Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy.

Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.

Directing GDNF-mediated neuronal signaling with proactively programmable cell-surface saccharide-free glycosaminoglycan mimetics.

A significant barrier to harnessing the power of cell-surface glycosaminoglycans (GAGs) to modulate glial cell-line-derived neurotrophic factor (GDNF) signaling is the difficulty in accessing key GAG structures involved. Here, we report tailored GDNF signaling using synthetic polyproline-based GAG mimetics (PGMs). PGMs deliver the much needed proactive programmability for GDNF recognition and effectively modulate GDNF-mediated neuronal processes in a cellular context.

An efficient strategy to enhance binding affinity and specificity of a known isozyme inhibitor.

The binding profile of a known inhibitor, benzenesulfonamide, against a family of carbonic anhydrase isozymes was efficiently enhanced via high-throughput screening of customized combinatorial one-bead-one-compound peptide libraries modified with the inhibitor molecule. The screening of the conjugate libraries recognized subtle variations in the microenvironments of the target enzyme and thus facilitated the identification of short peptide sequences that bind selectively to a close proximity of the active site. The identified peptide portions contributed significantly to the overall binding of the conjugate peptides with greatly enhanced affinity as well as improved specificity towards the target isozyme. The interactions between the inhibitors and the isozymes were validated by surface plasmon resonance (SPR), pull-down assay and enzymatic activity measurement. This high-throughput approach proved useful and efficient to enhance the binding profile of known inhibitors and may apply to developing effective inhibitors for a wide range of isozyme families.

Target identification of natural and traditional medicines with quantitative chemical proteomics approaches.

Natural and traditional medicines, being a great source of drugs and drug leads, have regained wide interests due to the limited success of high-throughput screening of compound libraries in the past few decades and the recent technology advancement. Many drugs/bioactive compounds exert their functions through interaction with their protein targets, with more and more drugs showing their ability to target multiple proteins, thus target identification has an important role in drug discovery and biomedical research fields. Identifying drug targets not only furthers the understanding of the mechanism of action (MOA) of a drug but also reveals its potential therapeutic applications and adverse side effects. Chemical proteomics makes use of affinity chromatography approaches coupled with mass spectrometry to systematically identify small molecule-protein interactions. Although traditional affinity-based chemical proteomics approaches have made great progress in the identification of cellular targets and elucidation of MOAs of many bioactive molecules, nonspecific binding remains a major issue which may reduce the accuracy of target identification and may hamper the drug development process. Recently, quantitative proteomics approaches, namely, metabolic labeling, chemical labeling, or label-free approaches, have been implemented in target identification to overcome such limitations. In this review, we will summarize and discuss the recent advances in the application of various quantitative chemical proteomics approaches for the identification of targets of natural and traditional medicines.

Effects of incorporation of azido moieties into the hydrophobic core of coiled coil peptides.

The secondary structure of the coiled coil peptides was regulated by altering the azido content at the hydrophobic core. These peptides were further investigated to form higher-order assemblies presumably via azido-mediated interactions.

Tailored chondroitin sulfate glycomimetics via a tunable multivalent scaffold for potentiating NGF/TrkA-induced neurogenesis.

The challenges inherent in the synthesis of large glycosaminoglycan (GAG) polysaccharides have made chemically accessible multivalent glycoligands a valuable tool in the field of GAG mimetics. However, the difficulty of positioning sulfated sugar motifs at desired sites has hindered efforts to precisely tailor their biofunctions. Here, we achieved precise orientation of sulfated disaccharide motifs by taking advantage of a structurally well-defined polyproline scaffold, and describe systematic explorations into the importance of the spatial arrangement of sulfated sugars along the scaffold backbone in designing multivalent glycoligands. Our protein binding studies demonstrate that the specific conformational display of pendant sugars is central to direct their multivalent interactions with NGF. By employing computational modeling and cellular studies, we have further applied this approach to engineer NGF-mediated signaling by regulating the NGF/TrkA complexation process, leading to enhanced neuronal differentiation and neurite outgrowth of PC12 cells. Our findings offer a promising strategy for the pinpoint engineering of GAG-mediated biological processes and a novel method of designing new therapeutic agents that are highly specific to GAG-associated disease.

Investigating fluorescent dyes in fluorescence-assisted screenings.

Screening of bead-based peptide libraries against fluorescent dye-labeled target proteins was found to be significantly influenced by the dye characteristics. Commercially available red fluorescent dyes with net negative charges adversely showed strong interactions with library beads. The introduction of zwitterionic dyes significantly reduced the unwanted interactions, which sheds light upon using the right fluorescent probe for acquisition of reliable results in various fluorescence-assisted applications.

Combinatorial bead-based peptide libraries improved for rapid and robust screenings.

In pursuit of utilizing combinatorial peptide libraries on beads, rapid and robust screening is one of the key steps for the success of high-throughput process. We have introduced improved structural features that greatly facilitate a MALDI-MS/MS-based sequencing, associated with easy and fast synthesis and analysis of such libraries. Whilst commonly used MS-based analysis involves in sophisticated procedures such as ladder synthesis, encoding tags are not required in our MS/MS-based sequencing platform. Fragment peaks in an acquired MS/MS should be outstanding in line with correct identification of parent mass in the preceding MS. To meet these requirements a one-bead-one-compound (OBOC) peptide library was designed by placing a positively charged arginine at C-terminus. As well as enhancing the overall ionization efficiency, arginine appended in all y-ion fragments generates a series of doublet peaks under MS/MS environments, which can speed up the sequencing process in conjunction with high accuracy. It is another strong benefit that the designed library significantly suppresses the adverse formation of sodium ion adducts, which seriously jeopardizes the sequencing, especially of peptides containing negatively charged amino acids. A peptide library constructed with D-amino acids was applied to screening against a clinically significant biomarker, C-reactive protein (CRP). Through the screening of focused libraries narrowed down from a comprehensive library, several hexamer peptide ligands were successfully identified and their binding affinity and specificity towards CRP were validated by surface plasmon resonance (SPR) and dot blot experiments.

Highly selective macrocycle formations by metathesis catalysts fixated in nanopores.

Ruthenium-based metathesis catalysts immobilized on mesocellular siliceous foam (MCF) bearing large nanopores proved highly efficient and selective for macrocyclic ring-closing metathesis (RCM). Kinetic studies revealed that the homogeneous counterpart exhibited far higher activity that accounted for more oligomerization pathways and resulted in less macrocyclization products. Meanwhile, the immobilized catalysts showed lower conversion rates leading to higher yields of macrocyclic products in a given reaction time, with conversion rates and yields dependent upon pore size, catalyst loading density, and linker length. The macrocycle formations via RCM were accelerated by increasing the pore size and decreasing the catalyst loading density while retaining the comparably high yield. The catalysts immobilized on MCF, of which silica surface is rigid and pores are relatively large, showed high conversion rates and yields compared with an analogue immobilized on TentaGel resins, of which backbone becomes flexible upon swelling in the reaction medium. It is noteworthy that the selectivity for the macrocyclic RCM can be significantly improved by tuning the catalyst initiation rates via immobilization onto the support materials in which well-defined three-dimentional network of large nanopores are deployed.

Preparation and characterization of manganese(IV) in aqueous acetic acid.

Mn(IV) acetate was generated in acetic acid solutions and characterized by UV-vis spectroscopy, magnetic susceptibility, and chemical reactivity. All of the data are consistent with a mononuclear manganese(IV) species. Oxidation of several substrates was studied in glacial acetic acid (HOAc) and in 95:5 HOAc-H(2)O. The reaction with excess Mn(OAc)(2) produces Mn(OAc)(3) quantitatively with mixed second-order kinetics, k (25.0 °C) = 110 ± 4 M(-1) s(-1) in glacial acetic acid, and 149 ± 3 M(-1) s(-1) in 95% AcOH, ΔH(‡) = 55.0 ± 1.2 kJ mol(-1), ΔS(‡) = -18.9 ± 4.1 J mol(-1) K(-1). Sodium bromide is oxidized to bromine with mixed second order kinetics in glacial acetic acid, k = 220 ± 3 M(-1) s(-1) at 25 °C. In 95% HOAc, saturation kinetics were observed.

Direct amide synthesis from either alcohols or aldehydes with amines: activity of Ru(II) hydride and Ru(0) complexes.

An in situ generated catalyst from readily available RuH(2)(PPh(3))(4), an N-heterocyclic carbene (NHC) precursor, NaH, and acetonitrile was developed. The catalyst showed high activity for the amide synthesis directly from either alcohols or aldehydes with amines. When a mixture of an alcohol and an aldehyde was reacted with an amine, both of the corresponding amides were obtained with good yields. Homogeneous Ru(0) complexes such as (eta(4)-1,5-cyclooctadiene)(eta(6)-1,3,5-cyclooctatriene)ruthenium [Ru(cod)(cot)] and Ru(3)(CO)(12) were also active in the amidation of an alcohol or an aldehyde with the help of an in situ generated NHC ligand.

Reactions of Mn(II) and Mn(III) with alkyl, peroxyalkyl, and peroxyacyl radicals in water and acetic acid.

The kinetics of oxidation of Mn(II) with acylperoxyl and alkylperoxyl radicals were determined by laser flash photolysis utilizing a macrocyclic nickel complex as a kinetic probe. Radicals were generated photochemically from the appropriate ketones in the presence of molecular oxygen. In both acidic aqueous solutions and in 95% acetic acid, Mn(II) reacts with acylperoxyl radicals with k = (0.5-1.6) x 10(6) M(-1) s(-1) and somewhat more slowly with alkylperoxyl radicals, k = (0.5-5) x 10(5) M(-1) s(-1). Mn(III) rapidly oxidizes benzyl radicals, k = 2.3 x 10(8) M(-1) s(-1) (glacial acetic acid) and 3.7 x 10(8) M(-1) s(-1) (95% acetic acid). The value in 3.0 M aqueous perchloric acid is much smaller, 1 x 10(7) M(-1) s(-1). The decarbonylation of benzoyl radicals in H(2)O has k = 1.2 x 10(6) s(-1).

Structural and kinetic study of reversible CO2 fixation by dicopper macrocyclic complexes. From intramolecular binding to self-assembly of molecular boxes.

A study of the reversible CO2 fixation by a series of macrocyclic dicopper complexes is described. The dicopper macrocyclic complexes [Cu2(OH)2(Me2p)](CF3SO3)2, 1(CF3SO3)2, and [Cu2(mu-OH)2(Me2m)](CF3SO3)2, 2(CF3SO3)2, (Scheme 1) containing terminally bound and bridging hydroxide ligands, respectively, promote reversible inter- and intramolecular CO2 fixation that results in the formation of the carbonate complexes [{Cu2(Me2p)}2(mu-CO3)2](CF3SO3)4, 4(CF3SO3)4, and [Cu2(mu-CO3)(Me2m)](CF3SO3)2, 5(CF3SO3)2. Under a N2 atmosphere the complexes evolve CO2 and revert to the starting hydroxo complexes 1(CF3SO3)2 and 2(CF3SO3)2, a reaction the rate of which linearly depends on [H2O]. In the presence of water, attempts to crystallize 5(CF3SO3)2 afford [{Cu2(Me2m)(H2O)}2(mu-CO3)2](CF3SO3)4, 6(CF3SO3)4, which appears to rapidly convert to 5(CF3SO3)2 in acetonitrile solution. [Cu2(OH)2(H3m)]2+, 7, which contains a larger macrocyclic ligand, irreversibly reacts with atmospheric CO2 to generate cagelike [{Cu2(H3m)}2(mu-CO3)2](ClO4)4, 8(ClO4)4. However, addition of 1 equiv of HClO4 per Cu generates [Cu2(H3m)(CH3CN)4]4+ (3), and subsequent addition of Et3N under air reassembles 8. The carbonate complexes 4(CF3SO3)4, 5(CF3SO3)2, 6(CF3SO3)4, and 8(ClO4)4 have been characterized in the solid state by X-ray crystallography. This analysis reveals that 4(CF3SO3)4, 6(CF3SO3)4, and 8(ClO4)4 consist of self-assembled molecular boxes containing two macrocyclic dicopper complexes, bridged by CO32- ligands. The bridging mode of the carbonate ligand is anti-anti-mu-eta1:eta1 in 4(CF3SO3)4, anti-anti-mu-eta2:eta1 in 6(CF3SO3)4 and anti-anti-mu-eta2:eta2 in 5(CF3SO3)2 and 8(ClO4)4. Magnetic susceptibility measurements on 4(CF3SO3)4, 6(CF3SO3)4, and 8(ClO4)4 indicate that the carbonate ligands mediate antiferromagnetic coupling between each pair of bridged CuII ions (J = -23.1, -108.3, and -163.4 cm-1, respectively, H = -JS1S2). Detailed kinetic analyses of the reaction between carbon dioxide and the macrocyclic complexes 1(CF3SO3)2 and 2(CF3SO3)2 suggest that it is actually hydrogen carbonate formed in aqueous solution on dissolving CO2 that is responsible for the observed formation of the different carbonate complexes controlled by the binding mode of the hydroxy ligands. This study shows that CO2 fixation can be used as an on/off switch for the reversible self-assembly of supramolecular structures based on macrocyclic dicopper complexes.

Nature of Cp*MoO2+ in water and intramolecular proton-transfer mechanism by stopped-flow kinetics and density functional theory calculations.

A stopped-flow study of the Cp*MoO3- protonation at low pH (down to zero) in a mixed H2O-MeOH (80:20) solvent at 25 degrees C allows the simultaneous determination of the first acid dissociation constant of the oxo-dihydroxo complex, [Cp*MoO(OH)2]+ (pKa1 = -0.56), and the rate constant of its isomerization to the more stable dioxo-aqua complex, [Cp*MoO2(H2O)]+ (k-2 = 28 s-1). Variable-temperature (5-25 degrees C) and variable-pressure (10-130 MPa) kinetics studies have yielded the activation parameters for the combined protonation/isomerization process (k-2/Ka1) from Cp*MoO2(OH) to [Cp*MoO2(H2O)]+, viz., DeltaH++= 5.1 +/- 0.1 kcal mol-1, DeltaS++ = -37 +/- 1 cal mol-1 K-1, and DeltaV++ = -9.1 +/- 0.2 cm3 mol-1. Computational analysis of the two isomers, as well as the [Cp*MoO2]+ complex resulting from the dissociation of water, reveals a crucial solvent effect on both the isomerization and the water dissociation energetics. Introducing a solvent model by the conductor-like polarizable continuum model and especially by explicitly inclusion of up to three water molecules in the calculations led to the stabilization of the dioxo-aqua species relative to the oxo-dihydroxo isomer and to the substantial decrease of the energy cost for the water dissociation process. The presence of a water dissociation equilibrium is invoked to account for the unusually low effective acidity (pKa1' = 4.19) of the [Cp*MoO2(H2O)]+ ion. In addition, the computational study reveals the positive role of external water molecules as simultaneous proton donors and acceptors, having the effect of dramatically lowering the isomerization energy barrier.

Influence of an extremely negatively charged porphyrin on the reversible binding kinetics of NO to Fe(III) and the subsequent reductive nitrosylation.

The polyanionic, water-soluble, and non-micro-oxo dimer-forming iron porphyrin (hexadecasodium iron 54,104,154,204-tetra-t-butyl-52,56,102,106,152,156,202,206-octakis[2,2-bis(carboxylato)ethyl]-5,10,15,20-tetraphenylporphyrin), (P16-)FeIII, with 16 negatively charged meso substituents on the porphyrin was synthesized and fully characterized by UV-vis and 1H NMR spectroscopy. A single pKa1 value of 9.90 +/- 0.01 was determined for the deprotonation of coordinated water in the six-coordinate (P16-)FeIII(H2O)2 and as attributed to the formation of the five-coordinate monohydroxo-ligated form, (P16-)FeIII(OH). The porphyrin complex reversibly binds NO in aqueous solution to yield the nitric oxide adduct, (P16-)FeII(NO+)(L), where L = H2O or OH-. The kinetics for the reversible binding of NO were studied as a function of pH, temperature, and pressure using the stopped-flow technique. The data for the binding of NO to the diaqua complex are consistent with the operation of a dissociative mechanism on the basis of the significantly positive values of DeltaS and DeltaV, whereas the monohydroxo complex favors an associatively activated mechanism as determined from the corresponding negative activation parameters. The rate constant, kon = 3.1 x 104 M-1 s-1 at 25 degrees C, determined for the NO binding to (P16-)FeIII(OH) at higher pH, is significantly lower than the corresponding value measured for (P16-)FeIII(H2O)2 at lower pH, namely, kon = 11.3 x 105 M-1 s-1 at 25 degrees C. This decrease in the reactivity is analogous to that reported for other diaqua- and monohydroxo-ligated ferric porphyrin complexes, and is accounted for in terms of a mechanistic changeover observed for (P16-)FeIII(H2O)2 and (P16-)FeIII(OH). The formed nitrosyl complex, (P16-)FeII(NO+)(H2O), undergoes subsequent reductive nitrosylation to produce (P16-)FeII(NO), which is catalyzed by nitrite produced during the reaction. Concentration-, pH-, temperature-, and pressure-dependent kinetic data are reported for this reaction. Data for the reversible binding of NO and the subsequent reductive nitrosylation reaction are discussed in reference to that available for other iron(III) porphyrins in terms of the influence of the porphyrin periphery.

Mechanistic studies on the nitrite-catalyzed reductive nitrosylation of highly charged anionic and cationic Fe(III) porphyrin complexes.

The nitrosyl complexes formed during the binding of NO to the (Pn)FeIII(H2O)2 (n = 8+ and 8-) complexes, viz., (P8-)FeII(H2O)(NO+) and (P8+)FeII(H2O)(NO+), undergo subsequent reductive nitrosylation reactions that were found to be catalyzed by nitrite, which was also produced during the reaction. The effect of the nitrite concentration, pH, temperature, and pressure on the nitrite-catalyzed reductive nitrosylation process was studied in detail for (P8-)FeIII(H2O)2, (P8+)FeIII(H2O)2, and (P8+)FeIII(OH)(H2O), from which rate and activation parameters were obtained. On the basis of these data, we propose mechanistic pathways for the studied reactions. The available results favor the operation of an innersphere electron-transfer process between nitrite and coordinated NO(+). By way of comparison, the cationic porphyrin complex (P8+)FeIII(L)2 (L = H2O or OH-) was found to react with NO2(-) to yield the nitrite adduct (P8+)FeIII(L)(NO2)(-)). A detailed kinetic studied revealed that nitrite binds to (P8+)FeIII(H2O)2 according to a dissociative mechanism, whereas nitrite binding to (P8+)FeIII(OH)(H2O) at higher pH follows an associative mechanism, similar to that reported for the binding of NO to these complexes.

A comparative mechanistic study of the reversible binding of NO to a water-soluble octa-cationic Fe(III) porphyrin complex.

The water-soluble, non-mu-oxo dimer-forming porphyrin, [5,10,15,20-tetrakis-4'-t-butylphenyl-2',6'-bis-(N-methylene-(4''-t-butylpyridinium))porphyrinato]iron(III) octabromide, (P(8+))Fe(III), with eight positively charged substituents in the ortho positions of the phenyl rings, was characterized by UV-vis and 1H NMR spectroscopy and 17O NMR water-exchange studies in aqueous solution. Spectrophotometric titrations of (P(8+))Fe(III) indicated a pKa1 value of 5.0 for coordinated water in (P(8+))Fe(III)(H2O)2. The monohydroxo-ligated (P(8+))Fe(III)(OH)(H2O) formed at 5 < pH < 12 has a weakly bound water molecule that undergoes an exchange reaction, k(ex) = 2.4 x 10(6) s(-1), significantly faster than water exchange on (P(8+))Fe(III)(H2O)2, viz. k(ex) = 5.5 x 10(4) s(-1) at 25 degrees C. The porphyrin complex reacts with nitric oxide to yield the nitrosyl adduct, (P(8+))Fe(II)(NO+)(L) (L = H2O or OH-). The diaqua-ligated (P(8+))Fe(III)(H2O)2 binds and releases NO according to a dissociatively activated mechanism, analogous to that reported earlier for other (P)Fe(III)(H2O)2 complexes. Coordination of NO to (P(8+))Fe(III)(OH)(H2O) at high pH follows an associative mode, as evidenced by negative deltaS(double dagger)(on) and deltaV(double dagger)(on) values measured for this reaction. The observed ca. 10-fold decrease in the NO binding rate on going from six-coordinate (P(8+))Fe(III)(H2O)2 (k(on) = 15.1 x 10(3) M(-1) s(-1)) to (P(8+))Fe(III)(OH)(H2O) (k(on) = 1.56 x 10(3) M(-1) s(-1) at 25 degrees C) is ascribed to the different nature of the rate-limiting step for NO binding at low and high pH, respectively. The results are compared with data reported for other water-soluble iron(III) porphyrins with positively and negatively charged meso substituents. Influence of the porphyrin periphery on the dynamics of reversible NO binding to these (P)Fe(III) complexes as a function of pH is discussed on the basis of available experimental data.

Kinetic and mechanistic studies on the reaction of nitric oxide with a water-soluble octa-anionic iron(III) porphyrin complex.

The polyanionic water-soluble and non-mu-oxo-dimer-forming iron porphyrin iron(III) 5(4),10(4),15(4),20(4)-tetra-tert-butyl-5(2),5(6),15(2),15(6)-tetrakis[2,2-bis(carboxylato)ethyl]-5,10,15,20-tetraphenylporphyrin, (P(8-))Fe(III) (1), was synthesized as an octasodium salt by applying well-established porphyrin and organic chemistry procedures to bromomethylated precursor porphyrins and characterized by standard techniques such as UV-vis and (1)H NMR spectroscopy. A single pK(a1) value of 9.26 was determined for the deprotonation of coordinated water in (P(8-))Fe(III)(H(2)O)(2) (1-H(2)()O) present in aqueous solution at pH <9. The porphyrin complex reversibly binds NO in aqueous solution to give the mononitrosyl adduct, (P(8-))Fe(II)(NO(+))(L), where L = H(2)O or OH(-). The kinetics of the binding and release of NO was studied as a function of pH, temperature, and pressure by stopped-flow and laser flash photolysis techniques. The diaqua-ligated form of the porphyrin complex binds and releases NO according to a dissociative interchange mechanism based on the positive values of the activation parameters DeltaS() and DeltaV() for the "on" and "off" reactions. The rate constant k(on) = 6.2 x 10(4) M(-1) s(-1) (24 degrees C), determined for NO binding to the monohydroxo-ligated (P(8-))Fe(III)(OH) (1-OH) present in solution at pH >9, is markedly lower than the corresponding value measured for 1-H(2)O at lower pH (k(on) = 8.2 x 10(5) M(-1) s(-1), 24 degrees C, pH 7). The observed decrease in the reactivity is contradictory to that expected for the diaqua- and monohydroxo-ligated forms of the iron(III) complex and is accounted for in terms of a mechanistic changeover observed for 1-H(2)O and 1-OH in their reactions with NO. The mechanistic interpretation offered is further substantiated by the results of water-exchange studies performed on the polyanionic porphyrin complex as a function of pH, temperature, and pressure.