Synthesis of optically active 3-oxa-carbacyclin precursors featuring asymmetric Horner-Emmons reaction

An enantioselective synthesis of 5 is described. Asymmetric Horner-Emmons reactions with the chiral phosphonate 6 are key steps in the synthesis of the allylic alcohols E-8 and E-11 from the ketones 5 and 9, respectively.     

Capillary electrophoretic separation and fractionation of hydrophobic peptides onto a pre-structured matrix assisted laser desorption/ ionization target for mass spectrometric analysis

A CE separation of hydrophobic peptides followed by fractionation onto a prestructured MALDI target and off-line MS analysis was performed. An improved and partially automated manufacturing procedure of the previously described MALDI target is presented. This target is structurally coated with silicone and especially developed for hydrophobic peptides and proteins. Here, the target plate was designed specifically for the CE fraction collection. Different solvents were evaluated to meet the requirements of peptide solubility and compatibility to both the CE and MALDI methods and to the fractionation procedure. CE-MALDI-MS analysis of nine highly hydrophobic peptides from cyanogen bromide-digested bacteriorhodopsin is demonstrated.     

Synthesis of strained cyclic peptides via an aza-Michael-acyl-transfer reaction cascade

A new method is presented to prepare strained lactams. Esterification of the C-terminus of a dipeptide with β-nitrostyrene or quinoline-type auxiliaries is followed by lactam formation by an intramolecular aza-Michael-acyl-transfer reaction cascade. Ultimately, the cyclic tetrapeptide cyclo[Phe-Tyr-Ala-Gly] has been prepared.     

The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin

The mechanism of cis-trans isomerization of prolyl peptides catalyzed by cyclophilin (CyP) was studied computationally via molecular dynamics (MD) simulations of the transition state (TS) and the cis and trans forms of the ground state (GS), when bound to CyP and when free in aqueous solution. The MD simulations include four enzyme-bound species of tetrapeptide (Suc-Ala-XC([double bond]O)-NPro-Phe-pNA; X = Gly, Trp, Ala, and Leu). In water, the prolyl amide bond is favorably planar with the presence of conformers exhibiting +/-20 degrees twist of the C-N dihedral. In the active site a hydrogen bond between the cis-prolyl amide carbonyl O and the backbone amide N-H of Asn102 retains the 20 degrees twist of the C-N dihedral. The TS structure is characterized by a 90 degrees twist of the amide C-N bond and a more favorable interaction with Asn102 due to the shorter distance between Asn102(HN) and the amide carbonyl O. The conformational change of cis --> TS also involves pyramidalization of the amide N, which results in the formation of a hydrogen bond between the amide N and the guanidino group of Arg55. Both Asn102 and Arg55 are held in the same position in CyP.cis-isomer as in CyP.TS. In the ligand-free CyP the Arg55 guanidino group is highly disorganized and Asn102 is displaced 1 A from the position in the ligand-bound CyP. Thus, the organization of Arg55 and Asn102 occurs upon substrate binding. The geometrical complimentarity of the organized enzyme structure to the TS structure is a result of preferential binding of the proline N and the amide carbonyl of the TS compared to that of GS. However, the N-terminal part (Suc-Ala) becomes repositioned in the TS such that two hydrogen bonds disappear, one hydrogen bond appears and two other hydrogen bonds becomes weaker on the conversion of CyP.cis to CyP.TS. During this conversion, total hydrophobic contact between enzyme and the peptide is preserved. Thus, the interaction energies of GS and TS with enzyme are, as a whole, much alike. This does not support the contention that TS is bound more tightly than GS by K(m)/K(TS) = 10(6) in the cis --> trans reaction. Repositioning of the N-terminal part of the peptide on CyP.TS formation becomes more pronounced when the substrate X residue is changed from Gly < Trp < Ala < Leu. We propose that the larger turning of the N-terminus is responsible for the larger value of the experimentally observed Delta S(++) and Delta H(++), which sum up to little change in Delta G(++). The positioning of the Arg55 and the degree of 20 degrees twist of the amide C-N bond are considered as criteria for Near Attack Conformers (NACs) in cis-trans isomerization. NACs account for approximately 30% of the total GS populations of the cis-isomer. Similar NAC populations were observed with four different substrates. This is consistent with the insensitivity of enzymatic activity to the nature of the X residue. Also, the NAC population in CyP.trans-AAPF was comparable to that in CyP.cis-AAPF, in accord with similar experimentally measured rates of the cis --> trans and trans --> cis reaction in CyP. These NACs, found in CyP.cis and CyP.trans, resemble only one of the four possible TS configurations in the water reaction. The identity of this TS structure (syn/exo) is in accord with experimentally determined KIE values in the enzymatic reaction. However, the geometry of the active site was also complementary to another TS structure (anti/exo) that was not detected in the active site by the same KIE measurements, implying that the geometrical fitness of the TS cannot be a single determining factor for enzymatic reactions.     

Green-/NIR-light-controlled rapid photochromism featuring reversible thermally activated delayed fluorescence and photoelectronic switching

Fluorescent dithienylethene-based photochromic materials have been attracting considerable attention owing to their wide applications in biological and materials sciences. However, the limitations of detrimental UV irradiation for photocyclization, short emission lifetime, and inefficient photoresponsive speed still need to be addressed. Herein, a novel dithienylethene photochromic molecule, BFBDTE, has been prepared by the incorporation of a difluoroboron β-diketonate (BF₂bdk) unit. The strong electron acceptor BF₂bdk not only reduces the energy gap of the open isomer, ensuring visible light-controlled fluorescence switching, but also promotes intersystem crossing for the generation of thermally activated delayed fluorescence (TADF). Upon alternating irradiation with green and NIR light, BFBDTE presents a rare example of photochromism, fluorescence and TADF switching in various polar solvents and a poly(methyl methacrylate) (PMMA) film. Meanwhile, it shows rapid and well repeatable cyclization (12 s) and cycloreversion reactions (20 s) in PMMA, accompanied by fast TADF switching within 11 s. Furthermore, photo-electrochemical measurements reveal a remarkable on-off photoelectronic response (photocurrent density ratio: I_light/I_dark = 684) between the open- and closed-form of BFBDTE. These remarkable merits make BFBDTE promising for photoswitchable molecular devices, optical memory storage systems, NIR detectors, and photoelectric switching.

Controlled by the alternating irradiation of green and NIR light, difluoroboron modifed dithienylethene shows rapid photochromism and photoelectronic switching.     

Effect of hydrophobic modifications in antimicrobial peptides

With increasing resistance development against conventional antibiotics, there is an urgent need to identify novel approaches for infection treatment. Antimicrobial peptides may offer opportunities in this context, hence there has been considerable interest in identification and optimization of such peptides during the last decade in particular, with the long-term aim of developing these to potent and safe therapeutics. In the present overview, focus is placed on hydrophobic modifications of antimicrobial peptides, and how these may provide opportunities to combat also more demanding pathogens, including multi-resistant strains, yet not provoking unacceptable toxic responses. In doing so, physicochemical factors affecting peptide interactions with bacterial and eukaryotic cell membranes are discussed. Throughout, an attempt is made to illustrate how physicochemical studies on model lipid membranes can be correlated to result from bacterial and cell assays, and knowledge from this translated into therapeutic considerations.     

Simultaneous separation of hydrophobic and hydrophilic peptides with a silica hydride stationary phase using aqueous normal phase conditions

The application of a silica hydride modified stationary phase with low organic loading has been investigated as a new type of chromatographic material suitable for the separation and analysis of peptides with electrospray ionization mass spectrometric detection. Retention maps were established to delineate the chromatographic characteristics of a series of peptides with physical properties ranging from strongly hydrophobic to very hydrophilic and encompassing a broad range of pI values (pI 5.5-9.4). The effects of low concentrations of two additives (formic acid and acetic acid) in the mobile phase were also investigated with respect to their contribution to separation selectivity and retention under comparable conditions. Significantly, strong retention of both the hydrophobic and the hydrophilic peptides was observed when high-organic low-aqueous mobile phases were employed, thus providing a new avenue to achieve high resolution peptide separations. For example, simultaneous separation of hydrophobic and hydrophilic peptides was achieved under aqueous normal phase (ANP) chromatographic conditions with linear gradient elution procedures in a single run, whilst further gradient optimization enabled improved peak efficiencies of the more strongly retained hydrophobic and hydrophilic peptides.     

Synthesis of nanosized silicon particles by a rapid metathesis reaction

A solid-state rapid metathesis reaction was performed in a bed of sodium silicofluoride (Na₂SiF₆) and sodium azide (NaN₃) powders diluted with sodium fluoride (NaF), to produce silicon nanoparticles. After a local ignition of Na₂SiF₆+4NaN₃+kNaF mixture (here k is mole number of NaF), the reaction proceeded in a self-sustaining combustion mode developing high temperatures (950–1000 °C) on very short time scales (a few seconds). Silicon nanoparticles prepared by the combustion process was easily separated from the salt byproducts by simple washing with distilled water. The structural and morphological studies on the nanoparticles were carried out using X-ray diffractometer (XRD) and field emission scanning electron microscope (FESEM). The mean size of silicon particles calculated from the FESEM image was about 37.75 nm. FESEM analysis also shows that the final purified product contains a noticeable amount of silicon fibers, dendrites and blocks, along with nanoparticles. The mechanism of Si nanostructures formation is discussed and a simple model for interpretation of experimental results is proposed.     

Thermomorphic system with non-fluorous phase-tagged Ru(BINAP) catalyst: facile liquid/solid catalyst separation and application in asymmetric hydrogenation

The thermomorphic BINAP derivative 1 tagged with long alkyl chains was prepared from (S)-5,5'-diamino BINAP and applied to Ru-catalyzed asymmetric hydrogenation of beta-ketoesters under homogeneous conditions in 3:1 (v/v) ethanol/1,4-dioxane at 60 degrees C with high enantioselectivity (up to 98% ee). Results indicated that the Ru(1) catalyst was easily recovered by simple cooling and precipitation and could be used for at least four cycles without any loss of enantioselectivity.     

Synthesis of porous aromatic framework with Friedel–Crafts alkylation reaction for CO_2 separation

A novel porous aromatic framework, PAF-8, derived from tetraphenylsilane as basic building unit, was successfully synthesized via Friedel–Crafts alkylation reaction. This PAF material had high thermal stability as well as high surface area(785 m~2g~(-1)) calculated from the Brunauer–Emmett–Teller(BET)model. Meanwhile, PAF-8 possessed high performances in gas sorption and especially for CO_2 separation.     

Cationic flocculants carrying hydrophobic functionalities: applications for solid/liquid separation

The flocculation behaviors of three series of polycations with narrow molecular weight distributions carrying hydrophobic substituents on their backbones [poly(N-vinylbenzyl-N,N,N-trimethylammonium chloride), poly(N-vinylbenzyl-N,N-dimethyl-N-butylammonium chloride), and poly(N-vinylbenzylpyridinium chloride)] were investigated in dispersions of monodisperse polystyrene latexes and kaolin. Apparently, the charge density of the polycations decreases with increasing substituent hydrophobicity and increasing molecular weight of the polyelectrolytes. The necessary amount of flocculant for phase separation in dispersions with high substrate surface charge densities increases with increasing hydrophobicity of the polyelectrolyte. Nevertheless, the introduction of hydrophobic functionalities is beneficial, resulting in a substantial broadening of the range between the minimum and maximum amounts of flocculant necessary for efficient flocculation (flocculation window). An increase in ionic strength supports this effect. When the substrate has a low charge density, the hydrophobic interactions play a much more significant role in the flocculation process. Here, the minimum efficient doses remained the same for all three polyelectrolytes investigated, but the width of the flocculation window increased as the polycation hydrophobicity and the molecular weight increased. The necessary amount of flocculant increased with an increase in particle size at constant solid content of the dispersion, as well as with a decreasing number of particles at a constant particle size.     

Interfacial interactions of hydrophobic peptides with lipid bilayers

Four hydrophobic laminin-related peptides and their corresponding parent peptides were synthesized to use them to target liposomes to tumoral cells. The peptide sequence was YIGSR((NH(2))), and hydrophobic residues linked to the alpha-amino terminal end were decanoyl, myristoyl, stearoyl, and cholesteryl-succinoyl. Before use in biological systems, a physicochemical study was carried out in order to determine their interaction with DPPC bilayers that could compromise both the toxicity and the stability of liposomal preparations. The experiments were based on DSC, fluorescence polarization, outer-membrane destabilization, and vesicle leakage. These peptides showed in general a low interaction with the vesicles, promoting in all cases the rigidification of bilayers. This lack of strong disturbances in the ordered state of phospholipid molecules seems more likely due to the similarity of peptide acyl chains with those of lipids than to the absence of interactions. The bulkiness of cholesteryl derivative as well as its tendency toward aggregation resulted in weak interaction levels except in thermograms. The binding of peptides to the surface of liposomes loaded with doxorubicin resulted in preparations with good entrapment yields and small size, required for long circulating vesicles (especially for the myristoyl derivative). The alternative method based on the reaction of parent peptide to the surface of liposomes through an amide linkage was slightly more efficient when the peptide was linked to the carboxy-terminal end of the DSPE-PEG-COOH-containing liposomes. Nevertheless, the final decision must be made with the simplicity of the procedure and reduction in losses during all the steps of the processes taken into consideration.     

Separations of hydrophobic synthetic peptides in counter-current chromatography

Synthetic peptides with many aromatic, aliphatic and especially acidic amino acid residues are not very soluble and require strong solvents for useful partitioning. A chloroform-methanol-acidic solvent system fractionates neutral and basically charged 26-mers to provide high yields. An insoluble 15-mer with 5 Trp residues and 60% overall hydrophobic amino acid content was purified in pyridine-acetic acid and in another basic t-butyl methyl ether-n-butanol-acetonitrile solvent system with high recovery. Two instruments were used, the eccentric-multi-layer hybrid coil planet centrifuge and the new spiral disk planet centrifuge that were able to retain the stationary phase of these solvent systems, some of which have low interfacial tension.     

Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces

The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.     

Synthesis of the C1-C52 fragment of amphidinol 3, featuring a beta-alkoxy alkyllithium addition reaction

An advanced intermediate for the synthesis of amphidinol 3 has been prepared. A cross-metathesis reaction was used to couple the C1-C12 and C13-C26 segments. An unusual beta-alkoxy alkyllithium reagent was generated from this segment and added to a Weinreb amide to assemble the C1-C52 section of amphidinol 3. These compounds represent some of the most advanced intermediates reported to date for the synthesis of amphidinol 3.     

Prediction of retention time of cutinases tagged with hydrophobic peptides in hydrophobic interaction chromatography

Hydrophobic interaction chromatography (HIC) is an important technique for protein purification, which exploits the separation of proteins based on hydrophobic interactions between the stationary phase ligands and hydrophobic regions on the protein surface. One way of enhancing the purification efficiency by HIC is the addition of short sequences of peptide tags to the target protein by genetic engineering, which could reduce the need for extra and expensive chromatographic steps. In the present work, a methodology for predicting retention times of cutinases tagged with hydrophobic peptides in HIC is presented. Cutinase from Fusarium solani pisi fused to tryptophan-proline (WP) tags, namely (WP)2 and (WP)4, and produced in Saccharomyces cerevisiae strains, were used as model proteins. From the simulations, the methodology based on tagged hydrophobic definition proposed by Simeonidis et al. (Phitagged), associated to a quadratic model for predicting dimensionless retention times, showed small differences (RMSE<0.022) between observed and estimated retention times. The difference between observed and calculated retention times being lower than 2.0% (RMSE<0.022) for the two tagged cutinases at three different stationary phases, except for the case of cut_(wp)2 in octyl sepharose-2 M ammonium sulphate. Therefore, we consider that the proposed strategy, based on tagged surface hydrophobicity, allows prediction of acceptable retention times of cutinases tagged with hydrophobic peptides in HIC.     

Synthesis of an adsorbed reversed-phase packing material for the separation of proteins and peptides

We have described the preparation and chromatographic evaluation of an adsorbed hydrophobic stationary phase suitable for reversed-phase chromatography of proteins and peptides. The synthetic procedure involves three steps: the adsorption of a polyamine to the silica surface; crosslinking of the adsorbed polyamine layer with a bis-phenyl difunctional epoxide; and the benzoylation of the remaining accessible amino groups. Performance of this chromatographic material compared favorably with SynChropak RP-8 silica (SynChrom, Linden, IN, U.S.A.) and was stable to 40% formic acid. Good separations were obtained between the components of sample mixtures containing proteins or the cyanogen bromide fragments of sperm whale myoglobin. However, in both cases, the adsorbed hydrophobic stationary phase was less retentive. Furthermore, this medium exhibited slightly different selectivity. Whereas the heme which was present in the cyanogen bromide digest of myoglobin desorbed as the second peak from the RP-8 column, it eluted last from the adsorbed stationary phase. Comparable performance, acid stability and alternate selectivity suggest that this material is an interesting alternative to organosilane reversed-phase coatings.     

High-performance liquid chromatographic method for the determination of prolyl peptides in urine

A rapid and accurate method is described for the determination of prolyl peptides in urine, with specific reference to the dipeptide prolylhydroxyproline, and free hydroxyproline and proline. Free amino acids and peptides were isolated from urine on cation-exchange minicolumns, and free imino acids and prolyl-N-terminal peptides were selectively derivatized with 4-chloro-7-nitrobenzofurazan, after reaction of amino acids and N-terminal aminoacyl peptides with o-phthalaldehyde. The highly fluorescent adducts of imino acids and prolyl peptides were separated on a Spherisorb ODS 2 column by isocratic elution for 12 min using as mobile phase 17.5 mM aqueous trifluoracetic acid solution containing 12.5% acetonitrile (eluent A), followed by gradient elution from eluent A to 40% of 17.5 mM aqueous trifluoroacetic acid solution containing 80% acetonitrile in 20 min. Analytes of interest, in particular the dipeptide prolylhydroxyproline, can be easily quantified by fluorimetric detection (epsilon ex = 470 nm, epsilon em = 530 nm) without interference from primary amino-containing compounds.     

Hydrogen/deuterium exchange of hydrophobic peptides in model membranes by electrospray ionization mass spectrometry

We demonstrate here that the hydrogen/deuterium solvent exchange (HDX) properties of the transmembrane fragment of the M2 protein of Influenza A (M2-TM) incorporated into lipid vesicles or detergent micelles can be studied with straightforward electrospray (ESI) and nanospray mass spectrometry (MS) configurations provided that key factors, including sample preparation techniques, are optimized. Small unilamellar vesicle preparations were obtained by solubilizing dimyristoyl phosphatidylcholine (DMPC) and the M2-TM peptide in aqueous solution with n-octyl-β-D-glycopyranoside, followed by dialysis to remove the detergent. Electron microscopy experiments revealed that subsequent concentration by centrifugation introduced large multilamellar aggregates that were not compatible with ESI-MS. By contrast, a lyophilization-based concentration procedure, followed by thawing above the liquid crystal transition temperature of the lipid component, maintained the liposome size profile and yielded excellent ion fluxes in both ESI-MS and nano-ESI-MS. Using these methods the global HDX profile of M2-TM in aqueous DMPC vesicles was compared with that in methanol, demonstrating that several amide sites were protected from exchange by the lipid membrane. We also show that hydrophobic peptides can be detected by ESI-MS in the presence of a large molar excess of the detergent Triton X-100. The rate of HDX of M2-TM in Triton X-100 micelles was faster than that in DMPC vesicles but slower than when the peptide had been denatured in methanol. These results indicate that the accessibility of backbone amide sites to the solvent can be profoundly affected by membrane protein structure and dynamics, as well as the properties of model bilayer systems.