Thermodynamic destabilization of azurin by four different tetramethylguanidinium amino acid ionic liquids.

The thermal unfolding of the copper redox protein azurin was studied in the presence of four different amino acid-based ionic liquids (ILs), all of which have tetramethylguanidium as cation. The anionic amino acid includes two with alcohol side chains, serine and threonine, and two with carboxylic acids, aspartate and glutamate. Control experiments showed that amino acids alone do not significantly change protein stability and pH changes anticipated by the amino acid nature have only minor effects on the protein. With the ILs, the protein is destabilized and the melting temperature is decreased. The two ILs with alcohol side chains strongly destabilize the protein while the two ILs with acid side chains have weaker effects. Unfolding enthalpy (ΔHunf°) and entropy (ΔSunf°) values, derived from fits of the unfolding data, show that some ILs increase ΔHunf°while others do not significantly change this value. All ILs, however, increase ΔSunf°. MD simulations of both the folded and unfolded protein conformations in the presence of the ILs provide insight into the different IL-protein interactions and how they affect the ΔHunf° values. The simulations also confirm that the ILs increase the unfolded state entropies which can explain the increased ΔSunf° values.

Hydrogen-Bonding Interactions at the DNA Terminus Promote Extension from Methylguanine Lesions by Human Extender DNA Polymerase ζ.

Chemically induced DNA lesions can become DNA replication substrates that are bypassed by low-fidelity DNA polymerases. Following nucleotide misinsertion opposite a DNA lesion, the extension step can contribute to preserving such errors and lead to genomic instability and cancer. DNA polymerase ζ, a B-family polymerase, is proficient as an extender polymerase that catalyzes elongation; however, the chemical factors that impact its DNA replication are not understood. This study addresses the question of how DNA polymerase ζ achieves extension by examining the ability of recombinant human DNA polymerase ζ to extend from a series of methylated guanine lesions. The influence of H-bonding was examined by placing structurally altered nucleoside analogues and canonical bases opposite G, O6-MeG, N1-MeG, and N2-MeG. We determined that terminal base pairs with the highest proclivity for H-bonding were most efficiently extended in both primer extension assays and steady-state kinetic analysis. In contrast, when no H-bonding was possible at the DNA terminus, the least efficient steady-state kinetics were observed. To evaluate H-bonding protein minor groove interactions that may underlie this phenomenon, we performed computational modeling with Escherichia coli DNA polymerase II, a homologue for DNA polymerase ζ. The modeling data together with the primer extension assays demonstrate the importance of having a carbonyl group on the primer strand that can interact with a lysine residue found to be conserved in many B-family polymerases, including human Pol ζ. These data provide a model whereby interbase H-bonding interactions at the DNA terminus promote lesion bypass and extension by human DNA polymerase ζ.

The Anticonvulsant Zonisamide Inhibits Hydroxyl Radical Generated from Methylguanidine.

Methylguanidine (MG) is a known nephrotoxin and neurotoxin, and an intracisternal injection of MG can induce convulsions in experimental animals. In this in vitro study, we examined the inhibitory effects of the antiepileptic agent zonisamide (ZNS) on hydroxyl radicals (•OH) generated from MG by using an electron spin resonance (ESR) technique. ZNS scavenged •OH generated from MG in a dose-dependent manner through direct scavenging during the auto-oxidation of MG. The rate constant of ZNS reacting with the •OH was at a near diffusion-controlled rate. These findings indicate that ZNS might detoxify MG and could thus protect against convulsive disorders.

N'-3-(Trifluoromethyl)phenyl Derivatives of N-Aryl-N'-methylguanidines as Prospective PET Radioligands for the Open Channel of the N-Methyl-d-aspartate (NMDA) Receptor: Synthesis and Structure-Affinity Relationships.

N-Methyl-d-aspartate (NMDA) receptor dysfunction has been linked to several neuropsychiatric disorders, including Alzheimer's disease, epilepsy, drug addiction, and schizophrenia. A radioligand that could be used with PET to image and quantify human brain NMDA receptors in the activated "open channel" state would be useful for research on such disorders and for the development of novel therapies. To date, no radioligands have shown well-validated efficacy for imaging NMDA receptors in human subjects. In order to discover improved radioligands for PET imaging, we explored structure-affinity relationships in N'-3-(trifluoromethyl)phenyl derivatives of N-aryl-N'-methylguanidines, seeking high affinity and moderate lipophilicity, plus necessary amenability for labeling with a positron-emitter, either carbon-11 or fluorine-18. Among a diverse set of 80 prepared N'-3-(trifluoromethyl)phenyl derivatives, four of these compounds (13, 19, 20, and 36) displayed desirable low nanomolar affinity for inhibition of [(3)H](+)-MK801 at the PCP binding site and are of interest for candidate PET radioligand development.

Structure and dynamics of a salt-bridge model system in water and DMSO.

We study the interaction between the ions methylguanidinium and trifluoroacetate dissolved in D2O and dimethylsulfoxide with linear infrared spectroscopy and femtosecond two-dimensional infrared spectroscopy. These ions constitute model systems for the side chains of arginine and glutamic and aspartic acid that are known to form salt bridges in proteins. We find that the salt-bridge formation of methylguanidinium and trifluoroacetate leads to a significant acceleration of the vibrational relaxation dynamics of the antisymmetric COO stretching vibration of the carboxyl moiety of trifluoroacetate. Salt-bridge formation has little effect on the rate of the spectral fluctuations of the CN stretching vibrations of methylguanidinium. The anisotropy of the cross peaks between the antisymmetric COO stretching vibration of trifluoroacetate and the CN stretching vibrations of methylguanidinium reveals that the salt-bridge is preferentially formed in a bidentate end-on configuration in which the two C=O groups of the carboxylate moiety form strong hydrogen bonds with the two -NH2 groups of methylguanidinium.

Emerging nitrogenous disinfection byproducts: Transformation of the antidiabetic drug metformin during chlorine disinfection of water.

As an environmental contaminant of anthropogenic origin metformin is present in the high ng/L- up to the low µg/L-range in most surface waters. Residues of metformin may lead to the formation of disinfection by-products during chlorine disinfection, when these waters are used for drinking water production. Investigations on the underlying chemical processes occurring during treatment of metformin with sodium hypochlorite in aqueous medium led to the discovery of two hitherto unknown transformation products. Both substances were isolated and characterized by HPLC-DAD, GC-MS, HPLC-ESI-TOF, (1)H-NMR and single-crystal X-ray structure determination. The immediate major chlorination product is a cyclic dehydro-1,2,4-triazole-derivate of intense yellow color (Y; C4H6ClN5). It is a solid chlorimine of limited stability. Rapid formation was observed between 10 °C and 30 °C, as well as between pH 3 and pH 11, in both ultrapure and tap water, even at trace quantities of reactants (ng/L-range for metformin, mg/L-range for free chlorine). While Y is degraded within a few hours to days in the presence of light, elevated temperature, organic solvents and matrix constituents within tap water, a secondary degradation product was discovered, which is stable and colorless (C; C4H6ClN3). This chloroorganic nitrile has a low photolysis rate in ambient day light, while being resistant to heat and not readily degraded in the presence of organic solvents or in the tap water matrix. In addition, the formation of ammonia, dimethylamine and N,N-dimethylguanidine was verified by cation exchange chromatography.

DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.

DNA molecules are highly charged semi-flexible polymers that are involved in a wide variety of dynamical processes such as transcription and replication. Characterizing the binding landscapes around DNA molecules is essential to understanding the energetics and kinetics of various biological processes. We present a curvilinear coordinate system that fully takes into account the helical symmetry of a DNA segment. The latter naturally allows to characterize the spatial organization and motions of ligands tracking the minor or major grooves, in a motion reminiscent of sliding. Using this approach, we performed umbrella sampling (US) molecular dynamics (MD) simulations to calculate the three-dimensional potentials of mean force (3D-PMFs) for a Na+ cation and for methyl guanidinium, an arginine analog. The computed PMFs show that, even for small ligands, the free energy landscapes are complex. In general, energy barriers of up to ~5 kcal/mol were measured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the minor groove. We shed light on the way the minor groove geometry, defined mainly by the DNA sequence, shapes the binding landscape around DNA, providing heterogeneous environments for recognition by various ligands. For example, we identified the presence of dissociation points or "exit ramps" that naturally would terminate sliding. We discuss how our findings have important implications for understanding how proteins and ligands associate and slide along DNA.

New N-aryl-N'-(3-(substituted)phenyl)-N'-methylguanidines as leads to potential PET radioligands for imaging the open NMDA receptor.

An expansive set of N-aryl-N'-(3-(substituted)phenyl)-N'-methylguanidines was prepared in a search for new leads to prospective PET ligands for imaging of the open channel of the N-methyl-d-aspartate (NMDA) receptor in vivo. The N-aryl rings and their substituents were varied, whereas the N-methyl group was maintained as a site for potential labeling with the positron-emitter, carbon-11 (t1/2=20.4min). At micromolar concentration, over half of the prepared compounds strongly inhibited the binding of [(3)H]TCP to its binding site in the open NMDA receptor in vitro. Four ligands displayed affinities that are similar or superior to those of the promising SPECT radioligand ([(123)I]CNS1261). The 3'-dimethylamino (19; Ki 36.7nM), 3'-trifluoromethyl (20; Ki 18.3nM) and 3'-methylthio (2; Ki 39.8nM) derivatives of N-1-naphthyl-N'-(phenyl)-N'-methylguanidine were identified as especially attractive leads for PET radioligand development.

The nonenzymatic decomposition of guanidines and amidines.

To establish the rates and mechanisms of decomposition of guanidine and amidine derivatives in aqueous solution and the rate enhancements produced by the corresponding enzymes, we examined their rates of reaction at elevated temperatures and used the Arrhenius equation to extrapolate the results to room temperature. The similar reactivities of methylguanidine and 1,1,3,3-tetramethylguanidine and their negative entropies of activation imply that their decomposition proceeds by hydrolysis rather than elimination. The influence of changing pH on the rate of decomposition is consistent with attack by hydroxide ion on the methylguanidinium ion (k2 = 5 × 10(-6) M(-1) s(-1) at 25 °C) or with the kinetically equivalent attack by water on uncharged methylguanidine. At 25 °C and pH 7, N-methylguanidine is several orders of magnitude more stable than acetamidine, urea, or acetamide. Under the same conditions, the enzymes arginase and agmatinase accelerate substrate hydrolysis 4 × 10(14)-fold and 6 × 10(12)-fold, respectively, by mechanisms that appear to involve metal-mediated water attack. Arginine deiminase accelerates substrate hydrolysis 6 × 10(12)-fold by a mechanism that (in contrast to the mechanisms employed by arginase and agmatinase) is believed to involve attack by an active-site cysteine residue.

Copper-catalyzed etherification of arene C-H bonds.

A method for direct, auxiliary-assisted alkoxylation and phenoxylation of ß-sp(2) C-H bonds of benzoic acid derivatives and γ-sp(2) C-H bonds of amine derivatives is reported. The reaction employs (CuOH)2CO3 catalyst, air as an oxidant, phenol or alcohol coupling partner, DMF, pyridine, or DMPU solvent, and K2CO3, tetramethylguanidine, or K3PO4 base at 70-130 °C.

Uraemic toxins generated in the presence of fullerene C60, carbon-encapsulated magnetic nanoparticles, and multiwalled carbon nanotubes.

Uraemic toxins-creatol and N-methylguanidine-are generated in conversion of creatinine in water in the presence of various forms of carbon such as fullerene C60, carbon-encapsulated magnetic nanoparticles, and multiwalled carbon nanotubes and oxygen. The conversion degree for creatinine was different for fullerene C60, CEMNPs, and MWCNTs and was 9% (3.6% creatol, 5.4% N-methylguanidine), 35% (12% creatol, 23% N-methylguanidine), and 75% (16% creatol, 59% N-methylguanidine), respectively.

Enhanced aqueous Suzuki-Miyaura coupling allows site-specific polypeptide 18F-labeling.

The excesses of reagents used in protein chemistry are often incompatible with the reduced or even inverse stoichiometries used for efficient radiolabeling. Analysis and screening of aqueous Pd(0) ligand systems has revealed the importance of a guanidine core and the discovery of 1,1-dimethylguanidine as an enhanced ligand for aqueous Suzuki-Miyaura cross-coupling. This novel Pd catalyst system has now allowed the labeling of small molecules, peptides, and proteins with the fluorine-18 prosthetic [(18)F]4-fluorophenylboronic acid. These findings now enable site-specific protein (18)F-labeling under biologically compatible conditions using a metal-triggered reaction.

The different interactions of lysine and arginine side chains with lipid membranes.

The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin, and cell-penetrating peptides. These roles are thought to stem from the strong interactions and disruptive influences of these amino acids on lipid membranes. In this study, we employ fully atomistic molecular dynamics simulations to observe, quantify, and compare the interactions of Lys and Arg with saturated phosphatidylcholine membranes of different thickness. We make use of both charged (methylammonium and methylguanidinium) and neutral (methylamine and methylguanidine) analogue molecules, as well as Lys and Arg side chains on transmembrane helix models. We find that the free energy barrier experienced by a charged Lys crossing the membrane is strikingly similar to that of a charged Arg (to within 2 kcal/mol), despite the two having different chemistries, H-bonding capability, and hydration free energies that differ by ∼10 kcal/mol. In comparison, the barrier for neutral Arg is higher than that for neutral Lys by around 5 kcal/mol, being more selective than that for the charged species. This can be explained by the different transport mechanisms for charged or neutral amino acid side chains in the membrane, involving membrane deformations or simple dehydration, respectively. As a consequence, we demonstrate that Lys would be deprotonated in the membrane, whereas Arg would maintain its charge. Our simulations also reveal that Arg attracts more phosphate and water in the membrane, and can form extensive H-bonding with its five H-bond donors to stabilize Arg-phosphate clusters. This leads to enhanced interfacial binding and membrane perturbations, including the appearance of a trans-membrane pore in a thinner membrane. These results highlight the special role played by Arg as an amino acid to bind to, disrupt, and permeabilize lipid membranes, as well as to sense voltages for a range of peptide and protein activities in nature and in engineered bionanodevices.

Liquid-vapor interfacial properties of aqueous solutions of guanidinium and methyl guanidinium chloride: influence of molecular orientation on interface fluctuations.

The guanidinium cation (C(NH2)3(+)) is a highly stable cation in aqueous solution due to its efficient solvation by water molecules and resonance stabilization of the charge. Its salts increase the solubility of nonpolar molecules ("salting-in") and decrease the ordering of water. It is one of the strongest denaturants used in biophysical studies of protein folding. We investigate the behavior of guanidinium and its derivative, methyl guanidinium (an amino acid analogue) at the air-water surface, using atomistic molecular dynamics (MD) simulations and calculation of potentials of mean force. Methyl guanidinium cation is less excluded from the air-water surface than guanidinium cation, but both cations show orientational dependence of surface affinity. Parallel orientations of the guanidinium ring (relative to the Gibbs dividing surface) show pronounced free energy minima in the interfacial region, while ring orientations perpendicular to the GDS exhibit no discernible surface stability. Calculations of surface fluctuations demonstrate that, near the air-water surface, the parallel-oriented cations generate significantly greater interfacial fluctuations compared to other orientations, which induces more long-ranged perturbations and solvent density redistribution. Our results suggest a strong correlation with induced interfacial fluctuations and ion surface stability. These results have implications for interpreting molecular-level, mechanistic action of this osmolyte's interaction with hydrophobic interfaces as they impact protein denaturation (solubilization).

An innovative strategy for sulfopeptides analysis using MALDI-TOF MS reflectron positive ion mode.

Sulfation of tyrosine residues is a key posttranslational modification in the regulation of various cellular processes. As such, the detection and localization of tyrosine sulfation is an essential step toward the elucidation of the physiological and pathological roles of this process. Despite substantial advances, intact sulfated peptides are still difficult to detect by MALDI-MS due to the extreme lability of the sulfo-moiety. The present report demonstrates for the first time how intact sulfated peptides can be directly and specifically detected by MALDI-MS in positive reflectron mode by using pyrenemethylguanidine (pmg) as a noncovalent derivatizing agent and an ionization enhancer. This new method allows the determination of the degree of sulfation of sulfopeptides pure or in mixtures. Moreover, the observation of specific peaks in the mass spectra enables a rapid and unambiguous discrimination between phospho- and sulfopeptides.

Theoretical studies on models of lysine-arginine cross-links derived from α-oxoaldehydes: a new mechanism for glucosepane formation.

Availability and high reactivity of α-oxoaldehydes have been approved by experimental techniques not only in vivo systems but also in foodstuffs. In this article we re-examine the mechanism of glucosepane formation by using computational model chemistry. Density functional theory has been applied to propose a new mechanism for glucosepane formation through reaction of α-oxoaldehydes with methyl amine (MA) and methyl guanidine (MGU) models of lysine and arginine residues respectively. This non enzymatic process can be described in three main steps: (1) Schiff base formation from methyl amine, methyl glyoxal (MGO) (2) addition of methyl guanidine and (3) addition of glyceraldehyde. We show that this process is thermodynamically possible and presents a rate-determining step with a reasonable free energy barrier equal to 37.8 kcal mol(-1) in water solvent. Comparisons were done with the mechanism formation of GODIC (glyoxal-derived imidazolium cross-link) and MODIC (methyl glyoxal-derived imidazolium cross-link), two other important cross-links in vivo.

Inhibitory effect of antioxidants on hydroxyl radical generation from methylguanidine: an ESR study.

Methylguanidine (MG) is known as not only a nephrotoxin but also as a neurotoxine. We have previously showed that MG itself generates hydroxyl radicals (*OH) in an in vitro study. In this study, we examined the inhibitory effects of ascorbate, EPC-K(1) (alpha-tocopheryl-L-ascorbate-2-O-phosphate diester), Trolox (water-soluble vitamin E analogue), and glutathione (GSH) on *OH generation from MG using an electron spin resonance (ESR) spectrometry with spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). It was found that these compounds have potent inhibitory effect on *OH generation from MG in the order of ascorbate > GSH > EPC-K(1) > Trolox.

Matrix-assisted laser desorption/ionization mass spectrometric analysis of polysulfated-derived oligosaccharides using pyrenemethylguanidine.

A better understanding of the biological roles of carbohydrates requires the use of tools able to provide efficient and rapid structural information. Unfortunately, highly acidic oligomers-such as polysulfated oligosaccharides-are very challenging to characterize because of their high polarity, structural diversity, and sulfate lability. These features pose special problems for matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis because polysulfated carbohydrates exhibit poor ionization efficiency and usually do not produce any signal. The present report demonstrates how MALDI-MS can be used to derive structural and compositional information from pure and mixed fractions of polysulfated oligosaccharides. Indeed, pyrenemethylguanidine (pmg, a derivatizing agent and ionization efficiency enhancer) was used for the analysis of di- to decasaccharides, carrying from two to nine sulfate groups. The method is applied to various highly sulfated chondroitin and carrageenan oligosaccharides as well as to the analysis of mixtures of compounds. In the mass spectra, the observation of a unique pmg-complexed ladder of peaks in both ionization modes allows an easy and rapid determination of both the number of sulfate groups carried by the analyte and its molecular weight. Moreover, we have developed a software tool for the rapid and automatic structural elucidation of carrageenans based on the mass spectra obtained.

Effect of N-[Imino(4-morpholyl)methyl]guanidine on the oxidative status in rats with toxic hepatitis.

The hepatoprotective and antioxidant properties of a synthetic biguanide N-[imino(4-morpholyl)methyl]guanidine (IMMG) were prognosticated by the method of computer prediction. Administration of IMMG was accompanied by a decrease in serum transaminase activity in rats with toxic hepatitis, which reflects inhibition of hepatocyte cytolysis. IMMG treatment was followed by a decrease in biochemiluminescence parameters reflecting the intensity of free radical oxidation. We revealed an increase in activity of aconitase, which was reduced during toxic hepatitis. The content of citrate in the liver and serum was returned to normal under these conditions. IMMG also increased activities of superoxide dismutase and catalase and total antioxidant activity in rat liver. Our results suggest that the hepatoprotective effect of IMMG is associated with its antioxidant activity.

A supramolecular fluorescence sensor for pyrovanadate as a functional model of vanadium haloperoxidase.

A novel basket-shaped tris(pyrene guanidinium) receptor was synthesized which binds pyrovanadate and pyrophosphate with Ka > 107 M-1. The binding of both anions is associated with quenching of the excimer fluorescence of the pyrenes. The supramolecular vanadate complex catalyzes the bromination of activated C-H bonds and hence is an enzyme mimic of vanadium haloperoxidases.