Stereochemistry of peptides containing 1-aminocyclopentane carboxylic acid (Acc5). Solution and solid state conformations of Boc-Acc5-Acc5-NHMe.

The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a ?-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III ?-turn conformation in the solid state stabilized by a 4 ? 1 hydrogen bond between the Boc CO and methylamide NH groups. The ?,? values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (?? ± 60°, ?? ±30°).

X-ray studies on crystalline complexes involving amino acids and peptides XIX. Effects of change in chirality in the complexes of succinic acid with dl- and l-arginine

Crystals of dl-arginine hemisuccinate dihydrate (I)(monoclinic; P21/c; a = 5.292, b = 16.296, c = 15.203 Å; α= 92.89°; Z = 4) and l-arginine hemisuccinate hemisuccinic acid monohydrate (II) (triclinic; P1; a = 5.099; b = 10.222, c = 14.626 Å; α= 77.31, β= 89.46, γ= 78.42°; Z = 2) were grown under identical conditions from aqueous solutions of the components in molar proportions. The structures were solved by direct methods and refined to R = 0.068 for 2585 observed reflections in the case of (I) and R = 0.036 for 2154 observed reflections in the case of (11). Two of the three crystallographically independent arginine molecules in the complexes have conformations different from those observed so far in the crystal structures containing arginine. The succinic acid molecules and the succinate ions in the structures are centrosymmetric and planar. The crystal structure of (II) is highly pseudosymmetric. Arginine-succinate interactions in both the complexes involve specific guanidyl-carboxylate interactions. The basic elements of aggregation in both the structures are ribbons made up of alternating arginine dimers and succinate ions. However, the ribbons pack in different ways in the two structures. (II) presents an interesting case in which two ionisation states of the same molecule coexist in a crystal. The two complexes provide a good example of the effect of change in chirality on stoichiometry, conformation, aggregation, and ionisation state in the solid state.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

Development of a Cationic Mucic Acid Polymer-Based Nanoparticle siRNA Delivery System

Cancer chemotherapy has advanced from highly toxic drugs to more targeted treatments in the last 70 years. Chapter 1 opens with an introduction to targeted therapy for cancer. The benefits of using a nanoparticle to deliver therapeutics are discussed. We move on to siRNA in particular, and why it would be advantageous as a therapy. Specific to siRNA delivery are some challenges, such as nuclease degradation, quick clearance from circulation, needing to enter cells, and getting to the cytosol. We propose the development of a nanoparticle delivery system to tackle these challenges so that siRNA can be effective.

Chapter 2 of this thesis discusses the synthesis and analysis of a cationic mucic acid polymer (cMAP) which condenses siRNA to form a nanoparticle. Various methods to add polyethylene glycol (PEG) for stabilizing the nanoparticle in physiologic solutions, including using a boronic acid binding to diols on mucic acid, forming a copolymer of cMAP with PEG, and creating a triblock with mPEG on both ends of cMAP. The goal of these various pegylation strategies was to increase the circulation time of the siRNA nanoparticle in the bloodstream to allow more of the nanoparticle to reach tumor tissue by the enhanced permeation and retention effect. We found that the triblock mPEG-cMAP-PEGm polymer condensed siRNA to form very stable 30-40 nm particles that circulated for the longest time – almost 10% of the formulation remained in the bloodstream of mice 1 h after intravenous injection.

Chapter 3 explores the use of an antibody as a targeting agent for nanoparticles. Some antibodies of the IgG1 subtype are able to recruit natural killer cells that effect antibody dependent cellular cytotoxicity (ADCC) to kill the targeted cell to which the antibody is bound. There is evidence that the ADCC effect remains in antibody-drug conjugates, so we wanted to know whether the ADCC effect is preserved when the antibody is bound to a nanoparticle, which is a much larger and complex entity. We utilized antibodies against epidermal growth factor receptor with similar binding and pharmacokinetics, cetuximab and panitumumab, which differ in that cetuximab is an IgG1 and panitumumab is an IgG2 (which does not cause ADCC). Although a natural killer cell culture model showed that gold nanoparticles with a full antibody targeting agent can elicit target cell lysis, we found that this effect was not preserved in vivo. Whether this is due to the antibody not being accessible to immune cells or whether the natural killer cells are inactivated in a tumor xenograft remains unknown. It is possible that using a full antibody still has value if there are immune functions which are altered in a complex in vivo environment that are intact in an in vitro system, so the value of using a full antibody as a targeting agent versus using an antibody fragment or a protein such as transferrin is still open to further exploration.

In chapter 4, nanoparticle targeting and endosomal escape are further discussed with respect to the cMAP nanoparticle system. A diboronic acid entity, which gives an order of magnitude greater binding (than boronic acid) to cMAP due to the vicinal diols in mucic acid, was synthesized, attached to 5kD or 10kD PEG, and conjugated to either transferrin or cetuximab. A histidine was incorporated into the triblock polymer between cMAP and the PEG blocks to allow for siRNA endosomal escape. Nanoparticle size remained 30-40 nm with a slightly negative ca. -3 mV zeta potential with the triblock polymer containing histidine and when targeting agents were added. Greater mRNA knockdown was seen with the endosomal escape mechanism than without. The nanoparticle formulations were able to knock down the targeted mRNA in vitro. Mixed effects suggesting function were seen in vivo.

Chapter 5 summarizes the project and provides an outlook on siRNA delivery as well as targeted combination therapies for the future of personalized medicine in cancer treatment.

Preliminary study on the photoproduction of hydroxyl radicals in aqueous solution with Aldrich humic acid, algae and Fe(III) under high-pressure mercury lamp irradiation

Under a high-pressure mercury lamp (HPML) and using an exposure time of 4 h, the photoproduction of hydroxyl radicals ((OH)-O-.) could be induced in an aqueous solution containing humic acid (HA). Hydroxyl radicals were determined by high-performance liquid chromatography using benzene as a probe. The results showed that (OH)-O-. photoproduction increased from 1.80 to 2.74 muM by increasing the HA concentration from 10 to 40 mg L-1 at an exposure time of 4 h (pH 6.5). Hydroxyl radical photoproduction in aqueous solutions of HA containing algae was greater than that in the aqueous solutions of HA without algae. The photoproduction of (OH)-O-. in the HA solution with Fe(111) was greater than that of the solution without Fe(III) at pH ranging from 4.0 to 8.0. The photoproduction of (OH)-O-. in HA solution with algae with or without Fe(111) under a 250 W HPML was greater than that under a 125 W HPML. The photoproduction of (OH)-O-. in irradiated samples was influenced by the pH. The results showed that HPML exposure for 4 h in the 4-8 pH range led to the highest (OH)-O-. photoproduction at pH 4.0.

Phase Behavior and self-assembly of poly[N-vinylformamide-co-(acrylic acid)] copolymers under highly acidic conditions

Copolymers of N-vinylformamide and acrylic acid were synthesized by conventional aqueous free-radical polymerization. The phase behavior of the copolymer solutions was investigated through the addition of hydrochloric acid and the variation of the temperature. With a moderate content of N-vinylformamide, the copolymers showed complex phase behaviors. Under low-acidity conditions, a suspending liquid was formed, whereas under high-acidity conditions, the random copolymers could assemble into round nanoparticles with a broad particle size distribution.

Novel temperature- and pH-responsive graft copolymers composed of poly(L-glutamic acid) and poly(N-isopropylacrylamide)

A series of novel temperature- and pH-responsive graft copolymers, poly(L-glutamic acid)-g-poly(N-isopropylacrylamide), were synthesized by coupling amino-semitelechelic poly(N-isopropylacrylamide) with N-hydroxysuccinimide-activated poly(L-glutamic acid). The graft copolymers and their precursors were characterized, by ESI-FTICR Mass Spectrum, intrinsic viscosity measurements and proton nuclear magnetic resonance (H-1 NMR). The phase-transition and aggregation behaviors of the graft copolymers in aqueous solutions were investigated by the turbidity measurements and dynamic laser scattering.

Antioxidant Sensors Based on Iron Diethylenetriaminepentaacetic Acid, Hematin, and Hemoglobin Modified TiO2 Nanoparticle Printed Electrodes

Antioxidant amperometric sensors based on iron-containing complexes and protein modified electrodes were developed. Indium tin oxide glass was printed with TiO2 nanoparticles, onto which iron-containing compounds and protein were adsorbed. When applied with negative potentials, the dissolved oxygen is reduced to H2O2 at the electrode surface, and the H2O2 generated in situ oxidizes Fe-II to Fe-III, and then electrochemical reduction of Fe-III therefore gives rise to a catalytic current. In the presence of antioxidants, H2O2 was scavenged, the catalytic current was reduced, and the decreased current signal was proportional to the quantity of existing antioxidants. A kinetic model was proposed to quantify the H2O2 scavenging capacities of the antioxidants. With the use of the sensor developed here, antioxidant measurements can be done quite simply: put the sensor into the sample solutions (in aerobic atmosphere), perform a cathodic polarization scan, and then read the antioxidant activity values. The present work can be complementary to the previous studies of antioxidant sensor techniques based on OH radicals and superoxide ions scavenging methods, but the sensor developed here is much easier to fabricate and use.

Triblock poly(lactic acid)-b-poly(ethylene glycol)-b-poly(lactic acid)/paclitaxel conjugates: Synthesis, micellization, and cytotoxicity

A triblock poly(lactic acid)-b-poly(ethylene glycol)-b-poly(lactic acid) (PLA-PEG-PLA)/paclitaxel (PTX) conjugate was synthesized by the reaction of carboxyl-terminated copolymer PLA-PEG-PLA with PTX in the presence of dicyclohexylcarbodiimide and dimethylaminopyridine. Carboxyl-terminated copolymer PLA-PEG-PLA was prepared by the reaction of the hydroxyl end groups in copolymer PLA-PEG-PLA with succinic anhydride. Its structure was confirmed by NMR and gel permeation chromatography. The PLA-PEG-PLA/PTX conjugates could self-assemble into micelles in aqueous solutions with a low critical micelle concentration. Dynamic light scattering and environmental scanning electron microscopy analyses of the PLA-PEG-PLA/PTX micelles revealed their spherical structure and size of 220 nm. The antitumor activity of the conjugate against woman Hela cancer cells, evaluated by the 3-(4,5-dimethylthiazol2-yl)-2,5-diphenyl tetrazolium bromide method, showed that the conjugates had an antitumor activity similar to that of pure PTX. The obtained PLA-PEG-PLA/PTX conjugates are expected to be used in clinical practice.

Polyelectrolyte complexes based on chitosan and poly(L-glutamic acid)

Polyelectrolyte complexes (PECs) were prepared by mixing aqueous solutions of chitosan (CS) and poly(L-glutamic acid) (PLGA) at various pH. It was found that the stoichiometry of the PECs depends on pH.An investigation of the PECs using Fourier transform infrared spectroscopy proved that the formation of the complexes is due to electrostatic interaction between –NH3 + groups of CS and –COO− groups of PLGA. The solid PECs were characterized using wide-angle X-ray diffraction, which suggested that a strong interaction occurs between the two polymers at pH = 4 or 5 and relatively weak interaction at pH = 3. These results were further confirmed by thermogravimetric analysis data. Transmission electron microscopy showed that the complexes have a spherical shape. The effect of ionic strength on the size of the PECs was also studied using dynamic light scattering. It was found that the size of the PECs is dependent on pH.

Extraction and separation of cadmium(II), iron(III), zinc(II), and europium(III) by Cyanex302 solutions using hollow fiber membrane modules

The mass transfer behaviors of Cd(II), Fe(III), Zn(II), and Eu(III) in sulfuric acid solution using microporous hollow fiber membrane (HFM) containing bis(2,4,4-trimethylpentyl)monothiophosphinic acid (commercial name Cyanex302) were investigated in this paper. The experimental results showed that the values of the mass transfer coefficients (K-w) decreased with an increase of H+ concentration and increased with an increase of extractant Cyanex302 concentration. The mass transfer resistance of Eu3+ was the largest because K-w value of Eu3+ was the smallest. The order of mass transfer rate of metal ions at low pH was Cd > Zn > Fe > Eu. Mixtures of Zn2+ and Eu3+ or of Zn2+ and Cd2+ were well separated in a counter-current circulation experiment using two modules connected in series at different initial acidity and concentration ratio. These results indicate that a hollow fiber membrane extractor is capable of separating the mixture compounds by controlling the acidity of the aqueous solution and by exploiting different mass transfer kinetics. The interfacial activity of Cyanex302 in sulfuric acid solution was measured and interfacial parameters were obtained according to Gibbs adsorption equation.

Copper hexacyanoferrate multilayer films on glassy carbon electrode modified with 4-aminobenzoic acid in aqueous solution

4-Aminobenzoic acid (4-ABA) was covalently grafted on a glassy carbon electrode (GCE) by amine cation radical formation during the electrooxidation process in 0.1 M KCl aqueous Solution. X-ray photoelectron spectroscopy (XPS) measurement proves the presence of 4-carboxylphenylamine on the GCE. Electron transfer processes of Fe(CN)(6)(3-) in solutions of various pHs at the modified electrode are studied by both cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Changing the solution pH would result in the variation of the terminal group's charge state, based on which the surface pK(a) values were estimated. The copper hexacyanoferrate (CuHCF) multilayer films were formed on 4-ABA/GCE prepared in aqueous solution, and which exhibit good electrochemical behavior with high stability.

Kinetics and mechanism of Yb(III) extraction and separation from Y(III) with mixtures of bis(2,4,4-trimethylpentyl)phosphinic acid and 2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester

The ytterbium(III) extraction kinetics and mechanism with mixtures of bis(2,4,4-trimethylpentyl)phosphinic acid (Cyanex272) and 2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester (P507) dissolved in heptane have been investigated by constant interfacial cell with laminar flow. The effects of the stirring rate, temperature, extractant concentration, and pH on the extraction with mixtures of Cyanex272 and P507 have been studied. The results are compared with those of the system with Cyanex272 or P507 alone. It is concluded that the Yb(III) extraction rate is enhanced with mixtures extractant of Cyanex272 and P507 according to their values of the extraction rate constant, which is due to decreasing the activation energy of the mixtures. At the same time, the mixtures exhibits no synergistic effects for Y(III), which provides better possibilities for Yb(III) and Y(III) separations at a proper conditions than anyone alone. Moreover, thermodynamic extraction separation Yb(III) and Y(III) by the mixtures has been discussed, which agrees with kinetics results. Extraction rate equations have also been obtained, and through the approximate solutions of the flux equation, diffusion parameters and thickness of the diffusion film have been calculated.