A general solution for the 2-pyridyl problem

Problem solved: an air-stable 2-pyridyl borane that can effectively couple to a wide range of aryl and heteroaryl halides and pseudohalides has evaded the synthesis community for decades. The discovery that Cu(DEA)(2) powerfully enables palladium-mediated cross-couplings with air-stable boronates 1 has finally provided a general solution to this problem. DEA=diethanolamine, DMF=N,N'-dimethylformamide, Tf=trifluoromethanesulfonyl.     

Exact solution to a general quantum mechanical problem with time-dependent boundary conditions

Exact analytical solutions are found for the quantum mechanical problem of a particle subject to a time-dependent potential with time-dependent boundary conditions. The method of solution employs time-dependent invariants, rescaling of space and time variables along with an unitary transformation. Several applications are discussed. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 827–833, 1997     

Synthesis of S-linked glycopeptides in aqueous solution

Investigation of direct S-glycosylation of homocysteine and cysteine containing peptides with O-acetyl protected glycosyl halides led under two-phase conditions in the presence of sodium carbonate as base to excellent results. Thus, from glucosyl bromide, galactosyl bromide, lactosyl bromide, sialyl chloride, and N-Troc protected 2-amino-2-deoxyglucosyl bromide S-glycosylated dipeptides 15, 18-21, 23, 24, and 26-29, respectively, were obtained in excellent yields. Alternatively, depending on the solubility of the peptide moiety, mixtures of DMF and water could be employed for successfully carrying out this reaction. Thus, S-glycosylated tripeptides 42-45 could be obtained. Combination of this method with chemical ligation was also successfully carried out.     

Sortase A-catalyzed peptide cyclization for the synthesis of macrocyclic peptides and glycopeptides

A chemoenzymatic method was developed for the synthesis of macrocyclic peptides and glycopeptides. Sortase A was found to mediate either head to tail cyclization or oligomerization and then head to tail cyclization of peptides and glycopeptides, depending on the peptide length, to produce 15-mer or higher cyclic peptides and glycopeptides.     

Mixed-mode chromatography for fractionation of peptides, phosphopeptides, and sialylated glycopeptides

A mixed-mode chromatographic (MMC) sorbent was prepared by functionalizing the silica sorbent with a pentafluorophenyl (PFP) ligand. The resulting stationary phase provided a reversed-phase (RP) retention mode along with a relatively mild strong cation-exchange (SCX) retention interaction. While the mechanism of interaction is not entirely clear, it is believed that the silanols in the vicinity of the perfluorinated ligand act as strongly acidic sites. The 2.1 mm x 150 mm column packed with such sorbent was applied to the separation of peptides. Linear RP gradients in combination with salt steps were used for pseudo two-dimensional (2D) separation and fractionation of tryptic peptides. An alternative approach of using linear cation-exchange gradients combined with RP step gradients was also investigated. Besides the attractive forces, the ionic repulsion contributed to the retention mechanism. The analytes with strong negatively charged sites (phosphorylated peptides, sialylated glycopeptides) eluted in significantly different patterns than generic tryptic peptides. This retention mechanism was employed for the isolation of phosphopeptides or sialylated glycopeptides from non-functionalized peptide mixtures. The mixed-mode column was utilized in conjunction with a phosphopeptide enrichment solid phase extraction (SPE) device packed with metal oxide affinity chromatography (MOAC) sorbent. The combination of MOAC and mixed-mode chromatography (MMC) provided for an enhanced extraction selectivity of phosphopeptides and sialylated glycopeptides peptides from complex samples, such as yeast and human serum tryptic digests.     

智能聚合物基材料富集磷酸化肽和糖肽的研究进展

翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如磷酸化肽和糖肽)丰度很低,且存在着强烈的背景干扰,很难直接用质谱进行分析,因此迫切需要开发高效的富集材料和技术来选择性富集翻译后修饰产物。近年来,智能聚合物基材料通过外部物理、化学或生物刺激可逆地改变其结构和功能,实现对磷酸化肽和糖肽高度可控的吸附和脱附,进而衍生开发出一系列新颖的富集方法,极大地吸引研究者们的兴趣。一方面,智能聚合物基材料的响应变化包括材料疏水性的增加或减少、形状和形貌的改变、表面电荷的重新分布以及亲和配体的暴露或隐藏等特性。这些特性使得目标物和智能聚合物基材料之间的亲和力可以通过简单改变外部条件(如温度、pH值、溶剂极性和生物分子等)实现更可控和更智能的精细调节。另一方面,智能聚合物基材料为集成功能模块提供了便捷的可扩展平台,例如特定的识别组件,显著提高了目标物质的分离选择性。智能聚合物基材料在分离方面展现出巨大的潜力,这为蛋白质翻译后修饰产物的分析和研究带来了希望。围绕上述主题,该文依据Web of Science近20年来近50篇代表性文献,概述了智能聚合物基材料在磷酸化肽和糖肽分离及富集中的发展方向。     

A solution to the cyclic aldol problem

[formula: see text] A protocol for achieving stereoselective aldol reactions with cyclic ketones is presented. In terms of yield, the process is particularly effective when a quaternary center at the alpha-carbon of the beta-hydroxy ketone product is created. The stereochemical outcome, anti or syn, is achieved by the Lewis acid-mediated ring expansion of stereochemically homogeneous epoxides in a reaction related to the pinacol rearrangement.     

A route to cyclic peptides and glycopeptides by native chemical ligation using in situ derived thioesters

The synthesis of cyclic peptides and glycopeptides by native chemical ligation using in situ derived thioesters is described.     

Chemoenzymatic synthesis of sialylated glycopeptides derived from mucins and T-cell stimulating peptides.

The Tn, T, sialyl-Tn, and 2,3-sialyl-T antigens are tumor-associated carbohydrate antigens expressed on mucins in epithelial cancers, such as those affecting the breast, ovary, stomach, and colon. Glycopeptides carrying these antigens are of interest for development of cancer vaccines and a short, chemoenzymatic strategy for their synthesis is reported. Building blocks corresponding to the Tn (GalNAc alpha-Ser/Thr) and T [Gal beta(1-->3)GalNAc alpha-Ser/Thr] antigens, which are relatively easy to obtain by chemical synthesis, were prepared and then used in the synthesis of glycopeptides on the solid phase. Introduction of sialic acid to give the sialyl-Tn [Neu5Ac alpha(2-->6)GalNAc alpha-Ser/Thr] and 2,3-sialyl-T [Neu5Ac alpha(2-->3)Gal beta(1-->3)GalNAc alpha-Ser/Thr] antigens is difficult when performed chemically at the building block level. Sialylation was therefore carried out with recombinant sialyltransferases in solution after cleavage of the Tn and T glycopeptides from the solid phase. In the same manner, the core 2 trisaccharide [Gal beta 1-->3(GlcNAc beta 1-->6)GalNAc] was incorporated in glycopeptides containing the T antigen by using a recombinant N-acetylglucosaminyltransferase. The outlined chemoenzymatic approach was applied to glycopeptides from the tandem repeat domain of the mucin MUC1, as well as to neoglycosylated derivatives of a T cell stimulating viral peptide.     

Modelling the electrophoretic migration behaviour of peptides and glycopeptides from glycoprotein digests in capillary electrophoresis-mass spectrometry

In this study, the classical semiempirical relationships between the electrophoretic mobility and the charge-to-mass ratio (m_e vs. q/M^α) were used to model the migration behaviour of peptides and glycopeptides originated from the digestion of recombinant human erythropoietin (rhEPO), a biologically and therapeutically relevant glycoprotein. The Stoke’s law (α = 1/3), the classical polymer model (α = 1/2) and the Offord’s surface law (α = 2/3) were evaluated to predict migration of peptides and glycopeptides, with and without sialic acids (SiA), in rhEPO digested with trypsin and trypsin–neuraminidase. The Stoke’s law resulted in better correlations for the set of peptides used to evaluate the models, while glycopeptides fitted better with the classical polymer model. Once predicted migration times with both models, it was easy to simulate their separation electropherogram. Results were later validated predicting migration and simulating separation of a different set of rhEPO glycopeptides and also human transferrin (Tf) peptides and glycopeptides. The excellent agreement between the experimental and the simulated electropherograms with rhEPO and Tf digests confirmed the potential applicability of this simple strategy to predict, in general, the peptide–glycopeptide electrophoretic map of any digested glycoprotein.     

Synthesis of α-S-linked glycopeptides in water containing solution

α-Thiols of N-acetylglucosamine and of N-acetylgalactosamine react with β-bromoalanine containing peptides at pH 8.5 under phase transfer conditions or, alternatively, in aqueous DMF, cleanly to α-S-linked glycopeptides. Thus, mimetics of important O-glycopeptides can be readily prepared.     

A solution to the pulse pileup and peak shape distortion problem

The pileup loss from the peak area and peak shape distortion effects are of considerable importance in routine activation analysis where the count rate may vary considerably from one sample to another. In this paper simple linear approximations for the peak shape change and efficiency loss have been used to show that correct results to within 2% are obtainable in the range 1000 cps to 10 000 cps.     

Engineering O-glycosylation points in non-extended peptides: implications for the molecular recognition of short tumor-associated glycopeptides

The ties that bind: The incorporation of non-natural residues in the peptide backbone allows the design of O-glycosylation points in helical segments. This strategy could help to modulate the binding properties between glycopeptides and their protein receptors, such as lectins and antibodies.     

Efficient synthesis of S-linked glycopeptides in aqueous solution by a convergent strategy

In naturally occurring glycopeptides and glycoproteins the glycan residues generally possess N- and O-linkages to the peptide backbone. Here we report the synthesis of the corresponding S-linked glycopeptides by a convergent strategy to provide compounds which should be quite stable to glycosidases. To this end, peptides that contain beta-bromoalanine and gamma-bromohomoalanine were generated either directly by bromination of serine and homoserine residues, respectively, or by standard ligation of the corresponding amino acids. 1-Thiosugars of O-acetyl protected GalNAc, GlcNAc, and lactose were prepared by known procedures. Reaction of the thiosugars with these peptides in an ethyl acetate/water two-phase system, which contained TBAHS and NaHCO(3), or in a one-phase system that consists of DMF/water and which contains NaHCO(3), led to the desired S-linked glycopeptides cleanly and in almost quantitative yield. This reaction also worked well for O-unprotected 1-thiosugars.     

On the solution of the N-completeness problem

A solution is given for the problem of N-completeness which arises in practical calculations for many electron systems because of the necessity of employing a finite basis set of antisymmetric two-particle functions.     

The problem of amino acid complementarity and antisense peptides

The review presents three hypotheses concerning the amino acid complementarity: 1) the Mekler-Blalock antisense hypothesis; 2) the Root-Bernstein approach based on stereochemical complementarity of amino acids and anti-amino acids coded by anticodons read in parallel with the coding DNA strand; 3) Siemion hypothesis resulting from the periodicity of the genetic code. The current state of knowledge as well as the results of the implementations of these hypotheses are compared. A special attention is given to Root-Bernstein and Siemion hypotheses, which differ in only few points of the complementarity prediction. We describe methods of investigation of peptide-antipeptide pairing, including circular dichroism, mass spectrometry, affinity chromatography and other techniques. The biological applications of complementarity principle are considered, such as search for bioeffector-bioreceptor interaction systems, the influence of peptide-antipeptide pairing on the activity of peptide hormones, and the application of antipeptides in immunochemistry. The possible role of amino acid-anti-amino acid interactions in the formation of the spatial structures of peptides, proteins and protein complexes is discussed. Such problems as the pairing preferences of protein-protein interfaces, the role of the pairing in the creation of disulfide bonds and the possible appearance of such interactions in beta-structure are also examined. The main intention of the paper is to bring the complementarity problem to the attention of the scientific community, as a possible tool in proteomics, molecular design and molecular recognition.     

An efficient approach for the characterization of mucin-type glycopeptides: the effect of O-glycosylation on the conformation of synthetic mucin peptides

Despite the growing importance of mucin core O-glycosylation in many biological processes including the protection of epithelial cell surfaces, the immune response, cell adhesion, inflammation, and tumorigenesis/metastasis, the regulation mechanism and conformational significance of the multiple introduction of α-GalNAc residues by UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAcTs) remains unclear. Here we report an efficient approach by combining MS and NMR spectroscopy that allows for the identification of O-glycosylation site(s) and the effect of O-glycosylation on the peptide backbone structures during enzymatic mucin domain assembly by using an isoform UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T2 (ppGalNAcT2) in vitro. An electron-capture dissociation device in a linear radio-frequency quadrupole ion trap (RFQ-ECD) combined with a time-of-flight (TOF) mass spectrometer was employed for the identification of Thr/Ser residues occupied by α-GalNAc branching among multiple and potential O-glycosylation sites in the tandem repeats of human mucin glycoproteins MUC4 (Thr-Ser-Ser-Ala-Ser-Thr-Gly-His-Ala-Thr-Pro-Leu-Pro-Val-Thr-Asp) and MUC5AC (Pro-Thr-Thr-Val-Gly-Ser-Thr-Thr-Val-Gly). In the present study, O-glycosylation was initiated specifically at Thr10 in naked MUC4 peptide and additional introduction of α-GalNAc proceeded preferentially but randomly at three other Thr residues to afford densely glycosylated MUC4 containing six α-GalNAc residues at Thr1, Ser2, Ser5, Thr6, Thr10, and Thr15. On the contrary, O-glycosylation of naked MUC5AC peptide occurred predominantly at consecutive Thr residues and led to MUC5AC with four α-GalNAc residues at Thr2, Thr3, Thr7, and Thr8. The solution structures determined by NMR spectroscopic studies elicited that the preferential introduction of α-GalNAc at Thr10 of MUC4 stabilizes specifically a β-like extended backbone structure at this area, whereas other synthetic models with a single α-GalNAc residue at Thr1, Thr6, or Thr15 did not exhibit any converged three-dimensional structure at the proximal peptide moiety. Such conformational impact on the underlying peptides was proved to be remarkable in the glycosylation at the consecutive Thr residues of MUC5AC.     

A solution to the component instability problem in the preparation of peptides containing C2-substituted cis-cyclobutane β-aminoacids: synthesis of a stable rhodopeptin analogue

Despite the inherent instability of C2-substituted cis-cyclobutane β-aminoacids, incorporation of such residues into peptides is shown to be possible through use of a 1-amino-2-(hydroxymethyl)cyclobutane derivative as a stable β-aminoacid surrogate. This synthetic strategy was validated by the synthesis of a rhodopeptin analogue.     

Thienamycin. A solution of the stereochemical problem

A new nitrone-based synthesis of β-lactams is described which makes provision for the 1-hydroxyethyl moiety in the potent antibiotic thienamycin. Moreover, the relative stereochemical features of the natural product are defined in a step involving the cycloaddition of a nitrone with methyl crotonate.