Chemical synthesis of Ser/Thr AMPylated peptides

A method for the solid phase chemical synthesis of AMPylated Ser/Thr containing peptides is described. Peptides were phosphonylated using the H-phosphonate method, then the adenosine moiety was introduced using 2′,3′-isopropylidene adenosine and the condensing reagent PyBOP. Oxidation with iodine yielded the desired AMPylated product in good yield following acidolytic cleavage from the resin support.     

Synthesis and characterization of acrylated phosphonates and their polymers having 1,3-dioxolane and 1,3-dioxane moieties derived from brominated cyclic acetals of polyols through the Arbuzov reaction. II

Glycerol, D -mannitol, and D -sorbitol were converted into their mono- and di-O-1,3-dioxolane and 1,3-dioxane bromoethylidene derivatives through a transacetalation reaction with bormoacetaldehyde diethyl acetal under controlled conditions. These brominated dioxolane or dioxane derivatives were subsequently phosphonylated through the Arbuzov reaction. The phosphonylated cyclic acetals were used as precursors for the synthesis of acrylated phosphonate monomers. All these compounds have been characterized by elemental analysis and spectroscopic (IR, ¹H-,¹³C-, ³¹P-NMR and mass) methods. A mixture of 1,3-dioxane and 1,3-dioxolane derivatives was obtained with D -sorbitol, whereas the reaction products with glycerol and D -mannitol yielded primarily the 1,3-dioxolane derivatives. The acrylated phosphonates of glycerol and mannitol have been polymerized and studied on the basis of gel permeation chromatography and their spectral and thermal properties. The acrylated phosphonates, monomers, and polymers, were shown to have a large capacity to solvate and dissolve heavy metal salts. This results in a dramatic increase (> 100°C) of the glass transition temperature of these polymers.     

铜催化炔丙醇酯与β-羰基膦酸酯的不对称[3+2]环加成反应合成手性膦酰化2,3-二氢呋喃

手性2,3-二氢呋喃衍生物是一类重要的杂环化合物,广泛存在于天然产物和生物活性分子中.它们也经常被用于手性四氢呋喃化合物的不对称合成.因此,人们发展了很多合成手性2,3-二氢呋喃化合物的方法,如有机小分子催化的多米诺迈克尔-烷基化反应、“中断的”Feist-Bénary反应或改进的 Feist-Bénary反应.此外,过渡金属催化的手性2,3-二氢呋喃的不对称合成在近些年引起了人们的极大关注. Ozawa等通过 Pd-催化2,3-二氢呋喃的动力拆分方法获得了手性2-芳基-2,3-二氢呋喃. Evans发展了一种 Sc-催化联烯硅和乙醛酸乙酯的[3+2]环加成反应合成手性2,3-二氢呋喃的方法.最近, Fu和 Tang等发展了 Cu催化烯酮和重氮化合物的[4+1]环加成反应合成手性2,3-二氢呋喃的方法.在 Nishibayashi和 van Maarseveen的开创性工作之后, Cu催化的不对称炔丙基转化反应取得了很大的进展.最近,我们发展了一类新的三齿手性 P,N,N-配体,在 Cu催化不对称炔丙基取代、脱羧炔丙基取代、[3+2]、[3+3]和[4+2]环加成反应中表现出优秀的对映和非对映选择性.其中,我们发现采用 Cu催化炔丙醇酯和β-酮酯的[3+2]环加成反应,能高对映选择性地获得手性2,3-二氢呋喃.我们设想,采用β-羰基膦酸酯代替β-酮酯,通过这种 Cu催化[3+2]环加成反应,将可以合成一类具有重要生物活性的手性膦酰化2,3-二氢呋喃化合物.基于这种设想,本文使用手性 P,N,N-配体,通过 Cu催化炔丙醇酯与β-羰基膦酸酯的不对称[3+2]环加成反应,以很好的收率和最高92% ee的对映选择性获得了一系列光学活性的膦酰化2,3-二氢呋喃化合物.我们以炔丙醇酯1a与β-羰基膦酸酯2a为标准底物,优化了反应条件,考察了配体、Cu盐、碱和反应温度等对反应收率和对映选择性的影响.我们确定了最佳的反应条件：以4b为配体,以 Cu(OTf)2为铜盐,以t-BuOK为碱,以 MeOH为溶剂,–20oC反应24 h.在此条件下,我们对β-羰基磷酸酯2的适用范围进行了考察.结果表明,各种苯基取代的β-羰膦磷酸酯均能得到很好的收率和对映选择性.苯环上取代基的空间效应对反应的对映选择性影响不大,但对反应收率影响较大,与相应3-取代或4-取代底物相比较,2-取代的底物获得的收率较低.苯环对位取代基的电子效应对反应的影响不大,给电子基或吸电子基的底物,均得到了较好的收率和对映选择性.杂环取代的底物同样适用于该反应,以90%的收率和89% ee的对映选择性获得了相应的[3+2]环加成产物.对于烷基底物,虽然反应的产率略低,但是得到了高达92% ee的产物.此外,我们对炔丙醇酯底物的适用范围也进行了考察.结果表明,该体系对于各种取代的炔丙醇酯底物均可以获得较高的收率和良好的对映选择性.总之,本文发展了一种铜催化炔丙醇酯与β-羰基膦酸酯的不对称[3+2]环加成反应的方法,成功合成了手性膦酰化2,3-二氢呋喃化合物.通过使用一个结构刚性的酮亚胺三齿 P,N,N-配体,以很好的收率和最高92% ee的对映选择性获得了一系列光学活性的膦酰化2,3-二氢呋喃化合物.     

Ring-closing metathesis and ring-closing metathesis-isomerisation approach to 1-phosphonylated 2-benzazocines

An RCM strategy has been developed for the synthesis of phosphonylated benzazocines and their corresponding isomerised analogues. The aminophosphonate precursors were obtained by a one-pot three-component condensation in moderate yield.     

V-type nerve agents phosphonylate ubiquitin at biologically relevant lysine residues and induce intramolecular cyclization by an isopeptide bond

Toxic organophosphorus compounds (e.g., pesticides and nerve agents) are known to react with nucleophilic side chains of different amino acids (phosphylation), thus forming adducts with endogenous proteins. Most often binding to serine, tyrosine, or threonine residues is described as being of relevance for toxicological effects (e.g., acetylcholinesterase and neuropathy target esterase) or as biomarkers for post-exposure analysis (verification, e.g., albumin and butyrylcholinesterase). Accordingly, identification of novel protein targets might be beneficial for a better understanding of the toxicology of these compounds, revealing new bioanalytical verification tools, and improving knowledge on chemical reactivity. In the present study, we investigated the reaction of ubiquitin (Ub) with the V-type nerve agents Chinese VX, Russian VX, and VX in vitro. Ub is a ubiquitous protein with a mass of 8564.8 Da present in the extra- and intracellular space that plays an important physiological role in several essential processes (e.g., proteasomal degradation, DNA repair, protein turnover, and endocytosis). Reaction products were analyzed by matrix-assisted laser desorption/ionization-time-of-flight- mass spectrometry (MALDI-TOF MS) and μ-high-performance liquid chromatography online coupled to UV-detection and electrospray ionization MS (μHPLC-UV/ESI MS). Our results originally document that a complex mixture of at least mono-, di, and triphosphonylated Ub adducts was produced. Surprisingly, peptide mass fingerprint analysis in combination with MALDI and ESI MS/MS revealed that phosphonylation occurred with high selectivity in at least 6 of 7 surface-exposed lysine residues that are essential for the biological function of Ub. These reaction products were found not to age. In addition, we herein report for the first time that phosphonylation induced intramolecular cyclization by formation of an isopeptide bond between the ε-amino group of a formerly phosphonylated lysine and the side chain of an adjacent acidic glutamic acid residue.

Metal-free entry to phosphonylated isoindoles by a cascade of 5-exo-dig cyclization, a [1,3]-alkyl shift, and aromatization under microwave heating

[reaction: see text] When o-ethynylbenzyl alpha-aminophosphonates are heated under microwave conditions, a rearrangement occurs which results in the formation of phosphonylated isoindoles. The rearrangement consists of a 5-exo-dig cyclization followed by a [1,3]-alkyl shift and finally aromatization.     

Determination of protein adducts of organophosphorus nerve agents in blood plasma

A comparative study of the efficiency of procedures for the determination of the biomarkers of organophosphorus agents (OPAs) in blood plasma was performed. It was found that the gas chromatography–mass spectrometry determination of OPAs reactivated from the composition of protein adducts is a rapid method for the detection of exposure to OPAs. The liquid chromatography–mass spectrometry determination of phosphonylated butyrylcholinesterase and albumin fragments modified with OPA residues provides an opportunity to perform more sensitive and retrospective analysis. The tyrosine adducts of OPAs with serum albumin and other blood plasma proteins are not prone to dealkylation in the course of aging; in the series of the test markers, they possess the greatest diagnostic value because they make it possible to determine the precise structure a toxic agent after the longest time interval after exposure. The tentative limit of detection of OPA markers varies from 0.1 to 1.0 ng/mL.     

Synthesis of New 2-Aryl-4-[1,2-bis(dialkoxyphosphoryl)vinyl]-5-ethoxy-1,3-oxazoles

Russian Journal of General Chemistry - A series of new substituted phosphonylated 1,3-oxazoles, 2-aryl-4-[1,2-bis(dialkoxyphosphoryl)vinyl]-5-ethoxy-1,3-oxazoles, was obtained by the reaction of...     

Reactivity of substituted 3‐(diethylphosphonyl)‐1‐(trialkylsilyl)alka‐1,3‐dienes: Regioselective epoxidation and cyclopropanation reactions

When treated with electrophilic m‐CPBA reagent, dienes 1 were efficiently epoxidized at the silylated 1,2‐double bond exclusively. Otherwise, regioselective cyclopropanation of the phosphonylated 3,4‐double bond was achieved by using the nucleophilic Corey's reagent. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10:231–236, 1999     

A direct method for the synthesis of nucleoside 5′-methylenebis(phosphonate)s from nucleosides

An efficient method for the preparation of nucleoside 5′-methylenebis(phosphonate)s has been developed. Unprotected nucleosides are phosphonylated directly with methylenebis(phosphonic dichloride). Reaction conditions were optimized to prevent side product formation.     

纳升级电喷雾离子源-四极杆-飞行时间质谱中磷酸化肽的离子抑制作用

目前磷酸化蛋白质组学研究中的主要技术是蛋白质酶解产生的磷酸化肽的质谱检测。但是实际样品中的磷酸化肽(特别是多磷酸化肽)很难被检测到。其原因普遍认为是由于质谱检测时,非磷酸化肽抑制磷酸化肽。但也有认为非磷酸化肽对磷酸化肽没有抑制作用。另外磷酸化肽之间是否存在离子抑制作用还没有报道。本文采用相同氨基酸序列的标准磷酸化肽和非磷酸化肽,将其单独和混合进行质谱检测,通过对比混合前后磷酸化肽的信号强度,证明了非磷酸化肽对磷酸化肽有离子抑制作用;单磷酸化肽对二磷酸化肽有一定的抑制作用,但不太显著;单磷酸化肽对三磷酸化肽、二磷酸化肽对三磷酸化肽均有显著的离子抑制作用。该研究为今后单磷酸化肽和多磷酸化肽的分段富集和检测提供了有力的证明。     

A novel class of chemically modified iodo-containing resins: design, synthesis and application to mass spectrometry-based proteome analysis

A novel class of chemically modified iodo-containing resins with isotope-labeled tagging for mass spectrometry-based proteome analysis is described. This iodo-containing resin contains a thiol-reactive group that is used to capture the cysteine (Cys)-containing peptides from peptide mixtures, one 'tag' amino acid, and an aminomethyl polystyrene resin with Rink Amide Linker. The 'tag' amino acid is synthesized in both heavy and light isotope-coded forms and therefore permits the direct relative quantification of peptides/proteins through mass spectrometric analysis. In the iodo-containing resin strategy, the Cys-containing peptides of two samples covalently captured by either light or heavy iodo-containing resin were mixed and washed extensively under stringent conditions. Then the Cys-containing peptides were retrieved by acid-catalyzed elution. Finally, the eluted peptides were directly analyzed by micro liquid chromatography/mass spectrometry for identification and relative quantification. The iodo-containing resins were synthesized by a simple but effective method. Their abilities to identify and quantify the Cys-containing part in two samples were proved by the analysis of mixtures of amino acids, peptides and proteins.     

超高效纳升液相色谱-电喷雾串联质谱鉴定重组人Ⅱ型肿瘤坏死因子受体-抗体融合蛋白

采用超高效纳升液相色谱-电喷雾串联质谱对重组人Ⅱ型肿瘤坏死因子受体-抗体融合蛋白进行了分析.样品经胰蛋白酶酶切后,进行液相色谱-串联质谱分析和数据库检索.结果表明, 分别有5个和7个肽段匹配于人肿瘤坏死因子受体和人Ig gamma-1 chain C region.比对分析表明,重组人Ⅱ型肿瘤坏死因子受体-抗体融合蛋白中检测到的人IgG的7个肽段完全与人IgG1的序列匹配,与其它3个亚型只有部分肽段匹配.说明重组人Ⅱ型肿瘤坏死因子受体-抗体融合蛋白一级结构正确,Fc片段确实为人IgG1的Fc片段.     

Mass-based classification (MBC) of peptides: Highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation

Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1,000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than +/-0.1 ppm. At a peptide mass of 1,500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution table of theoretical peptides. A mass distribution table of nonphosphorylated and monophosphorylated peptides with a bin width of 0.1 mu was made available via the open web site www.peptidecomposer.com.     

A new methodology for the synthesis of fluorinated exo-glycals and their time-dependent inhibition of UDP-galactopyranose mutase

Fluorinated carbohydrates constitute a very important class of mechanistic probes for glycosyl-processing enzymes. In this study, we describe the first synthesis of fluorinated and phosphonylated exo-glycals and their corresponding nucleotide sugars in the galactofuranose series. The synthetic protocol that we have developed is a Selectfluor-mediated fluorination/elimination sequence on phosphonylated exo-glycals, and it offers a new entry into fluorinated carbohydrate chemistry. The challenging E/Z stereochemical assignment of the resulting tetrasubstituted alkenes, which bear an alkoxy, an alkyl, a fluoro, and a phosphonyl group, has been achieved through NMR experiments. The corresponding (E)- and (Z)-nucleotide fluorosugars have been prepared and tested as inhibitors of UDP-galactopyranose mutase (UGM). UGM is a flavoenzyme that catalyzes the isomerization of uridine diphosphate(UDP)-galactopyranose into UDP-galactofuranose, a key step of the biosynthesis of important mycobacterial cell-wall glycoconjugates. The two diastereomeric molecules were found to display time-dependent inactivation of UGM, as expected from preliminary results using non-fluorinated exo-glycal nucleotides. The inhibitory properties of the two fluorinated molecules led us to suggest that the inactivation mechanism proceeds through two-electron processes, despite the presence of the flavin cofactor within the UGM catalytic site.     

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.     

Atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry of sulfonic acid derivatized tryptic peptides.

Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) and ion trap mass spectrometry have been used to study the fragmentation behavior of native peptides and peptide derivatives prepared for de novo sequencing applications. Sulfonic acid derivatized peptides were observed to fragment more extensively and up to 28 times more efficiently than the corresponding native peptides. Tandem mass spectra of native peptides containing aspartic or glutamic acids are dominated by cleavage on the C-terminal side of the acidic residues. This significantly limits the amount of sequence information that can be derived from those compounds. The MS/MS spectra of native tryptic peptides containing oxidized Met residues show extensive loss of CH(3)SOH and little sequence-specific fragmentation. On the other hand, the tandem mass spectra of derivatized peptides containing Asp, Glu and oxidized Met show much more uniform fragmentation along the peptide backbone. The AP-MALDI tandem mass spectra of some derivatized peptides were shown to be qualitatively very similar to the corresponding vacuum MALDI postsource decay mass spectra, which were obtained on a reflector time-of-flight instrument. However, the ion trap mass spectrometer offers several advantages for peptide sequencing relative to current reflector time-of-flight instruments including improved product ion mass measurement accuracy, improved precursor ion selection and MS(n). These latter capabilities were demonstrated with solution digests of model proteins and with in-gel digests of 2D-gel separated proteins.     

人肝癌细胞系HLE细胞表面抗原多肽的纳升电喷雾串联质谱从头测序分析

肿瘤细胞表面的抗原多肽能够被细胞毒T淋巴细胞特异性识别而引起免疫应答,因此有可能用于研制基于多肽的抗肿瘤疫苗。用弱酸将人肝癌细胞系HLE细胞表面抗原多肽和人正常肝细胞表面多肽洗脱后,经RP-HPLC分离,选择HLE细胞表面特异性多肽进行纳升电喷雾串联质谱(nanoESI-MS/MS)测序,共测定5个色谱峰中的20个多肽序列,分子量分布范围为1000~2000 Da。借助M asSeq软件分析出其中12个多肽的序列。经数据库查寻,其中的3个肽段分别来自钙调节蛋白、核蛋白S19和伴侣蛋白10。这些多肽的生物学功能及与肿瘤的关系值得深入研究。该研究表明nanoESI-MS/MS是测定微量混合多肽序列的最有效方法。     

Simultaneous Analysis of Phosphorylated Peptides by MALDI-TOF-MS

Six peptides with various phosphorylation sensitivities for protein kinase A (PKA) were used for the simultaneous analysis of phosphorylated peptides using matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. The mixture of six peptides was reacted with PKA and was analyzed by MALDI-TOF mass spectrometry. The intensity of all peaks except one phosphorylated peptide peak was very low (<20%). Moreover, we examined whether the addition of diammonium citrate to CHCA matrix at concentrations of 1–20 mg mL^?1 can increase the peak intensity of peptides and phosphorylated peptides. The addition of diammonium citrate increased the peak intensity of peptides and phosphorylated peptides, but an increase in the intensity was unsatisfactory. Our study strongly suggests that MALDI-TOF mass spectrometry is not suitable for the simultaneous analysis of phosphorylated peptides.     

Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.