Synthesis of sansalvamide A peptidomimetics: triazole, oxazole, thiazole, and pseudoproline containing compounds

Peptidomimetic-based macrocycles typically have improved pharmacokinetic properties over those observed with peptide analogs. Described are the syntheses of 13 peptidomimetic derivatives that are based on active Sansalvamide A structures, where these analogs incorporate heterocycles (triazoles, oxazoles, thiazoles, or pseudoprolines) along the macrocyclic backbone. The syntheses of these derivatives employ several approaches that can be applied to convert a macrocyclic peptide into its peptidomimetic counterpart. These approaches include peptide modifications to generate the alkyne and azide for click chemistry, a serine conversion into an oxazole, a Hantzsch reaction to generate the thiazole, and protected threonine to generate the pseudoproline derivatives. Furthermore, we show that two different peptidomimetic moieties, triazoles and thiazoles, can be incorporated into the macrocyclic backbone without reducing cytotoxicity: triazole and thiazole.     

More efficient Brownian dynamics algorithms

We examine the relative efficiencies of three- algorithms for performing Brownian Dynamics simulations without many-body hydrodynamics. We compare the conventional Brownian Dynamics algorithm of Ermak (CBD), Smart Monte Carlo (SMC) which incorporates Boltzmann sampling into essentially a CBD procedure, and the Stochastic Runge Kutta (SRK) method. We show, using the repulsive potential φ(r) = ε(σ/r) ⁿ , where n = 36 and 72, that the SRK algorithm gives the most accurate short-time dynamics for the mean-square displacements. The SRK algorithm static and dynamical properties converge better with a reducing time step to the exact values, than those generated by the CBD algorithm; giving efficiency gains typically of a factor of 3–4. Both CBD and SMC have the incorrect sign for the first correction term to the mean square displacement in a time step, whereas the SRK algorithm gives essentially the exact solution to order Δt ², where Δt is the simulation time step. In fact, these correction terms are almost equal and opposite in sign. Expressions for these terms were derived in terms of the average interaction energy per particle. The force, shear and bulk stress autocorrelation functions were calculated. The average energy per particle and time correlation functions at short time have values in excess of the exact values, while the corresponding quantities for SRK are below this. This difference in behaviour can be traced back to the extent of compliance of the particle trajectories with the exact expansion of the Smoluchowski equation. The accuracy, at a given value of the time step, of the stochastic algorithms can significantly depend on the form of the interaction potential between particles. It is also demonstrated that the long time limits of various correlation functions are fairly insensitive to a particular scheme (SRK or CBD) used in the simulations. All the correlation functions have a stretched exponential region at intermediate to long times, and the values of the exponents on density and force law steepness have been determined.     

A Fluorogenic Probe for Cell Surface Phosphatidylserine Using an Intramolecular Indicator Displacement Sensing Mechanism

The detection of externalized phosphatidylserine (PS) on the cell surface is commonly used to distinguish between living, apoptotic, and necrotic cells. The tools of choice for many researchers to study apoptosis are annexin V‐fluorophore conjugates. However, the use of this 35 kDa protein is associated with several drawbacks, including temperature sensitivity, Ca²⁺ dependence, and slow binding kinetics. Herein, a fluorogenic probe for cell surface PS, P‐IID , is described, which operates by an intramolecular indicator displacement (IID) mechanism. An intramolecularly bound coumarin indicator is released in the presence of cell surface PS, leading to a fluorescence “turn‐on” response. P‐IID demonstrates superior performance when compared to annexin V, for both fluorescence imaging and flow cytometry. This allows P‐IID to be used in time‐lapse imaging of apoptosis using confocal laser scanning microscopy and demonstrates the utility of the IID mechanism in live cells.     

Measurements of toluene and other aromatic hydrocarbons by differential-absorption LIDAR in the near-ultraviolet

The first measurements of toluene by differential-absorption LIDAR in the near-ultraviolet spectral region are reported. A pulse energy of 4.5 mJ was used for the measurement, generated by frequency-doubling the output from a tunable dye laser in beta-barium borate. The magnitude of spectral interference from other pollutant species has been calculated and the extension of the system to measure other aromatic hydrocarbons in the same spectral region is discussed.     

Amino-terminal dimerization of an erythropoietin mimetic peptide results in increased erythropoietic activity

Background: Erythropoietin (EPO), the hormone involved in red blood cell production, activates its receptor by binding to the receptor's extracellular domain and presumably dimerizing two receptor monomers to initiate signal transduction. EPO-mimetic peptides, such as EMP1, also bind and activate the receptor by dimerization. These mimetic peptides are not as potent as EPO, however. The crystal structure of the EPO receptor (EBP) bound to EMP1 reveals the formation of a complex consisting of two peptides bound to two receptors, so we sought to improve the biological activity of EPO-mimetic peptides by constructing covalent dimers of EMP1 and other peptide mimetics linked by polyethylene glycol (PEG).Results: The potency of the PEG-dimerized EPO peptide mimetics both in vitro and in vivo was improved up to 1,000-fold compared to the corresponding peptide monomers. The dinners were constructed using peptide monomers which have only one reactive amine per molecule, allowing us to conclude that the increase in potency can be attributed to a structure in which two peptides are linked through their respective amino termini to the difunctional PEG molecule. In addition, an inactive peptide was converted into a weak agonist by PEG-induced dimerization.Conclusions: The potency of previously isolated peptides that are modest agonists of the EPO receptor was dramatically increased by PEG-induced dimerization. The EPO receptor is thought to be dimerized during activation, so our results are consistent with the proposed 2:2 receptor : peptide stoichiometry. The conversion of an inactive peptide into an agonist further supports the idea that dimerization can mediate receptor activation.     

Ultraviolet-B radiation and plant competition: experimental approaches and underlying mechanisms

Under realistic stratospheric ozone depletion scenarios, ultraviolet-B radiation (280-320 nm) (UV-B) influences plant morphology and plant competitive interactions. Influence of UV-B on plant competition can be studied using a variety of experimental and analytical approaches including inverse yield-density models and allometric, neighborhood or size-structure analyses that provide links between plant and ecosystem responses. These approaches differ in their abilities to extract information regarding competitive interactions and their morphological underpinnings. Only a limited number of studies have been carried out to investigate UV-B effects on plant competition, and most of these have used the replacement series approach, which has received much criticism. Nonetheless, results to date indicate that slight differences in UV-B-induced morphological responses of species grown within associations can alter canopy structure thereby influencing photosynthetically active radiation (PAR) interception and relative competitive ability. Because the response of individuals of the same species is expected to be uniform, UV-B may influence intraspecific competition less than interspecific competition. Before we can make clear generalizations and predictions concerning the effects of this radiation on plant competition, an understanding is crucial of the mechanisms underlying UV-B-induced shifts in competitive interactions by assessing competition over time.     

Synthesis of the side chain cross-linked tyrosine oligomers dityrosine, trityrosine, and pulcherosine

[reaction: see text] An efficient synthesis of dityrosine and the first syntheses of the tyrosine trimers trityrosine and pulcherosine have been achieved. Protected 3-iodotyrosine underwent tandem Miyaura borylation-Suzuki coupling to give protected dityrosine. The choice of benzyl carbamate, ester, and ether protecting groups enabled a one-step global deprotection to give dityrosine. Suzuki coupling of protected 3,5-diiodotyrosine and tyrosine-3-boronic acid derivatives gave the corresponding trityrosine, but in low yield. However, use of a potassium tyrosine-3-trifluoroborate derivative in place of the corresponding pinacol boronate ester, in combination with protecting group variation, gave protected trityrosine in good yield. Access to pulcherosine was achieved through copper-catalyzed coupling of phenylalanine-4-boronic acid and 4-O-protected dopa derivatives to give an isodityrosine derivative. Selective halogenation followed by Suzuki coupling with the potassium tyrosine-3-trifluoroborate gave protected pulcherosine. Global deprotection of the protected trityrosine and pulcherosine derivatives completed the first syntheses of the corresponding tris-alpha-amino acids.     

The Simplified Component Technique: An Alternative to Rotated Principal Components

Abstract

It is fairly common, following a principal component analysis, to rotate components in order to simplify their structure. Here, we propose an alternative to this two-stage procedure which involves only one stage and combines the objectives of variance maximization and simplification. It is shown, using examples, that the new technique can provide alternative ways of interpreting a dataset. Some properties of the technique are investigated using a simulation study.