Pseudoprolines as removable turn inducers: tools for the cyclization of small peptides

The cyclization of small peptides which do not incorporate turn inducers is often difficult. We have developed a method involving the use of removable turn inducers, in the form of pseudoprolines, for the cyclization of difficult peptide sequences. The pseudoprolines induce a cisoid amide bond in the peptide backbone which facilitates cyclization. They are then readily removed to yield a cyclic peptide that does not contain any turn inducers.     

Investigating the scope of pseudoproline assisted peptide cyclization

The cyclization of linear peptides from six to nine amino acids in length and containing between two and four pseudoproline turn inducers derived from serine or threonine was investigated to determine the effect of peptide length, amino acid composition and spacing between the pseudoproline residues on macrocyclization yield.     

A Counterion‐Directed Approach to the Diels–Alder Paradigm: Cascade Synthesis of Tricyclic Fused Cyclopropanes

An approach to the intramolecular Diels–Alder reaction has led to a cascade synthesis of complex carbocycles composed of three fused rings and up to five stereocenters with complete stereocontrol. Computational analysis reveals that the reaction proceeds by a Michael/Michael/cyclopropanation/epimerization cascade in which size and coordination of the counterion is key.     

Assembly of a trinuclear metallo-capsule from a tripodal tris(beta-diketone) derivative and copper(II)

A new metallo-capsule has been synthesised that consists of three copper(II) ions and two molecules of a tris-deprotonated tripodal ligand in which three 2,4-pentanedione groups are linked via their gamma-carbons through thioether spacers to the 1,3,5-positions of a triazine core.     

Selective Removal of Sulfate from Water by Precipitation with a Rigid Bis-amidinium Compound

A simple, readily prepared biphenyl bis-amidinium compound ( 1⋅Cl₂ ) is able to selectively precipitate sulfate from water. The precipitant is effective at concentrations as low as 1 mM and shows complete selectivity against monovalent anions, and high selectivity even against CO₃²⁻ and HPO₄²⁻. It is highly effective (>90 % sulfate removed) in both seawater and highly acidic conditions relevant to mining waste-streams. X-ray crystallography reveals that 1⋅SO₄ forms a tightly packed, anhydrous, structure where each sulfate anion receives eight hydrogen bonds from amidinium N−H hydrogen bond donors.     

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.