Synthesis of the Phenylpyridal Scaffold as a Helical Peptide Mimetic

Phenylpyridal‐ and phenyldipyridal‐based scaffolds have been designed and synthesized as novel helical peptide mimetics. The synthesis required optimisation and selective alkylation in producing 2,6‐functionalized 3‐hydroxypyridine derivatives for a convergent scheme. The pyridine analogues were coupled by a series of Suzuki/Stille types cross‐coupling reactions. A series of biaryl and ter‐aryl substituted heterocycles were produced. The synthetic approach was concise and high yielding allowing large variability at the wanted side‐chain attachment points. A number of compounds were synthesised to show the versatility of the strategy.     

Iridium-catalyzed C-H activation/borylation/oxidation for the preparation of bis-protected phloroglucinol derivatives

The preparation of bis-protected phloroglucinol derivatives from a range of protected resorcinol substrates is presented. Functionalization was achieved via a two-step, one-pot iridium-catalyzed C-H activation/borylation/oxidation protocol. Our system gave high conversions to the arylboronic esters and good yields of the desired phenols following subsequent oxidation. A range of common protecting group categories was studied including alkyl, silyl, ether and ester.     

Tracking protein electrodenaturation fronts in the electrochemical treatment of tumors

Electrochemical reactions in the electrochemical treatment of tumors (EChT) induce extreme pH changes and, consequently, protein electrodenaturation fronts intimately related to tumor destruction. Here we introduce a new in vitro EChT collagen–macronutrient gel (CMG) model to study protein electrodenaturation fronts as a mean of assessing EChT effectiveness. Our CMG model shows that from an initial uniform condition two electrodenaturation fronts evolve expanding towards each other until collision. Moreover, electrodenaturation front tracking reveals that the front grows under a diffusion-controlled regime. Based on this evidence it is possible, in principle, to predict the time needed for tumor destruction without compromising healthy tissue. These results are consistent with those previously obtained with in vivo and in vitro EChT modeling. In contrast to previous simpler in vitro models, our CMG model represents a better structural and chemical approximation to a real tissue thus providing a better tool for validation of new in silico EChT models aimed at a more accurate prediction of tissue destruction level.     

Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.     

Automated data reduction for hydrogen/deuterium exchange experiments,enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm_50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins.     

SKATE: A docking program that decouples systematic sampling from scoring

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Modulated spin waves and robust quasi-solitons in classical Heisenberg rings

We investigate the dynamical behavior of finite rings of classical spin vectors interacting via nearest-neighbor isotropic exchange in an external magnetic field. Our approach is to utilize the solutions of a continuum version of the discrete spin equations of motion (EOM) which we derive by assuming continuous modulations of spin wave solutions of the EOM for discrete spins. This continuum EOM reduces to the Landau-Lifshitz equation in a particular limiting regime. The usefulness of the continuum EOM is demonstrated by the fact that the time-evolved numerical solutions of the discrete spin EOM closely track the corresponding time-evolved solutions of the continuum equation. It is of special interest that our continuum EOM possesses soliton solutions, and we find that these characteristics are also exhibited by the corresponding solutions of the discrete EOM. The robustness of solitons is demonstrated by considering cases where initial states are truncated versions of soliton states and by numerical simulations of the discrete EOM equations when the spins are coupled to a heat bath at finite temperatures.     

Slow-light enhanced correlated photon pair generation in a silicon photonic crystal waveguide

We report the generation of correlated photon pairs in the telecom C-band at room temperature from a dispersion-engineered silicon photonic crystal waveguide. The spontaneous four-wave mixing process producing the photon pairs is enhanced by slow-light propagation enabling an active device length of less than 100?μm. With a coincidence to accidental ratio of 12.8 at a pair generation rate of 0.006 per pulse, this ultracompact photon pair source paves the way toward scalable quantum information processing realized on-chip.     

Spectral parameter dependent Lax pairs for systems of Calogero–Moser type

Presentation of a method for generating Lax pairs for systems obtained by means of Hamiltonian reduction.