Two New Cyclic Tetrapeptides of Streptomyces rutgersensis T009 Isolated from Elaphodus davidianus Excrement

Two new cyclic tetrapeptides, cyclo(l ‐Val‐l ‐Leu‐l ‐Val‐l ‐Ile) ( 1 ) and cyclo(l ‐Leu‐l ‐Leu‐l ‐Ala‐l ‐Ala) ( 2 ), and 15 known compounds, cyclo(Gly‐l ‐Leu‐Gly‐l ‐Leu) ( 3 ), cyclo(l ‐Ser‐l ‐Phe) ( 4 ), cyclo(l ‐Leu‐l ‐Ile) ( 5 ), cyclo(l ‐Tyr‐l ‐Phe) ( 6 ), cyclo(Gly‐l ‐Trp) ( 7 ), cyclo(l ‐Leu‐l ‐Tyr) ( 8 ), cyclo(Gly‐l ‐Phe) ( 9 ), cyclo(l ‐Phe‐trans‐4‐hydroxy‐l ‐Pro) ( 10 ), cyclo(l ‐Leu‐l ‐Leu) ( 11 ), cyclo(l ‐Val‐l ‐Phe) ( 12 ), cyclo(l ‐Val‐l ‐Leu) ( 13 ), cyclo(l ‐Ile‐l ‐Ile) ( 14 ), cyclo(l ‐Tyr‐l ‐Tyr) ( 15 ), turnagainolide A ( 16 ), and bacimethrin ( 17 ) were isolated from the fermentation broth of Streptomyces rutgersensis T009 obtained from Elaphodus davidianus excrement. Their structures were identified on the basis of spectroscopic analysis. Meanwhile, the absolute configurations of the amino acid residues of compounds 1 and 2 were determined by advanced Marfey method. Compound 3 was obtained from a natural source for the first time. The X‐ray single crystal diffraction data of bacimethrin ( 17 ) were also reported for the first time. Compounds 1  –  17 exhibited no antimicrobial activities with the MICs > 100 μg/ml.     

南海红树林内生真菌ZSU-H26生物碱类代谢产物的研究

海洋微生物资源由于具有可持续开发性,而且其活性物质不像来源于其它海洋生物(如海绵、海藻、海兔、珊瑚等)产生的生物活性物质,其生产不受天然资源难再生的限制,能通过发酵进行胞外生产,与现代微生物技术相结合,较容易实现工业化生产,特别是其生产不对环境造成危害,符合当今绿色化学发展的方向.     

Two diketopiperazine cyclo(pro-phe) isomers from marine bacteria <Emphasis Type="Italic">Bacillus subtilis</Emphasis> sp. 13-2

Two bioactive diketopiperazines, cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe), against Bacillus subtilis (terrestrial), Staphylococcus aureus, and Escherichia coli DH5a were isolated from marine surface sediment bacteria Bacillus subtilis sp.13-2. To our knowledge, this was the first time that cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe) were isolated from Bacillus subtilis, and the first time that cyclo(R-Pro-S-Phe) was isolated from a natural source. These two compounds were established on the basis of ESI-MS spectral data, as well as NMR 1D and 2D (COSY, HMQC, and HMBC) spectral data.     

Synthesis,Properties, Structure and Reactivity of Sodium 2,3,4,5-Tetra- tert -butylcyclopentaphosphanide

The reaction between Na, t BuPCl 2 , and PCl 3 in thf gives Na[ cyclo -( t Bu 4 P 5 )] ( 1 ). 1 reacts with PCl 3 to yield ( cyclo - t Bu 3 P 4 ) t BuPCl ( 2 ), and with a proton source, such as HCl, NH 4 Cl, or t BuCl, to give cyclo - t Bu 4 P 5 H ( 3 ). The reaction of 1 with [MCl 2 (PRR' 2 ) 2 ] (M = Ni; R = R' = Et; M = Pd, Pt, R = Ph, R' = Me) gives [Ni{ cyclo -( t Bu 3 P 5 )}(PEt 3 ) 2 ] ( 4 ), [Pd{ cyclo -( t Bu 4 P 5 )} 2 ] ( 5 ), and [PtCl{ cyclo -( t Bu 3 P 4 ) t BuP}(PPhMe 2 )] ( 6 ). 1-6 were characterized by 31 P{ 1 H} NMR spectroscopy, and 1 and 4-6 were also characterized by X-ray crystallography.     

Quantification of cyclic dipeptides from cultures of Lactobacillus brevis R2Δ by HRGC/MS using stable isotope dilution assay

Lactic acid bacteria (LAB) play an important role as natural preservatives in fermented food and beverage systems, reducing the application of chemical additives. Thus, investigating their antifungal compounds, such as cyclic dipeptides, has gained prominence. Previous research has primarily focussed on isolation of these compounds. However, their precise quantification will provide further information regarding their antifungal performance in a complex system. To address this, deuterated labelled standards of the cyclic dipeptides cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) were synthesized, and stable isotope dilution assays were developed, enabling an accurate quantification of cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) in MRS-broth and wort. Quantitative results showed that, in the Lactobacillus brevis R2Δ fermented MRS-broth, the concentrations of cyclo(Leu-Pro), cyclo(Pro-Pro) and cyclo(Phe-Pro) were significantly higher (P?<?0.05), than in wort for cyclo (Leu-Pro) when compared with their controls. This indicates that the formation of these three cyclic dipeptides is related to L. brevis R2Δ metabolism. Furthermore, this represents the first report of cyclic dipeptides quantification using stable isotope dilution assays in LAB cultures both in vitro and in a food system.     

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.     

Two new cyclopeptides from stellaria yunnanensis

In the previous papers, we reported the isolation and structural elucidation of three new cyclopeptides, namely stellarin A, B and C, from the fresh roots of stellaria yunnanensis Franch. In a continued study on this plant, other two new cyclopeptides named stellarin D(1) and E(2) were obtained and their structures were established to be cyclo (Gly-Tyr-Leu-Phe-Pro-Ile-Pro)(1), cyclo(Gly-Ile-Pro-Tyr-Ile-Ala-Ala)(2), respectively.     

Two Cyclic Peptides Produced by the Endophytic Fungus # 2221 from Castaniopsis fissa on the South China Sea Coast

New cyclic peptides 1 and 2 were isolated from the endophytic fungus #2221 from Castaniopsisfissa on the south China sea coast. By 2D NMR methods and chiral HPLC technique, their structures were elucidated as cyclo (L-Val-L-Leu-L-Val-L-Leu) and cyclo(L-Leu-L-Ala-L-Leu-L-Ala), respectively.     

四齿四棱草根部环肽化合物的分离及鉴定

通过正相和反相硅胶柱层析,从四齿四棱草根部的乙醇提取物中分离纯化出4个环肽化合物,经波谱分析等鉴定了其结构,其中2个新化合物的结构分别为cyclo(-N-Pro¹-Pro²-Phe¹-Phe²-Leu¹-Ser-Thr-Leu²-CO)(1,四棱草肽C)和cyclo(-N-Pro¹-Pro²-His-Gly-Val-Asn-Ile-Trp-CO)(2,四棱草肽D).     

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.     

Unambiguous Stereochemical Assignment of Cyclo(Phe-Pro), Cyclo(Leu-Pro), and Cyclo(Val-Pro) by Electronic Circular Dichroic Spectroscopy

2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).     

Cyclo[n]pyrroles: size and site-specific binding to G-quadruplexes

Inhibiting the enzyme telomerase by stabilizing the G-quadruplex has potential in anticancer drug design. Diprotonated cyclo[n]pyrroles represent a set of expanded porphyrin analogues with structures similar to that of telomestatin, a natural product known to bind to and stabilize G-quadruplexes. As a first step toward testing whether cyclo[n]pyrroles display a similar function, a series of diprotonated cyclo[n]pyrroles (where n = 6, 7, and 8) was each added to the human telomere repeat sequence d(T(2)AG(3))(4) and examined with mass spectrometry, ion mobility, and molecular dynamics calculations. Nano-ESI-MS indicated that the smaller the cyclo[n]pyrrole, the more strongly it binds to the telomeric sequence. It was also found that cyclo[6]pyrrole bound to d(T(2)AG(3))(4) better than octaethylporphyrin, a finding rationalized by cyclo[6]pyrrole having a 2+ charge, while octaethylporphyrin bears no charge. Ion mobility measurements were used to measure the collision cross section of each d(T(2)AG(3))(4)/cyclo[n]pyrrole complex. Only one peak was observed in the arrival time distributions for all complexes, and the experimental cross sections indicated that only structures with d(T(2)AG(3))(4) in an antiparallel G-quadruplex arrangement and each cyclo[n]pyrrole externally stacked below the G-quartets occur under these experimental conditions. When the cyclo[n]pyrroles were intercalated or nonspecifically bound to the quadruplex, or if conformations different than antiparallel were considered for d(T(2)AG(3))(4), the theoretical cross sections did not match experiment. On this basis, it is inferred that (1) external stacking represents the dominant binding mode for the interaction of cyclo[n]pyrroles with d(T(2)AG(3))(4) and (2) the overall size and charge of the cyclo[n]pyrroles play important roles in defining the binding strength.     

Beta2-amino acids in the design of conformationally homogeneous cyclo-peptide scaffolds

Herein, we report studies on the influence of chiral beta(2)-amino acids in the design of conformationally homogeneous cyclic tetrapeptide scaffolds. The cyclic alpha-tetrapeptide cyclo(-Phe-D-Pro-Lys-Phe-) (1) and its four mixed analogues, having one of the alpha-Phe replaced by either an (S)- or an (R)-beta(2)hPhe residue (i.e., cyclo(-(R)-beta(2)hPhe-D-Pro-Lys-Phe) (2a), cyclo(-(S)-beta(2)hPhe-D-Pro-Lys-Phe-) (2b), cyclo(-Phe-D-Pro-Lys-(R)-beta(2)hPhe-) (3a), and cyclo(-Phe-D-Pro-Lys-(R)-beta(2)hPhe-) (3b)), were all synthesized through solid-phase procedures followed by solution-phase cyclization. Initially, all five cyclo-peptides were analyzed by (1)H NMR spectroscopic studies in different solvents and at variable temperatures. Subsequently, a detailed 2D NMR spectroscopic analysis of three of the mixed peptides in water was performed, and the information thus extracted was used as restraints in a computational study on the peptides' conformational preference. An X-ray crystallographic study on the side chain-protected (Boc) 2a revealed the solid-state structure of this peptide. The results presented herein, together with previous literature data on beta(3)-amino acid residues, conclusively demonstrate the potential of beta-amino acids in the design of conformationally homogeneous cyclic peptides that are homologous to peptides with known applications in biomedicinal chemistry and as molecular receptors.     

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.     

Antiparallel β-Sheet Conformation in Cyclopeptides Containing a Pseudo-amino Acid with a biphenyl moiety

The biphenyl-containing pseudo-amino acids 2′-(aminomethyl)biphenyl-2-carboxylic acid (Abc; 1 ) and 2′-(aminomethyl)biphenyl-2-acetic acid (Aba; 2 ) are used as rigid spacers in the backbone of the cyclic peptides cyclo (-Abc-Ala-Phe-Gly-)₂ ( 5 ), cyclo(-Abc-Ala-Val-Gly-)₂ ( 6 ), cyclo(-Aba-Gly-Phe-Ala-)₂ ( 7 ), and cyclo(-Aba-Ala-Phe-Gly-)₂( 8 ). Three different interconverting diastereoisomers are found in solutions of each of these cyclopeptides due to the atropisomerism of the biphenyl units. NMR Techniques and molecular-dynamics calculations allow to conclude that the major diastereoisomer of 5 (and 6 ) in (D₆)DMSO adopts a β-sheet conformation. It is proposed that the pseudo-amino acid 1 of (R)-chirality forms, with attached L -amino acids, a H-bonding pattern comparable to a β-turn (see D in Fig. 4 and F ).     

Theoretical UV circular dichroism of aliphatic cyclic dipeptides

Four cyclic dipeptides (piperazine-2,5-diones), cyclo(L-Pro-Gly), cyclo(L-Pro-L-Leu), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-L-Ala), were modeled from crystal structure data. Conformations resulting from energy minimization using molecular mechanics were compared with traditional ab initio and density functional theory geometric optimizations for each dipeptide. In all computational cases, the gas phase was assumed. The pi-pi transition feature of the UV circular dichroic (CD) spectra was predicted for each peptide structure via the classical dipole interaction model. The dipole interaction model predicted CD spectra that qualitatively agreed with experiment when MP2 or DFT geometries were used. By coupling MP2 or DFT geometric optimizations with the classical physics method of the dipole interaction model, significantly better CD spectra were calculated than those using geometries obtained by molecular mechanics. Thus, one can couple quantum mechanical geometries with a classical physics model for calculation of circular dichroism.     

Thermodynamic characterization of the osmolyte effect on protein stability and the effect of GdnHCl on the protein denatured state

To understand the biomolecular interactions of osmolytes or guanidine hydrochloride (GdnHCl) with protein functional groups, we have determined the apparent transfer free energies (Delta'(tr)) of a homologous series of cyclic dipeptides (CDs) from water to aqueous solutions of osmolytes or GdnHCl through solubility measurements, as a function of osmolyte or GdnHCl concentration at 25 degrees C under atmospheric pressure. The materials investigated in the present study included the CDs of cyclo(Gly-Gly), cyclo(Ala-Gly), cyclo(Ala-Ala), cyclo(Leu-Ala), and cyclo(Val-Val), the osmolytes of trimethylamine N-oxide (TMAO), sarcosine, betaine, proline, and sucrose, and the denaturant of GdnHCl. We observed positive values of (Delta'(tr)) for CDs from water to osmolyte, indicating that interactions between osmolytes and CDs are unfavorable. In contrast, negative (Delta'(tr)) contributions were observed for CDs from water to GdnHCl, revealing that favorable interactions are predominant. The experimental results were further used to estimate the transfer free energies (Delta'(tr)) of the peptide bond (-CONH-), the peptide backbone unit (-CH2C=ONH-), and various functional groups from water to aqueous solutions of osmolyte or GdnHCl.     

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.     

Four pairs of proline-containing cyclic dipeptides from Nocardiopsis sp. HT88, an endophytic bacterium of Mallotus nudiflorus L

Abstract

Strain HT88 was isolated from the fresh stems of Mallotus nudiflorus L, and it was identified as Nocardiopsis sp. by analyzing its morphology and the 16S rRNA sequence. The extracts of fermented HT88 showed potent antimicrobial activities. Bioassay guided separation of extracts led to eight proline (or hydroxyproline, Hyp)-containing cyclic dipeptides. Their structures were determined by 1D and 2D NMR spectroscopy and ESI mass spectrometry and further comparison with existing ¹H and ¹³C NMR, melting points and specific rotation data. The eight 2,5-diketopiperazines (DKPs) were identified as cyclo(L-Pro-L-Leu) (1), cyclo(Pro-Leu) (2), cyclo(L-trans-Hyp-L-Leu) (3), cyclo(D-trans-Hyp-D-Leu) (4), and cyclo(D-Pro-L-Phe) (5), cyclo(L-Pro-L-Phe) (6), and cyclo(D-cis-Hyp-L-Phe) (7), cyclo(L-trans-Hyp-L-Phe) (8), respectively. Up to date, this is the first isolation of four pairs of proline based DKPs from Nocardiopsis sp.