Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations.

Proteins and enzymes generally achieve their functions by creating well-defined 3D architectures that pre-organize reactive functionalities. Mimicking this approach to supramolecular pre-organization is leading to the development of highly versatile artificial chemical environments, including new biomaterials, medicines, artificial enzymes, and enzyme-like catalysts. The use of ß-turn and α-helical motifs is one approach that enables the precise placement of reactive functional groups to enable selective substrate activation and reactivity/selectivity that approaches natural enzymes. Our recent work has demonstrated that helical peptides can serve as scaffolds for pre-organizing two reactive groups to achieve enzyme-like catalysis. In this study, we used CYANA and AmberTools to develop a computational approach for determining how the structure of our peptide catalysts can lead to enhancements in reactivity. These results support our hypothesis that the bifunctional nature of the peptide enables catalysis by pre-organizing the two catalysts in reactive conformations that accelerate catalysis by proximity. We also present evidence that the low reactivity of monofunctional peptides can be attributed to interactions between the peptide-bound catalyst and the helical backbone, which are not observed in the bifunctional peptide.

A new depsidone from the neotricone-rich chemotype of the lichenised fungus Usnea fulvoreagens.

Individuals of Usnea fulvoreagens (Parmeliaceae, lichenised Ascomycota), a shrubby corticolous species that is widespread in Europe, East Asia and North America, produce medullary lichen acids in several distinct chemotypic patterns. One such chemotype reportedly contains an unidentified substance as the major secondary metabolite. We isolated this compound from Californian specimens of U. fulvoreagens and identified it as the rare depsidone neotricone. A co-occurring compound, conneotricone, was identified as 4,10-dihydroxy-5-(hydroxymethyl)-8-methyl-3,7-dioxo-1,3-dihydro-7H-isobenzofuro[4,5-b][1,4]benzodioxepine-11-carboxylic acid by NMR and HPLC-UV-MSn comparison with the material synthesised from salazinic acid.

Optimizing the Local Chemical Environment on a Bifunctional Helical Peptide Scaffold Enables Enhanced Enantioselectivity and Cooperative Catalysis.

We describe a proof-of-concept study in which peptide-bound enamine and thiourea catalysts are used to facilitate the conjugate addition of cyclohexanone to nitroolefins. Our bifunctional peptide scaffold is modified to optimize the local environment around both catalysts to enhance both reactivity and enantioselectivity, affording selectivities of ≤95% ee. Circular dichroism, nuclear magnetic resonance nuclear Overhauser effect studies, and molecular dynamics simulations verify the helical structure of our catalyst in solution and the importance of the secondary structure in catalysis.

Rapid, Quantitative Nuclear Magnetic Resonance Test for Oxygen-17 Enrichment in Water.

Nuclear magnetic resonance (NMR) studies involving 17O are increasingly important in molecular biology, material science, and other disciplines. A large number of these studies employ H217O as a source of 17O, and this reliance can be limiting because the high cost of H217O. To overcome this constraint, a recent study proposed a distillation scheme capable of producing significant quantities of H217O at a low cost. Although this method is reported to be effective, the reactions proposed to quantify percent of 17O enrichment are either time intensive or have a risk of errors due to the isotope effect. Here, an alternative reaction scheme is described to measure 17O water that ultimately creates methyl benzoate as the sole 17O-containing product. The proposed reaction is completed in a matter of minutes at room temperature, produces only one 17O product, and requires no clean-up step. The large isotope shift observed in solution NMR between the 13C═16O and 13C═17O resonances allows for integration of the individual peaks. This 13C NMR analysis is found to be highly accurate over a wide enrichment range and is accessible to most NMR spectroscopists.

Isolation and identification of compounds from Kalanchoe pinnata having human alphaherpesvirus and vaccinia virus antiviral activity.

CONTEXT: Kalanchoe pinnata (Lam.) Pers. (Crassulaceae) is a succulent plant that is known for its traditional antivirus and antibacterial usage. OBJECTIVE: This work examines two compounds identified from the K. pinnata plant for their antivirus activity against human alphaherpesvirus (HHV) 1 and 2 and vaccinia virus (VACV). MATERIALS AND METHODS: Compounds KPB-100 and KPB-200 were isolated using HPLC and were identified using NMR and MS. Both compounds were tested in plaque reduction assay of HHV-2 wild type (WT) and VACV. Both compounds were then tested in virus spread inhibition and virus yield reduction (VYR) assays of VACV. KPB-100 was further tested in viral cytopathic effect (CPE) inhibition assay of HHV-2 TK-mutant and VYR assay of HHV-1 WT. RESULTS: KPB-100 and KPB-200 inhibited HHV-2 at IC50 values of 2.5 and 2.9 µg/mL, respectively, and VACV at IC50 values of 3.1 and 7.4 µg/mL, respectively, in plaque reduction assays. In virus spread inhibition assay of VACV KPB-100 and KPB-200 yielded IC50 values of 1.63 and 13.2 µg/mL, respectively, and KPB-100 showed a nearly 2-log reduction in virus in VYR assay of VACV at 20 µg/mL. Finally, KPB-100 inhibited HHV-2 TK- at an IC50 value of 4.5 µg/mL in CPE inhibition assay and HHV-1 at an IC90 of 3.0 µg/mL in VYR assay. DISCUSSION AND CONCLUSION: Both compounds are promising targets for synthetic optimization and in vivo study. KPB-100 in particular showed strong inhibition of all viruses tested.

Novel synthetic (E)-2-methoxy-4-(3-(4-methoxyphenyl) prop-1-en-1-yl) phenol inhibits arthritis by targeting signal transducer and activator of transcription 3.

Rheumatoid arthritis (RA) is a severely debilitating chronic autoimmune disease that leads to long-term joint damage. Signal transducer and activator of transcription 3 (STAT3)-targeted small molecules have shown promise as therapeutic drugs for treating RA. We previously identified (E)-2,4-bis(p-hydroxyphenyl)-2-butenal (BHPB), a tyrosine-fructose Maillard reaction product, as a small molecule with potent anti-inflammatory and anti-arthritic properties, mediated through the inhibition of STAT3 activation. The aim of this study was to develop a novel BHPH derivative with improved anti-arthritic properties and drug-likeness. We designed and synthesised (E)-2-methoxy-4-(3-(4-methoxyphenyl) prop-1-en-1-yl) phenol (MMPP), a novel synthetic BHPB analogue, and investigated its anti-inflammatory and anti-arthritic activities in experimentally-induced RA. We showed that MMPP strongly inhibited pro-inflammatory responses by inhibiting in vitro STAT3 activation and its downstream signalling in murine macrophages and human synoviocytes from patients with RA. Furthermore, we demonstrated that MMPP exhibited potent anti-arthritic activity in a collagen antibody-induced arthritis (CAIA) mouse model in vivo. Collectively, our results suggest that MMPP has great potential for use in the treatment of RA.

Dirhodium-catalyzed C-H arene amination using hydroxylamines.

Primary and N-alkyl arylamine motifs are key functional groups in pharmaceuticals, agrochemicals, and functional materials, as well as in bioactive natural products. However, there is a dearth of generally applicable methods for the direct replacement of aryl hydrogens with NH2/NH(alkyl) moieties. Here, we present a mild dirhodium-catalyzed C-H amination for conversion of structurally diverse monocyclic and fused aromatics to the corresponding primary and N-alkyl arylamines using NH2/NH(alkyl)-O-(sulfonyl)hydroxylamines as aminating agents; the relatively weak RSO2O-N bond functions as an internal oxidant. The methodology is operationally simple, scalable, and fast at or below ambient temperature, furnishing arylamines in moderate-to-good yields and with good regioselectivity. It can be readily extended to the synthesis of fused N-heterocycles.

Characterization of a novel plasmid-borne thiopeptide gene cluster in Staphylococcus epidermidis strain 115.

Thiopeptides are small (12- to 17-amino-acid), heavily modified peptides of bacterial origin. This antibiotic family, with more than 100 known members, is characterized by the presence of sulfur-containing heterocyclic rings and dehydrated residues within a macrocyclic peptide structure. Thiopeptides, including micrococcin P1, have garnered significant attention in recent years for their potent antimicrobial activity against bacteria, fungi, and even protozoa. Micrococcin P1 is known to target the ribosome; however, like those of other thiopeptides, its biosynthesis and mechanisms of self-immunity are poorly characterized. We have discovered an isolate of Staphylococcus epidermidis harboring the genes for thiopeptide production and self-protection on a 24-kb plasmid. Here we report the characterization of this plasmid, identify the antimicrobial peptide that it encodes, and provide evidence of a target replacement-mediated mechanism of self-immunity.

Thermal maps of gases in heterogeneous reactions.

More than 85 per cent of all chemical industry products are made using catalysts, the overwhelming majority of which are heterogeneous catalysts that function at the gas-solid interface. Consequently, much effort is invested in optimizing the design of catalytic reactors, usually by modelling the coupling between heat transfer, fluid dynamics and surface reaction kinetics. The complexity involved requires a calibration of model approximations against experimental observations, with temperature maps being particularly valuable because temperature control is often essential for optimal operation and because temperature gradients contain information about the energetics of a reaction. However, it is challenging to probe the behaviour of a gas inside a reactor without disturbing its flow, particularly when trying also to map the physical parameters and gradients that dictate heat and mass flow and catalytic efficiency. Although optical techniques and sensors have been used for that purpose, the former perform poorly in opaque media and the latter perturb the flow. NMR thermometry can measure temperature non-invasively, but traditional approaches applied to gases produce signals that depend only weakly on temperature are rapidly attenuated by diffusion or require contrast agents that may interfere with reactions. Here we present a new NMR thermometry technique that circumvents these problems by exploiting the inverse relationship between NMR linewidths and temperature caused by motional averaging in a weak magnetic field gradient. We demonstrate the concept by non-invasively mapping gas temperatures during the hydrogenation of propylene in reactors packed with metal nanoparticles and metal-organic framework catalysts, with measurement errors of less than four per cent of the absolute temperature. These results establish our technique as a non-invasive tool for locating hot and cold spots in catalyst-packed gas-solid reactors, with unprecedented capabilities for testing the approximations used in reactor modelling.

A new species of Eimeria (Apicomplexa: Eimeriidae) from the eastern pipistrelle, Perimyotis subflavus (Chiroptera: Vespertilionidae), in Arkansas.

During November 2009 and March 2010, 20 adult eastern pipistrelles, Perimyotis (=  Pipistrellus) subflavus, were collected from Polk County, Arkansas, and their feces were examined for coccidian parasites. Two (10%) of the bats were found to be passing oocysts of an undescribed species of Eimeria. Oocysts of Eimeria heidti n. sp. were ovoidal to ellipsoidal, 26.1 × 20.5 µm (23-31 × 18-23 µm), with a bilayered wall, externally rough, internally smooth, and with a shape index of 1.3. Micropyle and oocyst residuum were absent, but a subspherical polar granule was often present. Sporocysts were ovoidal, 13.0 × 8.8 µm (11-15 × 7-13 µm), the shape index was 1.6, a Stieda body was present and sub-Stieda and para-Stieda bodies were absent. A sporocyst residuum consisting of multiple globules dispersed along the perimeter of the sporocyst and between the sporozoites were present, sporozoites were elongate, with a subspherical anterior refractile body and elongate posterior refractile body; a nucleus not discernible. This is the second coccidian reported from this host and the fourth instance of a coccidian species reported from an Arkansas bat.

A broad spectrum anticancer nucleoside with selective toxicity against human colon cells in vitro.

2',3'-Bis-O-tert-butyldimethylsilyl-5'-deoxy-5'-[N-(methylcarbamoyl)amino]-N(6)-(N-phenylcarbamoyl)adenosine, a new member of the N(6),5'-bis-ureidoadenosine class of anticancer nucleosides, is found to exhibit broad spectrum antiproliferative activity. A majority of the cell lines in the NCI-60 are inhibited with an average GI(50)=3.13 µM. Selective toxicity against human colon cancer cell lines (COLO 205, HCC-2998, HCT-116, HT29, KM12) was also exhibited (LC(50)'s=6-10 µM).

NMR imaging of catalytic hydrogenation in microreactors with the use of para-hydrogen.

Catalysis is vital to industrial chemistry, and the optimization of catalytic reactors attracts considerable resources. It has proven challenging to correlate the active regions in heterogeneous catalyst beds with morphology and to monitor multistep reactions within the bed. We demonstrate techniques, using magnetic resonance imaging and para-hydrogen (p-H2) polarization, that allow direct visualization of gas-phase flow and the density of active catalyst in a packed-bed microreactor, as well as control over the dynamics of the polarized state in space and time to facilitate the study of subsequent reactions. These procedures are suitable for characterizing reactors and reactions in microfluidic devices where low sensitivity of conventional magnetic resonance would otherwise be the limiting factor.

para-Hydrogen-induced polarization in heterogeneous hydrogenation reactions.

We demonstrate the creation and observation of para-hydrogen-induced polarization in heterogeneous hydrogenation reactions. Wilkinson's catalyst, RhCl(PPh3)3, supported on either modified silica gel or a polymer, is shown to hydrogenate styrene into ethylbenzene and to produce enhanced spin polarizations, observed through NMR, when the reaction was performed with H2 gas enriched in the para spin isomer. Furthermore, gaseous phase para-hydrogenation of propylene to propane with two catalysts, the Wilkinson's catalyst supported on modified silica gel and Rh(cod)(sulfos) (cod = cycloocta-1,5-diene; sulfos = -O3S(C6H4)CH2C(CH2PPh2)3) supported on silica gel, demonstrates heterogeneous catalytic conversion resulting in large spin polarizations. These experiments serve as a direct verification of the mechanism of heterogeneous hydrogenation reactions involving immobilized metal complexes and can be potentially developed into a practical tool for producing catalyst-free fluids with highly polarized nuclear spins for a broad range of hyperpolarized NMR and MRI applications.

Periodic boundary condition induced breakdown of the equipartition principle and other kinetic effects of finite sample size in classical hard-sphere molecular dynamics simulation.

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N-1)]1/2, and the ratio of average collision energy to average kinetic energy is increased by a factor of N/(N-1). Simulations in one, two, and three dimensions confirm the analytic results for arbitrary dimension.