Cyclopeptides and Amides from Pseudostellaria heterophylla (Caryophyllaceae)

From the roots of Pseudostellaria heterophylla, three cyclopeptides and three amides were isolated, besides heterophyllin A and B. Their structures were determined as cyclo (Ala‐Gly‐Pro‐Val‐Tyr‐) (heterophyllin J; 1 ), cyclo (Ala‐Gly‐Pro‐Tyr‐Leu‐) (pseudostellarin A; 2 ), cyclo (Gly‐Gly‐Gly‐Pro‐Pro‐Phe‐Gly‐Ile‐) (pseudostellarin B; 3 ), methyl γ‐hydroxypyroglutamate ( 4 ), methyl pyroglutamate ( 5 ), and pyroglutamic acid ( 6 ) on the basis of spectral data, especially 2D‐NMR data. Among them, compounds 1 and 4 are new compounds.     

1H and 13C NMR assignments of eight nitrogen containing compounds from Nocardia alba sp.nov (YIM 30243T)

An unprecedented new natural product named nocarsin A (1), 5H‐4a,6,7a‐triazacyclopenta[cd]indene‐5,7(6H)‐dione (1), together with seven known compounds lumichrome (2), cyclo (L ‐Leu‐L ‐Tyr) (3), cyclo (L ‐Ala‐L ‐Ile) (4), cyclo (L ‐Ala‐L ‐Leu) (5), cyclo (L ‐Val‐L ‐Ala) (6), 5‐methyluracil (7) and uracil (8), was isolated from Nocardia alba sp.nov (YIM 30243^T), which was isolated from a soil sample collected from Yunnan Province, P. R. China. NMR techniques including COSY, HSQC, ROESY, and HMBC were used to elucidate the structures of these compounds. We report the unambiguous assignments of the ¹H and ¹³C NMR spectra of the new compound nocarsin A (1). Copyright © 2009 John Wiley & Sons, Ltd.     

Amino acids of ricin and its polypeptides

Ricin and its corresponding polypeptides (A & B chain) were purified from castor seed. The molecular weight of ricin subunits were 29,000 and 28,000 daltons. The amino acids in ricin determined were Asp45 The22 Ser40 Glu53 Cys4 Gly96 His5 Ile21 Leu33 Lys20 Met4 Phe13 Pro37 Tyr11 Ala45 Val23 Arg20 indicating that ricin contains approximately 516 amino acid residues. The amino acids of the two subunits of ricin A and B chains were Asp23 The12 Ser21 Glu29 Cys2 Gly48 His3 Ile12, Leu17 Lys10 Met2 Phe6 Pro17 Tyr7 Ala35 Val13 Arg13 while in B chain the amino acids were Asp22 The10 Ser19 Glu25 Cys2 Gly47 His1 Ile10, Leu15 Lys11 Met1 Phe7 Pro6 Tyr5 Ala32Val11 Arg10. The total helical content of ricin came around 53.6% which is a new observation.     

Effective synthesis of cyclic peptide yunnanin C and analogues via Ser/Thr ligation (STL)-mediated peptide cyclization

Cyclic peptide yunnanin C isolated from the root of Stellaria yunnanensis was efficiently synthesized in which the linear peptide was prepared by Boc-SPPS and the cyclization was realized by serine/threonine ligation (STL)-mediated cyclization. In addition, nine yunnanin C analogues, including mutations of Tyr7Gly, Tyr7Val, Tyr7Pro, Tyr7Phe, Ser1Thr, Pro2Val, Gly5Pro, Phe6Ala and Ile4Ala, were prepared in the same fashion. Here, we demonstrated that STL-mediated peptide cyclization could be an effective approach to construct cyclic peptides. Except that proline at the C-terminus could retard the cyclization process, cyclization of yunnanin C analogues with various C-terminal amino acids proceeded with fast cyclization rate (<4 h) and only trace amount of dimers (<5%) at a working concentration of 5 mM.     

β‐Hairpins Generated from Hybrid Peptide Sequences Containing both α‐ and β‐Amino Acids

The incorporation of the β‐amino acid residues into specific positions in the strands and β‐turn segments of peptide hairpins is being systematically explored. The presence of an additional torsion variable about the C(α) C(β) bond (θ) enhances the conformational repertoire in β‐residues. The conformational analysis of three designed peptide hairpins composed of α/β‐hybrid segments is described: Boc‐Leu‐Val‐Val‐^DPro‐β Phe ‐Leu‐Val‐Val‐OMe ( 1 ), Boc‐Leu‐Val‐β Val ‐^DPro‐Gly‐β Leu ‐Val‐Val‐OMe ( 2 ), and Boc‐Leu‐Val‐β Phe ‐Val‐^DPro‐Gly‐Leu‐β Phe ‐Val‐Val‐OMe ( 3 ). 500‐MHz ¹H‐NMR Analysis supports a preponderance of β‐hairpin conformation in solution for all three peptides, with critical cross‐strand NOEs providing evidence for the proposed structures. The crystal structure of peptide 2 reveals a β‐hairpin conformation with two β‐residues occupying facing, non‐H‐bonded positions in antiparallel β‐strands. Notably, βVal(3) adopts a gauche conformation about the C(α) C(β) bond (θ=+65°) without disturbing cross‐strand H‐bonding. The crystal structure of 2 , together with previously published crystal structures of peptides 3 and Boc‐β Phe ‐β Phe ‐^DPro‐Gly‐β Phe ‐β Phe ‐OMe, provide an opportunity to visualize the packing of peptide sheets with local ‘polar segments' formed as a consequence of reversal peptide‐bond orientation. The available structural evidence for hairpins suggests that β‐residues can be accommodated into nucleating turn segments and into both the H‐bonding and non‐H‐bonding positions on the strands.     

A New Antifungal Cyclic Lipopeptide from Bacillus marinus B‐9987

A new cyclic lipopeptide, marihysin A ( 1 ), along with the three known cyclodipeptides cyclo(Ala‐Ile) ( 2 ), cyclo(Ala‐Leu) ( 3 ), and cyclo(Ala‐Tyr) ( 4 ), was isolated from the fermentation broth of the marine microorganism Bacillus marinus B‐9987 isolated from the tissues of rhizophere of Suaeda salsa in the intertidal zone of the Bohai Bay of P. R. China. Marihysin A ( 1 ) was established to be cyclo(Pro‐Gln‐Asn¹‐Ser‐Asn²‐Tyr‐Asn³‐β‐aminotetradecanoic acid) by spectroscopic analysis, and it exhibits broad‐spectrum but low activity against plant pathogens as determined by antifungal bioassay.     

Properties and Reactions of Substituted 1,2‐Thiazetidine 1,1‐Dioxides: Chiral Mono‐ and Bicyclic 1,2‐Thiazetidine 1,1‐Dioxides from α‐Amino Acids

New chiral mono‐ and bicyclic β‐sultams, valuable building blocks for drug synthesis, have been prepared from L ‐Ala, L ‐Val, L ‐Leu, L ‐Ile, L ‐Phe, L ‐Cys, L ‐Ser, L ‐Thr, and D ‐penicillamine by transformation of the COOH group into a methylsulfonyl chloride function, followed by cyclization under basic conditions. Selected properties, derivatives, and reactions of the β‐sultams are described.     

Studies on Synthesis of a Cycloheptapeptide and Effects of Different Metal Ions on the Cyclization

ＩｎｔｒｏｄｕｃｔｉｏｎＣｙｃｌｉｃｐｅｐｔｉｄｅｓ ,ｗｈｉｃｈａｒｅｃｏｎｓｔｒａｉｎｅｄｃｏｎｆｏｒｍａ ｔｉｏｎａｌｌｙａｎｄｍｏｒｅｒｅｓｉｓｔａｎｔｔｏｐｒｏｔｅａｓｅｄｉｇｅｓｔｉｏｎｓｔｈａｎｔｈｅｉｒｌｉｎｅａｒｐｒｅｃｕｒｓｏｒｓ ,ｈａｖｅｂｅｅｎｏｆｇｒｅａｔｉｎｔｅｒｅｓｔａｓｓｙｎｔｈｅｔｉｃｔａｒｇｅｔｓｂｏｔｈａｓｐｏｔｅｎｔｉａｌｄｒｕｇｌｅａｄｓａｎｄａｓｍｏｄｅｌｓｆｏｒｃｏｎ ｆｏｒｍａｔｉｏｎａｌａｎａｌｙｓｉｓ .1 4 Ｃｕｒｒｅｎｔｍｅｔｈｏｄｓｆｏｒｓｙｎｔ…     

Three new mixed‐ligand copper(II) complexes containing glycyl‐l‐valine and N,N‐aromatic heterocyclic compounds: Synthesis,characterization, DNA interaction,cytotoxicity and antimicrobial activity

Three novel copper(II) complexes, [Cu(Gly‐l ‐Val)(HPBM)(H₂O)]·ClO₄·H₂O ( 1 ), [Cu(Gly‐l ‐Val)(TBZ)(H₂O)]·ClO₄ ( 2 ) and [Cu(Gly‐l ‐Val)(PBO)(H₂O)]·ClO₄ ( 3 ) (Gly‐l ‐Val = glycyl‐l ‐valine anion, HPBM = 5‐methyl‐2‐(2′‐pyridyl)benzimidazole, TBZ = 2‐(4′‐thiazolyl)benzimidazole, PBO = 2‐(2′‐pyridyl)benzoxazole), have been prepared and characterized with elemental analyses, conductivity measurements as well as various spectroscopic techniques. The interactions of these copper complexes with calf thymus DNA were explored using UV–visible, fluorescence, circular dichroism, thermal denaturation, viscosity and docking analyses methods. The experimental results showed that all three complexes could bind to DNA via an intercalative mode. Moreover, the cytotoxic effects were evaluated using the MTT method, and the antimicrobial activity of these complexes was tested against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The results showed that the activities are consistent with their DNA binding abilities, following the order of 1 > 2 > 3 .     

Determination of diketopiperazines of Burkholderia cepacia CF-66 by gas chromatography–mass spectrometry

Bacteria communicate with each other by a process termed “quorum sensing” (QS), and diffusible, low-molecular-weight chemicals, called signal molecules, are used as the communication languages. In cell-free Burkholderia cepacia CF-66 culture supernatants, five compounds suspected of being signal molecules were identified. The gene (cepI) related with AHLs synthesis were not detected by polymerase chain reaction (PCR) using specific primers. Gas chromatography–mass spectrometry (GC–MS) revealed that these compounds were not AHLs but the diketopiperazines (DKPs) cyclo(Pro–Phe), cyclo(Pro–Tyr), cyclo(Ala–Val), cyclo(Pro–Leu), and cyclo(Pro–Val), all of which were both d and l-type. Four kinds of DKPs had been isolated from other Gram-negative bacteria, but the other was a novel kind discovered in CF-66, and l-cyclo (Pro–Phe) was quantified by GC–MS. It was found that exogenous DKPs had a negative effect on the candidacidal activity of the culture supernatant extracts.     

Indirect reversed‐phase high‐performance liquid chromatographic and direct thin‐layer chromatographic enantioresolution of (R,S)‐Cinacalcet

Enantioresolution of the calcimimetic drug (R,S)‐Cinacalcet was achieved using both indirect and direct approaches. Six chiral variants of Marfey's reagent having l ‐Ala‐NH₂, l ‐Phe‐NH₂, l ‐Val‐NH₂, l ‐Leu‐NH₂, l ‐Met‐NH₂ and d ‐Phg‐NH₂ as chiral auxiliaries were used as derivatizing reagents under microwave irradiation. Derivatization conditions were optimized. Reversed‐phase high‐performance liquid chromatography was successful using binary mixtures of aqueous trifluoroacetic acid and acetonitrile for separation of diastereomeric pairs with detection at 340 nm. Thin silica gel layers impregnated with optically pure l ‐histidine and l ‐arginine were used for direct resolution of enantiomers. The limit of detection was found to be 60 pmol in HPLC while in TLC it was found to be in the range of 0.26–0.28 µg for each enantiomers. Copyright © 2010 John Wiley & Sons, Ltd.     

Two New Cyclopeptides from Arenaria oreophila (Caryophyllaceae)

Two new cyclopeptides, named arenariphilin A ( 1 ) and arenariphilin B ( 2 ), were isolated from the whole plants of Arenaria oreophila. Their structures were determined as cyclo‐(Thr‐Gly) ( 1 ) and cyclo‐(Ser₁‐Gly ‐Ser₂‐Ile ‐Phe₁‐Phe₂) ( 2 ) on the basis of spectral data, especially by 2D‐NMR.     

On the sodium and lithium ion affinities of some α-amino acids

The decomposition of 59 different cluster ions (generated by fast atom bombardment) consisting of two different amino acids and a sodium ion was analysed. The only fragment ions of significant abundance could be assigned to sodium ion-bound amino acids. Assuming that the most abundant ion in the fragment ion spectrum corresponds to the amino acid with the highest sodium ion affinity (SIA), the 20 common α-amino acids could be ordered with increasing sodium ion affinity as follows: Gly, Ala, Cys, Val, (Leu, Ile), Ser, Met, Thr, (Phe, Pro), Asp, Tyr, (Glu, Lys), Trp, Asn, Gln, His, Arg. Quantitative determinations were carried out by comparison of the lithium ion affinity (LIA) of Ala with that of dimethylformamide (DMF) in a fragment ion scan of the ion-bound dimer Ala—Li⁺—DMF. LIA(Ala) was calculated from LIA(Ala) = LIA(DMF) – (1/C)ln[I(AlaLi⁺)/I(DMF—Li⁺)], where the constant C was estimated from measurements of proton-bound amine–amino acid clusters. From fragment ion analysis of nine other Li⁺-bound α-amino acid dimers, the following lithium ion affinities were obtained: Gly 51.0, Ala 52.6, Sar 53.5, α-aminobutyric acid 53.7, glycine methyl ester 54.7 and Val 54.8. SIA(Ala) was estimated to be 75% of the lithium ion affinity and from fragment ion analysis of ten Na⁺-bound α-amino acid dimers the following sodium ion affinities were obtained: Gly 37.9, Ala 39.4, α-aminobutyric acid 40.3, Val 41.0, glycine methylster 41.0 and Sar 41.2.     

Megastigmane Glycosides from Docynia indica and Their Anti‐inflammatory Activities

Using various chromatographic methods, three new megastigmane glycosides, docynicasides A – C ( 1  –  3 ) and ten known, (6S,9R)‐vomifoliol 9‐O‐β‐d ‐xylopyranosyl‐(1′′→6′)‐O‐β‐d ‐glucopyranoside ( 4 ), hyperin ( 5 ), quercitrin ( 6 ), quercetin 3‐α‐l ‐arabinofuranoside ( 7 ), naringenin 7‐O‐β‐d ‐glucopyranoside ( 8 ), phloridzin ( 9 ), phloretin 2′‐O‐β‐d ‐xylopyranosyl‐(1→6)‐β‐d ‐glucopyranoside ( 10 ), pinosylvin 3‐O‐β‐d ‐glucopyranoside ( 11 ), tormentic acid ( 12 ), and chlorogenic acid methyl ester ( 13 ) were isolated from the fruits of Docynia indica. Their chemical structures were elucidated by physical and chemical methods. All the isolated compounds were evaluated for the inhibitory activity on NO production in LPS‐stimulated BV2 cells. As the results, compounds 3  –  5 showed significant inhibitory activity on LPS‐stimulated NO production in BV2 cells with the IC₅₀ values ranging from 21.0 to 29.3 μm .     

CE‐ESI‐MS coupled with dynamic pH junction online concentration for analysis of peptides in human urine samples

In this article, an approach has been developed for the analysis of some small peptides with similar pI values by CE‐ESI‐MS based on the online concentration strategy of dynamic pH junction. The factors affected on the separation, detection and online enrichment, such as BGE, injection pressure, sheath flow liquid and separation voltage have been investigated in detail. Under the optimum conditions, i.e. using 0.5 mol/L formic acid (pH 2.15) as the BGE, preparing the sample in 50 mM ammonium acetate solution (pH 7.5), 50 mbar of injection pressure for 300 s, using 7.5 mM of acetic acid in methanol–water (80% v/v) solution as the sheath flow liquid and 20 kV as the separation voltage, four peptides with similar pI values, such as L ‐Ala‐L ‐Ala (pI=5.57), L ‐Leu‐D ‐Leu (pI=5.52), Gly‐D ‐Phe (pI=5.52) and Gly‐Gly‐L ‐Leu (pI=5.52) achieved baseline separation within 18.3 min with detection limits in the range of 0.2–2.0 nmol/L. RSDs of peak migration time and peak area were in the range of 1.45–3.57 and 4.93–6.32%, respectively. This method has been applied to the analysis of the four peptides in the spiked urine sample with satisfactory results.     

Versuche zur Anwendung von Thermitase als Katalysator zur Knüpfung der Peptidbindung

The utility of thermitase, a thermophilic proteolytic enzyme fromThermoactinomyces vulgaris, as a catalyst for peptide synthesis has been studied using several N-benzyloxycarbonyl dipeptide esters as carboxyl components and Leu-NH₂ as nucleophile. Couplings were most successful with substrates containing Met, Leu, Ala, Phe, Tyr in P₁-position, and Val, Ala, Pro in P₂, whereas the substrates with Val, Ile, Pro in P₁ failed to couple.

     

Phenylethanoid Glycosides from the Roots of Digitalis ciliata Trautv.

Three new phenylethanoid glycosides, named digicilisides A – C ( 1  –  3 , resp.), have been isolated from the roots of Digitalis ciliata, along with five known phenylethanoid glycosides. The structures of 1  –  3 were identified as 2‐(4‐hydroxy‐3‐methoxyphenyl)ethyl β‐d ‐glucopyranosyl‐(1→3)‐[α‐l ‐rhamnopyranosyl‐(1→6)]‐4‐O‐[(E)‐feruloyl]‐β‐d ‐glucopyranoside ( 1 ), 2‐(3,4‐dihydroxyphenyl)ethyl α‐l ‐arabinopyranosyl‐(1→2)‐[β‐d ‐glucopyranosyl‐(1→3)]‐[α‐l ‐rhamnopyranosyl‐(1→6)]‐4‐O‐[(E)‐feruloyl]‐β‐d ‐glucopyranoside ( 2 ), and 2‐(3,4‐dihydroxyphenyl)ethyl β‐d ‐glucopyranosyl‐(1→3)‐{6‐O‐[(E)‐feruloyl]‐β‐d ‐glucopyranosyl‐(1→6)}‐4‐O‐[(E)‐caffeoyl]‐β‐d ‐glucopyranoside ( 3 ).     

Enantioselective Solid‐Phase Peptide Synthesis Using Traceless Chiral Coupling Reagents and Racemic Amino Acids

The enantioselective condensing reagent 4,6‐dimethoxy‐1,3,5‐triazine (DMT)/strychnine/BF$\rm{{_{4}^{-}}}$ was obtained by treatment of 2‐chloro‐4,6‐dimethoxy‐1,3,5‐triazine (CDMT) with strychnine tetrafluoroborate. The reagent was useful under typical conditions of solid‐phase peptide synthesis (SPPS) with enantiomerically homogeneous substrates. By SPPS, desired dipeptides were obtained in 84–94% yield using 4 equiv. of racemic Fmoc‐Ala, Fmoc‐Phe, and/or Fmoc‐Tyr for 1 equiv. of Wang resin loaded with Gly, Ala, Leu, Phe, Glu(^tBu), and/or Pro, respectively. For all three Fmoc‐protected amino acids, the configuration of the enantiomer preferred under SPPS conditions was independent of the structure of the acylated component and identical to that established in condensations proceeding in solution. In all cases, the enantiomer ratios L /D (er) were in a similar range, and varied from 9 : 92 to 2 : 98 for alanine, and from 90 : 10 to 100 : 0 for aromatic amino acids. The synthesis of Ac‐L ‐Lys(Ac)‐D ‐Ala‐D ‐Ala‐OH from racemic Fmoc‐Ala gave an L /D ratio of 10 : 90 for the esterification of Wang resin, and 0 : 100 for the formation of peptide bonds.     

Imidazole‐initiated polymerizations of α‐amino acid N‐carboxyanhydrides – simultaneous chain‐growth and step‐growth polymerization

The N‐carboxyanhydrides (NCAs) of sarcosine (Sar), D ,L ‐leucine (D ,L ‐Leu), D ,L ‐phenylalanine (D ,L ‐Phe), and L ‐alanine (L ‐Ala) were polymerized in dioxane. Imidazole served as initiator and the NCA/initiator ratio was varied from 1/1 to 40/1. The isolated polypeptides were characterized by ¹H NMR spectroscopy, by MALDI‐TOF mass spectrometry, by viscosity measurements, and by SEC measurements in the case of poly(sarcosine). Cyclic oligopeptides were found in all reaction products and in the case of polySar, poly(D ,L ‐Leu), and poly(D ,L ‐Phe) the cycles were the main products. In the case of poly(L ‐Ala), rapid precipitation of β‐sheet lamellaes prevented efficient cyclizations and stabilized imidazolide endgroups. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5690–5698, 2005     

Putative One‐Pot Prebiotic Polypeptides with Ribonucleolytic Activity

KIA7, a peptide with a highly restricted set of amino acids (Lys, Ile, Ala, Gly and Tyr), adopts a specifically folded structure. Some amino acids, including Lys, Ile, Ala, Gly and His, form under the same putative prebiotic conditions, whereas different conditions are needed for producing Tyr, Phe and Trp. Herein, we report the 3D structure and conformational stability of the peptide KIA7H, which is composed of only Lys, Ile, Ala, Gly and His. When the imidazole group is neutral, this 20‐mer peptide adopts a four‐helix bundle with a specifically packed hydrophobic core. Therefore, one‐pot prebiotic proteins with well‐defined structures might have arisen early in chemical evolution. The Trp variant, KIA7W, was also studied. It adopts a 3D structure similar to that of KIA7H and its previously studied Tyr and Phe variants, but is remarkably more stable. When tested for ribonucleolytic activity, KIA7H, KIA7W and even short, unstructured peptides rich in His and Lys, in combination with Mg⁺⁺, Mn⁺⁺ or Ni⁺⁺ (but not Cu⁺⁺, Zn⁺⁺ or EDTA) specifically cleave the single‐stranded region in an RNA stem–loop. This suggests that prebiotic peptide–divalent cation complexes with ribonucleolytic activity might have co‐inhabited the RNA world.