Lysine Derivatives Research Articles

Methods of the site-selective solid phase synthesis of peptide-derived Amadori products

Two procedures of glycated peptides' synthesis have been developed. The first method involves reductive alkylation of the epsilon-amino groups of lysine with 2,3:4,5-di-O-isopropylidene-beta-D-arabino-hexos-2-ulo-2,6-pyranose in the presence of sodium cyanoborohydride on solid support. The second one uses a new fully protected lysine derivative, which is a building block designed for direct introduction of the glycated lysine moiety into a peptide, according to the standard solid phase synthesis protocol. The applicability of the proposed methods for the synthesis of peptide-derived Amadori products is discussed. The structure of the synthesized glycated peptides was confirmed by high-resolution mass spectrometry and enzymatic hydrolysis. Circular dichroism studies, performed in water solution, revealed that the formation of the Amadori rearrangement product in the lysine side chain does not influence significantly the conformational preferences of the peptides studied. However, when the solvent was changed to trifluoroethanol, the glycated peptides preferred beta-turn conformation.

IBX/TBAB-Mediated Oxidation of Primary Amines to Nitriles

The combination of o-iodoxybenzoic acid (IBX) and tetrabutylammonium bromide (TBAB) efficiently oxidizes primary amines to the corresponding nitriles in good to excellent yield under mild conditions. The reaction is racemization-free when applied to a chiral lysine derivative.

Lipeo-sCT: A novel reversible lipidized salmon calcitonin derivative, its biophysical properties and hypocalcemic activity

We have previously described the design and synthesis of Mal-sCT and compared its biological activity with its reversible counterpart, REAL-sCT. Mal-sCT was salmon calcitonin (sCT) conjugated with two molecules of an ɛ-maleimido lysine derivative of palmitic acid via non-reversible thioether bonds at its cysteine residues while REAL-sCT was sCT conjugated with two molecules of a cysteine derivative of palmitic acid via reducible disulfide bonds at its cysteine residues. Neither compounds when dissolved in water could reproducibly improved the oral deliverability of sCT. The purpose of this study was to characterize and evaluate Lipeo-sCT, a novel sCT analog conjugated via reducible disulfide bonds with two amphiphilic groups consisting of a hydrophobic hexadecyl moiety attached via an ether bond to a hydrophilic triethylene glycol moiety. Lipeo-sCT was successfully synthesized by a 4-step reaction, purified and identified by ESI–MS. Analysis by dynamic light scattering (DLS) and transmission electron microscopy (TEM) suggested it had a propensity to form aggregates in water, although the aggregation behavior was controllable by modulating solvent polarity. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay indicated a lack of cytotoxicity against the Caco-2 cells at up to 100 μM. Compared with sCT, Lipeo-sCT lowered plasma calcium to comparable levels when injected subcutaneously at 0.15 mg/kg into female Wistar rats, but the hypocalcemic activity of Lipeo-sCT was prolonged by at least 6 more hours. This was attributable to a continual regeneration of sCT from Lipeo-sCT. sCT was detectable in plasma 8 h following subcutaneous injection of Lipeo-sCT (1.90 mg/kg), while Lipeo-sCT was not observed in plasma at all time points. By comparison, sCT was detectable in plasma for less than 2.5 h following subcutaneous injection at an equivalent dose (1.50 mg/kg). Data from this study complement those of previous studies, and add to the body of knowledge correlating the in vivo activity of lipidized peptides to their physical properties.

Propargyl 4-[18F]fluorobenzoate: A Putatively More Stable Prosthetic Group for the Fluorine-18 Labeling of Biomolecules via Click Chemistry

Faster and more efficient approaches for radiolabeling biomolecules with short-lived (18)F are in dire need. Herein we report a new (18)F-labeled prosthetic group containing an acetylene function that permits the labeling of biomolecules via click chemistry. This template, propargyl 4-[(18)F]fluorobenzoate ([(18)F]PFB) was synthesized from a quaternary salt precursor in decay-corrected radiochemical yields of 58 +/- 31%. Several model compounds containing an azide moiety-benzyl azide, two lysine derivatives and a transglutaminase-reactive peptide-were labeled using [(18)F]PFB via a click reaction in decay-corrected radiochemical yields of 88 +/- 4%, 79 +/- 33%, 75 +/- 5%, and 37 +/- 31%, respectively. Our results suggest that the novel agent [(18)F]PFB is a potentially useful template for the (18)F-labeling of biomolecules via click chemistry.

Recognition of Non-α-amino Substrates by Pyrrolysyl-tRNA Synthetase

Pyrrolysyl-tRNA synthetase (PylRS), an aminoacyl-tRNA synthetase (aaRS) recently found in some methanogenic archaea and bacteria, recognizes an unusually large lysine derivative, l-pyrrolysine, as the substrate, and attaches it to the cognate tRNA (tRNAPyl). The PylRS–tRNAPyl pair interacts with none of the endogenous aaRS–tRNA pairs in Escherichia coli, and thus can be used as a novel aaRS–tRNA pair for genetic code expansion. The crystal structures of the Methanosarcina mazei PylRS revealed that it has a unique, large pocket for amino acid binding, and the wild type M. mazei PylRS recognizes the natural lysine derivative as well as many lysine analogs, including Nɛ-(tert-butoxycarbonyl)-l-lysine (Boc-lysine), with diverse side chain sizes and structures. Moreover, the PylRS only loosely recognizes the α-amino group of the substrate, whereas most aaRSs, including the structurally and genetically related phenylalanyl-tRNA synthetase (PheRS), strictly recognize the main chain groups of the substrate. We report here that wild type PylRS can recognize substrates with a variety of main-chain α-groups: α-hydroxyacid, non-α-amino-carboxylic acid, Nα-methyl-amino acid, and d-amino acid, each with the same side chain as that of Boc-lysine. In contrast, PheRS recognizes none of these amino acid analogs. By expressing the wild type PylRS and its cognate tRNAPyl in E. coli in the presence of the α-hydroxyacid analog of Boc-lysine (Boc-LysOH), the amber codon (UAG) was recoded successfully as Boc-LysOH, and thus an ester bond was site-specifically incorporated into a protein molecule. This PylRS–tRNAPyl pair is expected to expand the backbone diversity of protein molecules produced by both in vivo and in vitro ribosomal translation.

Molecular Clip and Tweezer Introduce New Mechanisms of Enzyme Inhibition

Artificial molecular clips and tweezers, designed for cofactor and amino acid recognition, are able to inhibit the enzymatic activity of alcohol dehydrogenase (ADH). IC50 values and kinetic investigations point to two different new mechanisms of interference with the NAD(+)-dependent oxidoreductase: While the clip seems to pull the cofactor out of its cleft, the tweezer docks onto lysine residues around the active site. Both modes of action can be reverted to some extent, by appropriate additives. However, while cofactor depletion by clip 1 was in part restored by subsequent NAD(+) addition, the tweezer (2) inhibition requires the competitive action of lysine derivatives. Lineweaver-Burk plots indicate a competitive mechanism for the clip, with respect to both substrate and cofactor, while the tweezer clearly follows a noncompetitive mechanism. Conformational analysis by CD spectroscopy demonstrates significant ADH denaturation in both cases. However, only the latter case (tweezer-lysine) is reversible, in full agreement with the above-detailed enzyme switch experiments. The complexes of ADH with clips or tweezer can be visualized in a nondenaturing gel electrophoresis, where the complexes migrate toward the anode, in contrast to the pure enzyme which approaches the cathode. Supramolecular chemistry has thus been employed as a means to control protein function with the specificity of artificial hosts opening new avenues for this endeavor.

Monosaccharide-Based Water-Soluble Fluorescent Tags

Monosaccharides are fluorescently labeled under microwave irradiation by N-(coumarin-3-carbonyl)benzotriazole 4. 1,2:3,4-di- O-isopropylidene-alpha- d-galactopyranose 9 gives 12 (90%), 1,2:5,6-di- O-isopropylidene- d-glucose 10 gives 13 (89%), 2,3:5,6-di- O-isopropylidene-alpha- d-mannofuranose 11 gives 14 (65%) (all by O-acylation) and 2,3,4,5-tetra- O-pivaloyl-beta- d-galactopyranosylamine 15 gives 16 (60%) (by N-acylation). Similarly, the coumarin-containing activated lysine derivatives 7 and 8 afford the l-lysine-scaffold based coumarin labeled sugars 17, 18a, b, and 19 (67-85%) which, after removal of the diisopropylidene groups, provide water-soluble fluorescent derivatives.

Protein Adduct Formation by Glucuronide Metabolites of Permethrin

Biomonitoring of exposure to the insecticide permethrin is usually performed by analysis of its urinary metabolites 3-phenoxybenzoic acid (3-PBA) or cis/ trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane-1-carboxylic acid (Cl 2 CA). We are engaged in the development of a methodology to assess the cumulative internal dose of exposure to permethrin, which is based on the assumption that (reactive) glucuronide conjugates of the major permethrin metabolites 3-PBA and Cl 2 CA will form persistent (weeks to months) adducts to proteins, in analogy with the glucuronide conjugates of structurally related drugs. The 3-PBA and Cl 2 CA beta-glucuronide metabolites of permethrin have been successfully chemically and enzymatically synthesized. Their identities have been assessed by means of (1)H NMR spectroscopy and liquid chromatography-tandem mass spectrometry. The reactivity of these metabolites with various amino acids, peptides, and albumin in human plasma has been studied. Several distinct adducts could be identified by liquid chromatography-tandem mass spectrometry. After pronase digestion of albumin isolated from exposed human plasma, various lysine derivatives resulted with favorable mass spectrometric and chromatographic properties. Covalent binding was quantified by using [(14)C]-3-PBA glucuronide; >1.5% of total radioactivity was bound to proteins. It is envisaged that the obtained results can form a firm basis for the development of a protein adduct-based methodology for biomonitoring exposure to permethrin. In view of the widespread use of permethrin, the toxicological relevance of protein binding by its metabolites will be addressed in more detail in future work.

Protein N-Acylation: H2O2-Mediated Covalent Modification of Protein by Lipid Peroxidation-Derived Saturated Aldehydes

Various lines of evidence indicate that the oxidative modification of protein and the subsequent accumulation of the degenerated proteins have been found in cells and tissues during aging, oxidative stress, and in a variety of pathological states. The critical agents that give rise to this protein degeneration may be represented by aldehydes. Although the covalent modification of proteins by aldehydes alone has been well-studied, the effect of reactive oxygen species, such as H2O2, upon aldehyde modification of the protein has received little attention. We have now established a unique protein modification in which H2O2 and, to a lesser extent, alkyl hydroperoxides mediate the binding of alkanals to the lysine residues of protein to generate structurally unusual N-acylation products. Upon the reaction of a lysine-containing peptide, N(alpha)-benzoylglycyl-lysine, with hexanal in the presence of H2O2, a product containing one molecule of hexanal per peptide was detected. On the basis of the chemical and spectroscopic evidence, the product was identified to be the acylation product, N(epsilon)-hexanoyllysine. H2O2 mediated the N-acylation of the lysine derivative by the saturated aldehydes of 1-6 carbons in length. The H2O2-mediated acylation of the protein was immunochemically confirmed by reaction of the proteins with hexanal in the presence of H2O2. Furthermore, the enhanced N-acylations (N-acetylation and N-hexanoylation) were also observed in the kidney of rats exposed to ferric nitrilotriacetate, a well-characterized inducer of oxidative stress. Mechanistic studies using a phosphonium lysine derivative suggest a Baeyer-Villiger-like reaction proceeding through peroxide addition to the aldehyde Schiff base. These data suggest that the hydroperoxides, including H2O2, might be involved not only in the oxidative modification of protein but also in the covalent binding of the saturated aldehydes to proteins under oxidative stress.

Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases

We report a method for site-specifically incorporating l-lysine derivatives into proteins in mammalian cells, based on the expression of the pyrrolysyl-tRNA synthetase (PylRS)-tRNA Pyl pair from Methanosarcina mazei. Different types of external promoters were tested for the expression of tRNA Pyl in Chinese hamster ovary cells. When tRNA Pyl was expressed from a gene cluster under the control of the U6 promoter, the wild-type PylRS-tRNA Pyl pair facilitated the most efficient incorporation of a pyrrolysine analog, N ε - tert-butyloxycarbonyl- l-lysine (Boc-lysine), into proteins at the amber position. This PylRS-tRNA Pyl system yielded the Boc-lysine-containing protein in an amount accounting for 1% of the total protein in human embryonic kidney (HEK) 293 cells. We also created a PylRS variant specific to N ε -benzyloxycarbonyl- l-lysine, to incorporate this long, bulky, non-natural lysine derivative into proteins in HEK293. The recently reported variant specific to N ε -acetyllysine was also expressed, resulting in the genetic encoding of this naturally-occurring lysine modification in mammalian cells.

Targeted drug delivery by in vivo coupling to endogenous albumin: an albumin-binding prodrug of methotrexate (MTX) is better than MTX in the treatment of murine collagen-induced arthritis

Objective:To examine the effect of an albumin-binding prodrug of methotrexate (MTX) in the treatment of murine collagen-induced arthritis (CIA).Methods:The prodrug AWO54 with the formula EMC-d-Ala-Phe-Lys-Lys-MTX binds selectively to the cysteine-34...

Three-input chemical logic circuits based on a new fluorescent sensor for ATP and Cu2+in aqueous solution

Abstract A new l -lysine derivative featuring an anthracene unit is synthesized and characterized by elemental analysis, ESI-MS, 1H-NMR, and 13C-NMR. It can selectively bind ATP in acidic aqueous solutions, and be used as a highly selective fluorescent chemosensor for Cu2+ at neutral pH, resulting in fluorescence quenching. According to these characters, two combinational logic circuits are fabricated on a single molecule with three chemical inputs [H+(IN1), OH−(IN2), ATP (IN31)] and [H+(IN1), OH−(IN2), Cu2+(IN32)], respectively.

Model Studies on Protein Glycation

Mixtures of N alpha-hippurylarginin, N alpha-hippuryllysine, and glyoxal were incubated in the absence and presence of N alpha-acetylcysteine in order to assess the individual reactivity of these nucleophilic amino acid residues. The incubations were performed under atmospheric and high hydrostatic pressure (400 MPa), and, at the same time, beta-casein was reacted with glyoxal. The results showed that arginine is the main partner for glyoxal in the absence of cysteine, whereas a lysine derivatization was not apparent. In the presence of cysteine, however, arginine was almost completely protected from the reaction, whereas a noticeable formation of lysine derivatives, mainly carboxymethyllysine, was observed. Based on these findings, a reaction mechanism is proposed to explain the influence of cysteine on the reaction.

Solid phase and solution synthesis of NvocLys(CO(CH2)5NH–NBD)OCH2CN, a trifunctional fluorescent lysine derivative

Herein, we describe a general strategy for the facile synthesis of a multifunctional amino acid derivative bearing both fluorescent and photolabile groups such as the lysine derivative NvocLys(CO(CH2)5NH-NBD)OCH2CN (1) that can be used as a biophysical tool for studying protein structure. The synthetic strategy involves functionalization of the amine groups while the amino acid is attached to a solid support, followed by esterification of the carboxylic acid in solution. The solid support protects the caboxylic acid, preventing a side reaction associated with the synthesis in solution and obviating the need for chromatographic purification of several intermediates. This synthetic strategy can be used for the preparation of a variety of amino acid derivatives with unusual alpha-amine and side chain functionalities.

ChemInform Abstract: N‐Trifluoroacyl Lysine Derivatives in the Synthesis of L‐Lysyl‐L‐glutamic Acid.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase

Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the “22nd” genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA Pyl with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the “open” states to the “closed” states upon AMPPNP binding. On the other hand, the β7-β8 hairpin exhibits multiple conformational states, the open, intermediate (β7-open/β8-open and β7-closed/β8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the β7-β8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the β7-β8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA Pyl. Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and α-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.

Supramolecular Gels Formed by Amphiphilic Low‐Molecular‐Weight Gelators of Nα,Nε‐Diacyl‐L‐Lysine Derivatives

Simple L-lysine derivatives, N(alpha)-hexanoyl-N(epsilon)-lauroyl-L-lysine (1), its alkali metal salts (2-4), and two-component compounds that consist of 1 with 2 to 4, were synthesized and their hydrogelation and organogelation properties were studied. Addition of hydrochloric acid to an aqueous solution of the alkali metal salt at room temperature produced a translucent hydrogel. This hydrogelation occurred as a result of a change in nanostructure from micelle-like aggregates to nanofibers, which was induced by partial protonation of the carboxylate to form a carboxylic acid. On the other hand, two-component low-molecular-weight gelators exhibited amphiphilic gelation behavior and functioned as not only hydrogelators, but also as organogelators. FTIR studies revealed that lateral ionic interactions between the carboxylate, alkali metal cation, carboxylic acid, and protons, in addition to hydrogen-bonding and van der Waals interactions play a very important role in hydrogelation. Furthermore, it was found that the water-insoluble carboxylic acid compound underwent a precipitation-dissolution transition with a thermally reversible sol-gel transition in the two-component gelator systems.

Adsorption of Metal Ions on an Activated Carbon/L‐Lysine Derivative Hybrid Compound

AbstractThe new compound Nϵ‐(4‐amino‐1,6‐dihydro‐1‐methyl‐5‐nitroso‐6‐oxopyrimidin‐2‐yl)‐L‐lysine (H2L) has been synthesised and its molecular structure determined by single‐crystal X‐ray diffraction methods. The Brönsted acid/base character of H2L has been determined in water in the pH range 2.5–10.0, and the nature of the observed protonation steps determined by potentiometric and spectrophotometric methods. The adsorption of H2L on a commercial activated carbon (AC) in aqueous solution is irreversible, mainly due to the electronic behaviour of the π system of the pyrimidine moiety. The adsorption of H2L on the AC provides a route to develop NH3+‐CHR‐COO–‐type functions on the AC surface, thereby yielding a new hybrid material with an enhanced adsorption capacity for metal ions in aqueous solution. The adsorption of NiII, CuII, ZnII and CdII ions on the functionalised AC has been studied and the results analysed on the basis of the reactivity data for several pyrimidine ligand/metal ion systems. The results, which show an enhancement of the adsorption capacity of the new material with respect to the unfunctionalised AC, are compared with analogous materials studied previously.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Succination of Protein Thiols during Adipocyte Maturation

Although obesity is a risk factor for development of type 2 diabetes and chemical modification of proteins by advanced glycoxidation and lipoxidation end products is implicated in the development of diabetic complications, little is known about the chemical modification of proteins in adipocytes or adipose tissue. In this study we show that S-(2-succinyl)cysteine (2SC), the product of chemical modification of proteins by the Krebs cycle intermediate, fumarate, is significantly increased during maturation of 3T3-L1 fibroblasts to adipocytes. Fumarate concentration increased > or =5-fold during adipogenesis in medium containing 30 mm glucose, producing a > or =10-fold increase in 2SC-proteins in adipocytes compared with undifferentiated fibroblasts grown in the same high glucose medium. The elevated glucose concentration in the medium during adipocyte maturation correlated with the increase in 2SC, whereas the concentration of the advanced glycoxidation and lipoxidation end products, N(epsilon)-(carboxymethyl)lysine and N(epsilon)-(carboxyethyl)lysine, was unchanged under these conditions. Adipocyte proteins were separated by one- and two-dimensional electrophoresis and approximately 60 2SC-proteins were detected using an anti-2SC polyclonal antibody. Several of the prominent and well resolved proteins were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. These include cytoskeletal proteins, enzymes, heat shock and chaperone proteins, regulatory proteins, and a fatty acid-binding protein. We propose that the increase in fumarate and 2SC is the result of mitochondrial stress in the adipocyte during adipogenesis and that 2SC may be a useful biomarker of mitochondrial stress in obesity, insulin resistance, and diabetes.

Trypsin Activity Measurement in Fish and Mammals

Trypsin activity is usually measured using synthetic substrates, principally amide and ester derivatives of the amino acids lysine or arginine. The aim of this study was to compare trypsin activity measurements done with two assays using amide substrates and two assays using ester substrates. The activity of purified commercial enzyme extracts (bovine and Atlantic cod, Gadus morhua) were measured as was the activity in animal tissues (mice and Atlantic cod) at 5, 15, 25, and 35°C. The results clearly showed the potential impact of the substrate choice on the results when comparing different taxonomic groups at different temperatures. The sensitivity, the measurement reproducibility and even the thermal sensitivity of the enzyme varies according to the assay used.