies in releasing noradrenalin and dopamine, but higher potencies in releasing serotonin than amphetamine. In March 2013, the EU Council decided on an EU-wide control based on the European Monitoring Centre for Drugs and Drug Addiction risk assessment report documenting that 4-MA was sold as amphetamine on the illicit market and detected in several fatal cases. Therefore, 4-MA and its isomers should be covered by drug testing in clinical and forensic toxicology. The aims of the presented work were to study the metabolism and detectability of each isomer in urine samples. For metabolism studies, rat urine samples were isolated by solid-phase extraction without and after enzymatic cleavage of conjugates. The phase I metabolites were separated and identified after acetylation by gas chromatography–mass spectrometry (GC-MS) and/or liquid chromatography–high resolution-linear ion trap mass spectrometry (LC-HR-MS ⁿ ) and the phase II metabolites by LC-HR-MS ⁿ . From the identified phase I and II metabolites, the following main metabolic pathways were deduced: aromatic hydroxylation, hydroxylation of the phenylmethyl group followed by oxidation to the corresponding carboxylic acid, hydroxylation of the side chain, and glucuronidation and/or sulfation of the hydroxy and carboxy groups. CYP2D6 was involved in the aromatic hydroxylation. Finally, the intake of a commonly used dose of the MAs could be confirmed in rat urine using the authors’ GC-MS and the LC-MS ⁿ standard urine screening approaches. Differentiation of the isomers to confirm the intake of a specific isomer was possible with an additional workup in rat urine.     

Evaluation of novel ZnO–Ag cathode for CO2 electroreduction in solid oxide electrolyser

CO₂ and steam/CO₂ electroreduction to CO and methane in solid oxide electrolytic cells (SOEC) has gained major attention in the past few years. This work evaluates, for the very first time, the performance of two different ZnO–Ag cathodes: one where ZnO nanopowder was mixed with Ag powder for preparing the cathode ink (ZnO_mix–Ag cathode) and the other one where Ag cathode was infiltrated with a zinc nitrate solution (ZnO_inf –Ag cathode). ZnO_mix–Ag cathode had a better distribution of ZnO particles throughout the cathode, resulting in almost double CO generation while electrolysing both dry CO₂ and H₂/CO₂ (4:1 v/v). A maximum overall CO₂ conversion of 48% (in H₂/CO₂) at 1.7 V and 700 °C clearly indicated that as low as 5 wt% zinc loading is capable of CO₂ electroreduction. It was further revealed that for ZnO_inf –Ag cathode, most of CO generation took place through RWGS reaction, but for ZnO_mix–Ag cathode, it was the synergistic effect of both RWGS reaction and CO₂ electrolysis. Although ZnO_inf –Ag cathode produced trace amount of methane at higher voltages, with ZnO_mix–Ag cathode, there was absolutely no methane. This seems to be due to strong electronic interaction between Zn and Ag that might have suppressed the catalytic activity of the cathode towards methanation.

     

Capillary electrophoresis method for analysis of inorganic and organic anions related to habitability and the search for life

In situ missions of exploration require analytical methods that are capable of detecting a wide range of molecular targets in complex matrices without a priori assumptions of sample composition. Furthermore, these methods should minimize the number of reagents needed and any sample preparation steps. We have developed a method for the detection of metabolically relevant inorganic and organic anions that is suitable for implementation on in situ spaceflight missions. Using 55 mM acetic acid, 50 mM triethylamine, and 5% glycerol, more than 21 relevant anions are separated in less than 20 min. The method is robust to sample ionic strength, tolerating high concentrations of background salts (up to 900 mM NaCl and 300 mM MgSO₄). This is an important feature for future missions to ocean worlds. The method was validated using a culture of Escherichia coli and with high salinity natural samples collected from Mono Lake, California.     

Critical Sets of Elliptic Equations

Given a solution u to a linear, homogeneous, second‐order elliptic equation with Lipschitz coefficients, we introduce techniques for giving improved estimates of the critical set ??(u)u {x :|δu|(x) = 0}, as well as the first estimates on the effective critical set ??_r(u), which roughly consists of points x such that the gradient of u is small somewhere on B_r(x) compared to the nonconstancy of u. The results are new even for harmonic functions on ?ⁿ. Given such a u, the standard first‐order stratification {l^k} of u separates points x based on the degrees of symmetry of the leading‐order polynomial of u‐u(x). In this paper we give a quantitative stratification of u, which separates points based on the number of almost symmetries of approximate leading‐order polynomials of u at various scales. We prove effective estimates on the volume of the tubular neighborhood of each , which lead directly to (n‐2 + ?)‐Minkowski type estimates for the critical set of u. With some additional regularity assumptions on the coefficients of the equation, we refine the estimate to give new proofs of the uniform (n‐2)‐Hausdorff measure estimate on the critical set and singular sets of u.© 2014 Wiley Periodicals, Inc.     

Long‐Lived Spin States for Low‐Field Hyperpolarized Gas MRI

Parahydrogen induced polarization was employed to prepare a relatively long‐lived correlated nuclear spin state between methylene and methyl protons in propane gas. Conventionally, such states are converted into a strong NMR signal enhancement by transferring the reaction product to a high magnetic field in an adiabatic longitudinal transport after dissociation engenders net alignment (ALTADENA) experiment. However, the relaxation time T₁ of ～0.6 s of the resulting hyperpolarized propane is too short for potential biomedical applications. The presented alternative approach employs low‐field MRI to preserve the initial correlated state with a much longer decay time T_LLSS=(4.7±0.5) s. While the direct detection at low‐magnetic fields (e.g. 0.0475 T) is challenging, we demonstrate here that spin‐lock induced crossing (SLIC) at this low magnetic field transforms the long‐lived correlated state into an observable nuclear magnetization suitable for MRI with sub‐millimeter and sub‐second spatial and temporal resolution, respectively. Propane is a non‐toxic gas, and therefore, these results potentially enable low‐cost high‐resolution high‐speed MRI of gases for functional imaging of lungs and other applications.     

Unprecedented 1,14‐seco‐Crotofolanes from Croton insularis: Oxidative Cleavage of Crotofolin C by a Putative Homo‐Baeyer–Villiger Rearrangement

EBC‐162 isolated from Croton insularis, obtained from the northern rainforest of Australia, was structurally affirmed as crotofolin C ( 4 ). Novel oxidative degradation products, EBC‐233 and EBC‐300, which are the first crotofolane endoperoxides, were also isolated. Both endoperoxides were found to be stable intermediates, which are proposed to undergo an unprecedented homo‐Baeyer–Villiger biosynthetic rearrangement to give a new class of 1,14‐seco‐crotofolane diterpenes. Prolonged storage of all isolates assisted in authenticating their natural product status. Anticancer activities of reported compounds are presented.     

Surface Design for Immobilization of an Antimicrobial Peptide Mimic for Efficient Anti-Biofouling

Microbial surface attachment negatively impacts a wide range of devices from water purification membranes to biomedical implants. Mimics of antimicrobial peptides (AMPs) constituted from poly(N-substituted glycine) „peptoids“ are of great interest as they resist proteolysis and can inhibit a wide spectrum of microbes. We investigate how terminal modification of a peptoid AMP-mimic and its surface immobilization affect antimicrobial activity. We also demonstrate a convenient surface modification strategy for enabling alkyne–azide „click“ coupling on amino-functionalized surfaces. Our results verified that the N- and C-terminal peptoid structures are not required for antimicrobial activity. Moreover, our peptoid immobilization density and choice of PEG tether resulted in a „volumetric“ spatial separation between AMPs that, compared to past studies, enabled the highest AMP surface activity relative to bacterial attachment. Our analysis suggests the importance of spatial flexibility for membrane activity and that AMP separation may be a controlling parameter for optimizing surface anti-biofouling.     

B‐MWW Zeolite: The Case Against Single‐Site Catalysis

Boron‐containing materials have recently been identified as highly selective catalysts for the oxidative dehydrogenation (ODH) of alkanes to olefins. It has previously been demonstrated by several spectroscopic characterization techniques that the surface of these boron‐containing ODH catalysts oxidize and hydrolyze under reaction conditions, forming an amorphous B₂(OH)_xO_(3?x/2) (x=0–6) layer. Yet, the precise nature of the active site(s) remains elusive. In this Communication, we provide a detailed characterization of zeolite MCM‐22 isomorphously substituted with boron (B‐MWW). Using ¹¹B solid‐state NMR spectroscopy, we show that the majority of boron species in B‐MWW exist as isolated BO₃ units, fully incorporated into the zeolite framework. However, this material shows no catalytic activity for ODH of propane to propene. The catalytic inactivity of B‐MWW for ODH of propane falsifies the hypothesis that site‐isolated BO₃ units are the active site in boron‐based catalysts. This observation is at odds with other traditionally studied catalysts like vanadium‐based catalysts and provides an important piece of the mechanistic puzzle.