Mild method for cleavage of dehydroalanine units: highly efficient conversion of nocathiacin I to nocathiacin IV

Thiazolyl peptide antibacterial nocathiacin I (1) was converted to nocathiacin IV (4) in high yield using iodomethane and hydriodic acid in THF at 45 degrees C. Several simplified dehydroalanine-containing systems undergo dehydroalanine cleavage under the same conditions, although in these cases iodomethane is not needed for efficient conversion. The mild reaction conditions are in contrast with other methods described in the literature.     

Separation of structurally similar nocathiacin analogues by reversed phase chromatography

The complete separation of structurally similar compounds has been a challenge due mainly to their similarity on physical and chemical properties. In the present study, a simple and effective chromatographic method to separate and purify nocathiacin acid from its structural analogue nocathiacin I was developed. After evaluating mobile phase compositions on the retention characteristics by reversed phase high-performance liquid chromatography (HPLC), the elution order of nocathiacin I and nocathiacin acid was completely reversed, and the resolution value between the two analogues was improved, by varying pH value and ionic strength, to greater than 10 from merged peaks under initial conditions. In addition, a preparative isolation of nocathiacin acid was performed by reversed phase column chromatography under the guidance of the HPLC study. This chromatographic method resulted in an efficient process to obtain pure nocathiacin acid with a recovery rate of 83%. The present approach offers a new methodology for the separation of structurally closely related secondary metabolites.     

Observation of O-H...N scalar coupling across a hydrogen bond in nocathiacin I

We report here the observation of O-H...N hydrogen-bond (1h)J(N,OH) scalar coupling in a biologically active natural product. The intramolecular hydrogen bond between the threonine hydroxyl (Thr-OH) group and the thiazolyl nitrogen at the second thiazole ring (Thz-2) in nocathiacin I was directly detected by a 1H-15N HMBC NMR experiment. The magnitude of the scalar coupling constant (1h)J(N,OH) was accurately measured to be 1.8 +/- 0.1 Hz by a J-resolved 1H-15N HMBC experiment. By adding the O-H...N distance restraint, the 3D solution structure of nocathiacin I was refined. The structure refinement indicated that the distance between the Thr-3 hydroxyl hydrogen and the Thz-2 nitrogen is or= 0.23 A. The presence of an intramolecular hydrogen bond in nocathiacin I is further supported by a number of NMR parameters and additional NMR experiments. This observation provides valuable information for characterizing molecular conformations, and for studying structure-activity relationships.     

Conformation and absolute configuration of nocathiacin I determined by NMR spectroscopy and chiral capillary electrophoresis

Nocathiacin I (BMS-249524) is a highly cross-linked thiazolyl peptide that displays potent activity against Gram-positive bacteria, including a number of antibiotic-resistant strains. This natural product contains 10 chiral centers. NMR studies have been performed to characterize the solution structure of nocathiacin I. A uniformly 13C,15N-labeled sample was used to obtain NMR assignments. Restrained simulated annealing calculations were performed by using accurately determined NOE distance restraints. All of the chiral centers were allowed to float during the simulated annealing protocol. Two clusters of structures were obtained that satisfy the NOE restraints very well and that are reasonably consistent with vicinal J-coupling constants. Within each cluster, all 10 chiral centers are uniquely defined. The two clusters are effectively mirror images of each other: all chiral centers that have the R(S) configuration in one cluster have the S(R) configuration in the other. The single threonine residue in nocathiacin I was subsequently determined to be l-threonine by chiral capillary electrophoresis, allowing the absolute configurations of all 10 chiral centers to be defined.     

New synthetic technology for the construction of N-hydroxyindoles and synthesis of nocathiacin I model systems

A new synthetic method providing expedient access to a wide range of polyfunctionalized N-hydroxyindoles (IV) is reported. These unique constructs are assembled by nucleophilic additions to in situ generated α,β-unsaturated nitrones (III) through carbon-carbon and carbon-heteroatom bond formation. The new synthetic technology was applied to the synthesis of nocathiacin I (1) model systems (2 and 3a-c) containing the N-hydroxyindole structural motif.     

Synthesis of novel nocathiacin-class antibiotics. Condensation of glycolaldehyde with primary amides and tandem reductive amination of amadori-rearranged 2-oxoethyl intermediates

Nocathiacin I (1) and nocathiacin IV (2) are novel indole-containing thiazolyl peptide antibiotics, which exhibit potent activity against key Gram-positive bacterial pathogens, including multi drug-resistant Staphylococcus aureus, Streptococcus pneumoniae, and Enterococcus faecium. New nocathiacins 7-12 were prepared from 2 by a condensation with glycolaldehyde followed by tandem reductive amination of the 2-oxoethyl intermediate 4. The latter was formed via Amadori rearrangement from initial 2-hydroxyethylideneamide 3. This transformation readily tolerates the complex architecture of nocathiacins and allows selective incorporation of water solubilizing groups to the primary amide in 2 without protecting group manipulation.     

Tryptic hydrolysis of inorcanic pyrophosphate modified by phosphate and O-phosphoethanolamine

By the peptide map method, a phosphorylated peptide has been isolated from a tryptic hydrolysate of phosphorylated yeast inorganic pyrophosphatase (I), and this is a direct proof of the formation of a covalent bond between (I) and phosphate in the course of this reaction. The isolation and analysis of the peptide from the tryptic hydrolysate shows that the phosphate acceptor is probably the aspartic acid residue 240 or 248. Analysis of a tryptic hydrolysate of (I) modified with O-phosphoethanolamine has shown that O-phosphoethanolamine forms an amide bond with the carboxy group of the same aspartic acid residue. In an alkaline medium, the phosphate residue migrates to the imidazole ring of a histidine residue, apparently that present in position 222.     

Reevaluation of copper(I) affinity for amyloid-β peptides by competition with ferrozine--an unusual copper(I) indicator

The association constant of ferrozine (5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine-4,4'-disulfonic acid) with Cu(I) to form the chromophoric [Cu(I)(Fz)(2)](3-) complex was determined by UV/Vis titration experiments in Hepes buffer (0.1 M, pH 7.4). An association constant close to 10(12) M(-2), which is significantly weaker than those of the well-known, water-soluble, Cu(I) chelators bicinchoninic acid and 2,9-dimethyl-4,7-diphenyl-1,10-phenantroline disulfonic acid, was found. The [Cu(I)(Fz)(2)](3-) chromophore was used in UV/Vis competition experiments to determine Cu(I) binding affinity for the amyloid-β peptide involved in Alzheimer's disease and for a series of pertinent mutants. An association constant of approximately 10(7) M(-1) was found; this is much weaker than that reported for dithiothreitol and confirms that imidazoles are harder ligands than thiolates. Each His mutation (H6A, H13A, and H14A) impacts the peptide affinity for Cu(I). The native human amyloid-β peptide was found to be a fourfold-stronger Cu(I) ligand than the murine peptide, which differs by three point mutations (R5G, Y10F, and H13R) from the human one.     

Total synthesis of microcin B17 via a fragment condensation approach

The total synthesis of the 43 amino acid antibacterial peptide Microcin B17 (MccB17) is described. The natural product was synthesized via a convergent approach from a heterocycle-derived peptide and peptide thioester fragments prepared via Fmoc-strategy solid phase peptide synthesis (SPPS). Final assembly was achieved in an efficient manner using two Ag(I)-assisted peptide ligation reactions to afford MccB17 in excellent overall yield.     

爱滋病病毒中肽段的酶促合成

为了进一步研究酶促合成在多肽合成中的实际应用,选择合成了爱滋病病毒(人类免疫缺损病毒,HIV-I)的gp41中氨基酸序列598-609的三个肽段,该部分是HIV-I中的2个抗原决定簇部分,H-Leu-Glg-Leu-Trp-Glg-cgs-Ser-Glg-Lgs-Leu-Ile-Cgs-OH可以作为抗原来检测HIV抗体.     

Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation

Binding between major histocompatibility complex (MHC) class I molecules and immunogenic epitopes is one of the most important processes for cell-mediated immunity. Consequently, computational prediction of amino acid sequences of MHC class I binding peptides from a given sequence may lead to important biomedical advances. In this study, an efficient structure-based method for predicting peptide binding to MHC class I molecules was developed, in which the binding free energy of the peptide was evaluated by two individual docking simulations. An original penalty function and restriction of degrees of freedom were determined by analysis of 361 published X-ray structures of the complex and were then introduced into the docking simulations. To validate the method, calculations using a 50-amino acid sequence as a prediction target were performed. In 27 calculations, the binding free energy of the known peptide was within the top 5 of 166 peptides generated from the 50-amino acid sequence. Finally, demonstrative calculations using a whole sequence of a protein as a prediction target were performed. These data clearly demonstrate high potential of this method for predicting peptide binding to MHC class I molecules.     

Structure of the peptide moiety of verticillin

The amino acid sequence of the peptide moiety of verticillin (I) - a phytotoxic metabolite of the causative agent of verticillium wilt of the cotton plant - has been determined. On the basis of the determination of the amino acid sequences of five short peptides isolated from the products of incomplete acid hydrolysis of oxidized desferriverticillin, the structure cyclo[L-glycyl-L-seryl-L-glycyl(L--N-hydroxyornithyl)] has been established for the peptide moiety of (I).     

Azidomethyl-ruthenocene: facile synthesis of a useful metallocene derivative and its application in the 'click' labelling of biomolecules

A convenient synthesis of azidomethyl-ruthenocene and its use in the covalent labelling of amino acids, peptides and a peptide nucleic acid (PNA) monomer derivative by Cu(I) catalyzed azide-alkyne coupling (Cu-AAC, "click chemistry") are described.     

Synthesis and biological evaluation of two chemically modified peptide epitopes for the class I MHC protein HLA-B*2705

The T-cell receptor of a CD8(+) T-cell recognises peptide epitopes bound by class I major histocompatibility complex (MHC) glycoproteins presented in a groove on their upper surface. Within the groove of the MHC molecule are 6 pockets, two of which mostly display a high degree of specificity for binding amino acids capable of making conserved and energetically favourable contacts with the MHC. One type of MHC molecule, HLA-B*2705, preferentially binds peptides containing an arginine at position 2. In an effort to increase the affinity of peptides for HLA-B*2705, potentially leading to better immune responses to such a peptide, we synthesised two modified epitopes where the amino acid at position 2 involved in anchoring the peptide to the class I molecule was replaced with the alpha-methylated beta,gamma-unsaturated arginine analogue 2-(S)-amino-5-guanidino-2-methyl-pent-3-enoic acid. The latter was prepared via a multi-step synthetic sequence, starting from alpha-methyl serine, and incorporated into dipeptides which were fragment-coupled to resin-bound heptameric peptides yielding the target nonameric sequences. Biological characterisation indicated that the modified peptides were poorer than the native peptides at stabilising empty class I MHC complexes, and cells sensitised with these peptides were not recognised as well by cognate CD8(+) T-cells, where available, compared to those sensitised with the native peptide. We suggest that the modifications made to the peptide have decreased its ability to bind to the peptide binding groove of HLA-B*2705 molecules which may explain the decrease in recognition by cytotoxic T-cells when compared to the native peptide.     

Facile chemoselective synthesis of dehydroalanine-containing peptides

Useful methodology is described for the synthesis of dehydroalanine residues (II) within peptides. The unnatural amino acid (Se)-phenylselenocysteine (I) can be incorporated into growing peptide chains via standard peptide synthesis procedures. Subsequent oxidative elimination affords a dehydroalanine at the desired position. The oxidation conditions are mild and tolerate functionalities commonly found in peptides, including variously protected cysteine residues. To illustrate its utility, cyclic lanthionines have been synthesized by this method.     

Self-assembly of short peptide amphiphiles: the cooperative effect of hydrophobic interaction and hydrogen bonding

The interplay between hydrogen bonding, hydrophobic interaction and the molecular geometry of amino acid side-chains is crucial to the development of nanostructures of short peptide amphiphiles. An important step towards developing their practical use is to understand how different amino acid side-chains tune hydrophobic interaction and hydrogen bonding and how this process leads to the control of the size and shape of the nanostructures. In this study, we have designed and synthesized three sets of short amphiphilic peptides (I(3)K, LI(2)K and L(3)K; L(3)K, L(4)K and L(5)K; I(3)K, I(4)K and I(5)K) and investigated how I and L affected their self-assembly in aqueous solution. The results have demonstrated a strong tendency of I groups to promote the growth of β-sheet hydrogen bonding and the subsequent formation of nanofibrillar shapes. All I(m)K (m = 3-5) peptides assembled into nanofibers with consistent β-sheet conformation, whereas the nanofiber diameters decreased as m increased due to geometrical constraint in peptide chain packing. In contrast, L groups had a weak tendency to promote β-sheet structuring and their hydrophobicity became dominant and resulted in globular micelles in L(3)K assembly. However, increase in the number of hydrophobic sequences to L(5)K induced β-sheet conformation due to the cooperative hydrophobic effect and the consequent formation of long nanofibers. The assembly of L(4)K was, therefore, intermediate between L(3)K and L(5)K, similar to the case of LI(2)K within the set of L(3)K, LI(2)K and I(3)K, with a steady transition from the dominance of hydrophobic interaction to hydrogen bonding. Thus, changes in hydrophobic length and swapping of L and I can alter the size and shape of the self-assembled nanostructures from these simple peptide amphiphiles.     

Deprotection of the S-trimethylacetamidomethyl (Tacm) group using silver tetrafluoroborate: application to the synthesis of porcine brain natriuretic peptide-32 (pBNP-32)

Silver tetrafluoroborate (AgBF4) in trifluoroacetic acid (TFA) has been found to cleave the S-trimethyl-acetamidomethyl (Tacm) group or the S-acetamidomethyl (Acm) group without affecting other functional groups in a peptide chain. A newly isolated porcine brain natriuretic peptide-32 (pBNP-32) was synthesized by the combined use of the S-Tacm group and AgBF4 deprotection. The synthetic pBNP-32 was obtained in better yield by the AgBF4 procedure than by the standard I2 procedure. The synthetic pBNP-32 has the highest chick rectum relaxant activity among the known members of the atrial natriuretic peptide-brain natriuretic peptide (ANP-BNP) families. Somatostatin was also synthesized by the Fmoc-based solid-phase method using S-Tacm and AgBF4. In this synthesis, the recently developed reagent tetrafluoroboric acid (HBF4) was applied to cleave the peptide from the resin.     

抗菌肽IB-367的固相合成与抑菌活性

采用固相合成方法,以Rink Amide树脂为载体,Fmoc保护氨基酸为原料,经苯并三唑-1-四甲基六氟磷酸酯(HBTU)/N,N-二异丙基乙胺(DIEA)缩合,三氟乙酸/苯甲硫醚/乙二硫醇/苯甲醚裂解体系脱除保护基制得IB-367线性肽(4); 4经双氧水氧化制得IB-367一环肽(5); 5经碘乙醇溶液氧化合成抗菌肽IB-367(6),收率34.1%,纯度＞95.0%,其结构经MS(ESI)和氨基酸组成分析确证。抑菌活性研究结果表明：6对大肠杆菌和金黄色葡萄球菌的最小抑菌浓度为5.0 μg·mL^-1。     

Impurity identification and determination for the peptide hormone angiotensin I by liquid chromatography–high-resolution tandem mass spectrometry and the metrological impact on value assignments by amino acid analysis

It is common practice to quantify the mass concentration of a peptide solution through quantitative determination of selected chemically stable amino acids produced following complete hydrolysis of the parent peptide. This is because there is generally an insufficient quantity of material available to allow for the obvious alternative of a direct purity analysis characterization of the parent peptide, and the subsequent constitution of a calibration solution. However, selected accurately characterized pure peptide reference materials are required to establish reference points for the dissemination of metrologically traceable measurements and to develop reference measurement systems for laboratory medicine. In principle, purity assignment of a peptide can be performed by using the so-called mass balance approach, by employing a range of analytical techniques to obtain an estimate of the mass fraction content of all impurities present in the intact peptide, and by utilizing the difference from the theoretical limit value to assign the mass fraction content of the main peptide. Liquid chromatography–high-resolution tandem mass spectrometry (LC-hrMS/MS) is a key technique for the detection, identification, and determination of structurally related impurities present in a peptide material, and experiments characterizing the model peptide hormone angiotensin I (ANG I) are described in the present work. Degradation products that were generated from ANG I after storage at elevated temperatures were screened. The formation of peptide fragments such as ANG II or ANG III was determined by comparison of measured mass values with calculated mass values. The use of a data-dependent acquisition technique enabled the detection and structural characterization of ANG II and other peptide fragments as major impurities in the same LC-hrMS/MS analysis run. Subsequent quantification using external calibration allowed the mass fraction of the major impurities in a candidate reference material to be estimated as 10.4 mg/g. Failure to correct for these impurities would lead to a 1 % error in the determination of the concentration of the peptide in solution by amino acid analysis techniques.

Peptide reagent design based on physical and chemical properties of amino acid residues

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so-called AABPD (amino acid based-peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three-dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three-dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C-like proteinase and the affinity prediction for epitope-peptides with Class I MHC molecules are studied by using the peptide reagent design strategy.